META-INF/
META-INF/MANIFEST.MF
org/
org/jmol/
org/jmol/adapter/
org/jmol/adapter/readers/
org/jmol/adapter/readers/cifpdb/
org/jmol/adapter/readers/molxyz/
org/jmol/adapter/readers/more/
org/jmol/adapter/readers/xml/
org/jmol/adapter/smarter/
org/jmol/api/
org/jmol/applet/
org/jmol/appletwrapper/
org/jmol/atomdata/
org/jmol/bspt/
org/jmol/console/
org/jmol/export/
org/jmol/g3d/
org/jmol/geodesic/
org/jmol/i18n/
org/jmol/jvxl/
org/jmol/jvxl/api/
org/jmol/jvxl/calc/
org/jmol/jvxl/data/
org/jmol/jvxl/readers/
org/jmol/minimize/
org/jmol/minimize/forcefield/
org/jmol/modelset/
org/jmol/modelsetbio/
org/jmol/popup/
org/jmol/quantum/
org/jmol/shape/
org/jmol/shapebio/
org/jmol/shapespecial/
org/jmol/shapesurface/
org/jmol/smiles/
org/jmol/symmetry/
org/jmol/translation/
org/jmol/translation/JmolApplet/
org/jmol/translation/JmolApplet/ar/
org/jmol/translation/JmolApplet/ca/
org/jmol/translation/JmolApplet/cs/
org/jmol/translation/JmolApplet/da/
org/jmol/translation/JmolApplet/de/
org/jmol/translation/JmolApplet/el/
org/jmol/translation/JmolApplet/en_GB/
org/jmol/translation/JmolApplet/es/
org/jmol/translation/JmolApplet/et/
org/jmol/translation/JmolApplet/fr/
org/jmol/translation/JmolApplet/hu/
org/jmol/translation/JmolApplet/it/
org/jmol/translation/JmolApplet/ko/
org/jmol/translation/JmolApplet/nb/
org/jmol/translation/JmolApplet/nl/
org/jmol/translation/JmolApplet/pl/
org/jmol/translation/JmolApplet/pt/
org/jmol/translation/JmolApplet/pt_BR/
org/jmol/translation/JmolApplet/sl/
org/jmol/translation/JmolApplet/sv/
org/jmol/translation/JmolApplet/tr/
org/jmol/translation/JmolApplet/uk/
org/jmol/translation/JmolApplet/zh_CN/
org/jmol/translation/JmolApplet/zh_TW/
org/jmol/util/
org/jmol/viewer/
JmolApplet.class
<Unknown>
package
public JmolApplet extends org.jmol.appletwrapper.AppletWrapper implements org.jmol.api.JmolAppletInterface {
private static final String[] preloadClasses
public void <init> ()
public java.lang.String getPropertyAsString (java.lang.String)
public java.lang.String getPropertyAsString (java.lang.String, java.lang.String)
public java.lang.String getPropertyAsJSON (java.lang.String)
public java.lang.String getPropertyAsJSON (java.lang.String, java.lang.String)
public java.lang.Object getProperty (java.lang.String)
public java.lang.Object getProperty (java.lang.String, java.lang.String)
public java.lang.String loadInlineArray (java.lang.String[], java.lang.String, boolean)
public java.lang.String loadInlineString (java.lang.String, java.lang.String, boolean)
public java.lang.String loadInline (java.lang.String)
public java.lang.String loadInline (java.lang.String, java.lang.String)
public java.lang.String loadInline (java.lang.String[])
public java.lang.String loadInline (java.lang.String[], java.lang.String)
public java.lang.String loadNodeId (java.lang.String)
public java.lang.String loadDOMNode (netscape.javascript.JSObject)
public void script (java.lang.String)
public void syncScript (java.lang.String)
public java.awt.Graphics setStereoGraphics (boolean)
public java.lang.String scriptNoWait (java.lang.String)
public java.lang.String scriptCheck (java.lang.String)
public java.lang.String scriptWait (java.lang.String)
public java.lang.String scriptWait (java.lang.String, java.lang.String)
public java.lang.String scriptWaitOutput (java.lang.String)
static void <clinit> ()
}
jmol75x29x8.gif
org/jmol/adapter/readers/cifpdb/CifReader.class
<Unknown>
package org.jmol.adapter.readers.cifpdb
public org.jmol.adapter.readers.cifpdb.CifReader extends org.jmol.adapter.smarter.AtomSetCollectionReader implements org.jmol.api.JmolLineReader {
private org.jmol.util.CifDataReader tokenizer
private String thisDataSetName
private String chemicalName
private String thisStructuralFormula
private String thisFormula
private boolean iHaveDesiredModel
private java.util.Hashtable htHetero
public static final String[] cellParamNames
private static final String[] TransformFields
private String key
private String data
private java.util.Hashtable atomTypes
private static final byte ATOM_TYPE_SYMBOL
private static final byte ATOM_TYPE_OXIDATION_NUMBER
private static final String[] atomTypeFields
private static final byte NONE
private static final byte TYPE_SYMBOL
private static final byte LABEL
private static final byte AUTH_ATOM
private static final byte FRACT_X
private static final byte FRACT_Y
private static final byte FRACT_Z
private static final byte CARTN_X
private static final byte CARTN_Y
private static final byte CARTN_Z
private static final byte OCCUPANCY
private static final byte B_ISO
private static final byte COMP_ID
private static final byte ASYM_ID
private static final byte SEQ_ID
private static final byte INS_CODE
private static final byte ALT_ID
private static final byte GROUP_PDB
private static final byte MODEL_NO
private static final byte DUMMY_ATOM
private static final byte DISORDER_GROUP
private static final byte ANISO_LABEL
private static final byte ANISO_U11
private static final byte ANISO_U22
private static final byte ANISO_U33
private static final byte ANISO_U12
private static final byte ANISO_U13
private static final byte ANISO_U23
private static final byte ANISO_MMCIF_U11
private static final byte ANISO_MMCIF_U22
private static final byte ANISO_MMCIF_U33
private static final byte ANISO_MMCIF_U12
private static final byte ANISO_MMCIF_U13
private static final byte ANISO_MMCIF_U23
private static final byte U_ISO_OR_EQUIV
private static final byte ANISO_B11
private static final byte ANISO_B22
private static final byte ANISO_B33
private static final byte ANISO_B12
private static final byte ANISO_B13
private static final byte ANISO_B23
private static final byte ANISO_Beta_11
private static final byte ANISO_Beta_22
private static final byte ANISO_Beta_33
private static final byte ANISO_Beta_12
private static final byte ANISO_Beta_13
private static final byte ANISO_Beta_23
private static final byte ADP_TYPE
private static final String[] atomFields
private static final byte GEOM_BOND_ATOM_SITE_LABEL_1
private static final byte GEOM_BOND_ATOM_SITE_LABEL_2
private static final byte GEOM_BOND_SITE_SYMMETRY_2
private static final String[] geomBondFields
private static final byte NONPOLY_ENTITY_ID
private static final byte NONPOLY_NAME
private static final byte NONPOLY_COMP_ID
private static final String[] nonpolyFields
private String[] hetatmData
private static final byte CHEM_COMP_ID
private static final byte CHEM_COMP_NAME
private static final String[] chemCompFields
private static final byte CONF_TYPE_ID
private static final byte BEG_ASYM_ID
private static final byte BEG_SEQ_ID
private static final byte BEG_INS_CODE
private static final byte END_ASYM_ID
private static final byte END_SEQ_ID
private static final byte END_INS_CODE
private static final byte STRUCT_ID
private static final byte SERIAL_NO
private static final String[] structConfFields
private static final byte SHEET_ID
private static final byte STRAND_ID
private static final String[] structSheetRangeFields
private static final byte SITE_ID
private static final byte SITE_COMP_ID
private static final byte SITE_ASYM_ID
private static final byte SITE_SEQ_ID
private static final byte SITE_INS_CODE
private static final String[] structSiteRangeFields
private int siteNum
private java.util.Hashtable htSites
private static final byte SYMOP_XYZ
private static final byte SYM_EQUIV_XYZ
private static final String[] symmetryOperationsFields
String field
private char firstChar
private int[] propertyOf
private byte[] fieldOf
private int propertyCount
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
private void processDataParameter ()
private void processChemicalInfo (java.lang.String) throws java.lang.Exception
private void processSymmetrySpaceGroupName () throws java.lang.Exception
private void processCellParameter () throws java.lang.Exception
private void processUnitCellTransformMatrix () throws java.lang.Exception
private boolean getData () throws java.lang.Exception
private void processLoopBlock () throws java.lang.Exception
private void processAtomTypeLoopBlock () throws java.lang.Exception
boolean processAtomSiteLoopBlock () throws java.lang.Exception
private void processGeomBondLoopBlock () throws java.lang.Exception
private void processNonpolyData ()
private void processChemCompLoopBlock () throws java.lang.Exception
private void processNonpolyLoopBlock () throws java.lang.Exception
private void addHetero (java.lang.String, java.lang.String)
private void processStructConfLoopBlock () throws java.lang.Exception
private void processStructSheetRangeLoopBlock () throws java.lang.Exception
private void processStructSiteBlock () throws java.lang.Exception
private void processSymmetryOperationsLoopBlock () throws java.lang.Exception
private int fieldProperty (int)
private void parseLoopParameters (java.lang.String[]) throws java.lang.Exception
public java.lang.String readLine () throws java.lang.Exception
private void disableField (int)
private void skipLoop () throws java.lang.Exception
private static boolean isMatch (java.lang.String, java.lang.String)
static void <clinit> ()
}
org/jmol/adapter/readers/cifpdb/PdbReader.class
<Unknown>
package org.jmol.adapter.readers.cifpdb
public org.jmol.adapter.readers.cifpdb.PdbReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
int lineLength
boolean isNMRdata
final java.util.Hashtable htFormul
java.util.Hashtable htHetero
java.util.Hashtable htSites
protected String fileType
String currentGroup3
String compnd
java.util.Hashtable htElementsInCurrentGroup
int maxSerial
int[] chainAtomCounts
private static final String lineOptions
java.util.Vector biomolecules
java.util.Vector biomts
int atomCount
String lastAtomData
int lastAtomIndex
boolean haveMappedSerials
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
private void header ()
private void compnd ()
private void setBiomoleculeAtomCounts ()
private void remark350 () throws java.lang.Exception
void atom ()
protected int readOccupancy ()
protected float readBFactor ()
protected float readPartialCharge ()
protected float readRadius ()
java.lang.String deduceElementSymbol (boolean)
void conect ()
void structure ()
private int getModelNumber ()
void model (int)
void cryst1 () throws java.lang.Exception
float getFloat (int, int) throws java.lang.Exception
void scale (int) throws java.lang.Exception
void expdta ()
void formul ()
void het ()
void hetnam ()
void anisou ()
private void site ()
public void applySymmetryAndSetTrajectory () throws java.lang.Exception
}
org/jmol/adapter/readers/molxyz/MolReader.class
<Unknown>
package org.jmol.adapter.readers.molxyz
public org.jmol.adapter.readers.molxyz.MolReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
String header
private static final String isotopeMap0
private static final String isotopeMap1
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
void processMolSdHeader () throws java.lang.Exception
void processRgHeader () throws java.lang.Exception
void processCtab () throws java.lang.Exception
void flushLines () throws java.lang.Exception
void readAtoms (int) throws java.lang.Exception
void readBonds (int, int) throws java.lang.Exception
}
org/jmol/adapter/readers/molxyz/XyzReader.class
<Unknown>
package org.jmol.adapter.readers.molxyz
public org.jmol.adapter.readers.molxyz.XyzReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
private void skipAtomSet (int) throws java.lang.Exception
private int readAtomCount () throws java.lang.Exception
private void readAtomSetName () throws java.lang.Exception
private void readAtoms (int) throws java.lang.Exception
}
org/jmol/adapter/readers/more/AdfReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.AdfReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
String energy
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
private void readCoordinates () throws java.lang.Exception
private void readFrequencies () throws java.lang.Exception
}
org/jmol/adapter/readers/more/AimsReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.AimsReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
private void setUnitCellFromLatticeVectors (javax.vecmath.Vector3f[])
}
org/jmol/adapter/readers/more/AlchemyReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.AlchemyReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
int atomCount
int bondCount
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
private void readAtoms () throws java.lang.Exception
private void readBonds () throws java.lang.Exception
}
org/jmol/adapter/readers/more/CastepReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.CastepReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
private String[] tokens
private float a
private float b
private float c
private float alpha
private float beta
private float gamma
private javax.vecmath.Vector3f[] abc
private static final String[] lengthUnitIds
private static final float[] lengthUnitFactors
private static final int lengthUnits
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
private void readLatticeAbc () throws java.lang.Exception
private void readLatticeCart () throws java.lang.Exception
private void readPositionsFrac () throws java.lang.Exception
private void readPositionsAbs () throws java.lang.Exception
private float readLengthUnit () throws java.lang.Exception
private void readAtomData (float) throws java.lang.Exception
private int tokenizeCastepCell () throws java.lang.Exception
static void <clinit> ()
}
org/jmol/adapter/readers/more/CsfReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.CsfReader extends org.jmol.adapter.readers.more.MopacDataReader {
int nAtoms
String atomicNumbers
int fieldCount
int nVibrations
int nGaussians
int nSlaters
private java.util.Hashtable propertyItemCounts
int[] fieldTypes
static final byte objCls1
static final byte objID1
static final byte objCls2
static final byte objID2
static final String[] connectorFields
static final byte[] connectorFieldMap
java.util.Hashtable connectors
static final byte ID
static final byte sym
static final byte anum
static final byte chrg
static final byte xyz_coordinates
static final byte pchrg
static final String[] atomFields
static final byte[] atomFieldMap
static final byte bondType
static final String[] bondFields
static final byte[] bondFieldMap
int nBonds
static final byte normalMode
static final byte vibEnergy
static final byte transitionDipole
static final String[] vibFields
static final byte[] vibFieldMap
static final byte eig_val
static final byte mo_occ
static final byte eig_vec
static final byte eig_vec_compressed
static final byte coef_indices
static final byte bfxn_ang
static final byte sto_exp
static final byte contractions
static final byte gto_exp
static final byte shell
static final String[] moFields
static final byte[] moFieldMap
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
private void processObjectClass () throws java.lang.Exception
private void processLocalTransform () throws java.lang.Exception
int getPropertyCount (java.lang.String)
private int parseLineParameters (java.lang.String[], byte[]) throws java.lang.Exception
private void fillCsfArray (java.lang.String, java.lang.String[], int, java.lang.Object) throws java.lang.Exception
void processConnectorObject () throws java.lang.Exception
void processAtomObject () throws java.lang.Exception
void processBondObject () throws java.lang.Exception
void processVibrationObject () throws java.lang.Exception
void processMolecularOrbitalObject () throws java.lang.Exception
void processBasisObject (java.lang.String) throws java.lang.Exception
void createSlaterByType (int, int, java.lang.String, float, float)
static void <clinit> ()
}
org/jmol/adapter/readers/more/CubeReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.CubeReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
boolean negativeAtomCount
int atomCount
boolean isAngstroms
final int[] voxelCounts
final float[] origin
final float[][] voxelVectors
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
void readTitleLines () throws java.lang.Exception
void readAtomCountAndOrigin () throws java.lang.Exception
void readVoxelVectors () throws java.lang.Exception
void readVoxelVector (int) throws java.lang.Exception
void readAtoms () throws java.lang.Exception
void readExtraLine () throws java.lang.Exception
}
org/jmol/adapter/readers/more/FFReader.class
<Unknown>
package org.jmol.adapter.readers.more
abstract org.jmol.adapter.readers.more.FFReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
private static final String ffTypes
private static final String twoChar
private static final String specialTypes
private static final String secondCharOnly
private String userAtomTypes
private java.util.Properties atomTypes
void <init> ()
protected void setUserAtomTypes ()
protected boolean getElementSymbol (org.jmol.adapter.smarter.Atom, java.lang.String)
}
org/jmol/adapter/readers/more/FoldingXyzReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.FoldingXyzReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
private static final boolean useAutoBond
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
void readAtoms (int) throws java.lang.Exception
}
org/jmol/adapter/readers/more/GamessReader.class
<Unknown>
package org.jmol.adapter.readers.more
public abstract org.jmol.adapter.readers.more.GamessReader extends org.jmol.adapter.readers.more.MOReader {
protected java.util.Vector atomNames
private java.util.Hashtable calcOptions
private boolean isTypeSet
public void <init> ()
protected abstract void readAtomsInBohrCoordinates () throws java.lang.Exception
protected void readGaussianBasis (java.lang.String, java.lang.String) throws java.lang.Exception
protected abstract java.lang.String fixShellTag (java.lang.String)
protected void readFrequencies () throws java.lang.Exception
private void readComponents (int, float[])
protected static java.lang.String fixBasisLine (java.lang.String)
protected void setCalculationType ()
protected void readControlInfo () throws java.lang.Exception
protected void readBasisInfo () throws java.lang.Exception
private void readCalculationInfo (java.lang.String) throws java.lang.Exception
}
org/jmol/adapter/readers/more/GamessUKReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.GamessUKReader extends org.jmol.adapter.readers.more.GamessReader {
private java.util.Vector symmetries
private java.util.Vector occupancies
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
protected boolean checkLine () throws java.lang.Exception
protected void readAtomsInBohrCoordinates () throws java.lang.Exception
protected java.lang.String fixShellTag (java.lang.String)
private void readOrbitalSymmetryAndOccupancy () throws java.lang.Exception
private void setOrbitalSymmetryAndOccupancy ()
}
org/jmol/adapter/readers/more/GamessUSReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.GamessUSReader extends org.jmol.adapter.readers.more.GamessReader {
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
protected boolean checkLine () throws java.lang.Exception
protected void readMolecularOrbitals (int) throws java.lang.Exception
protected void readEFPInBohrCoordinates () throws java.lang.Exception
protected void readAtomsInBohrCoordinates () throws java.lang.Exception
private void readAtomsInAngstromCoordinates () throws java.lang.Exception
protected java.lang.String fixShellTag (java.lang.String)
void readPartialCharges () throws java.lang.Exception
void readDipoleMoment () throws java.lang.Exception
}
org/jmol/adapter/readers/more/GaussianReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.GaussianReader extends org.jmol.adapter.readers.more.MOReader {
private static final int STD_ORIENTATION_ATOMIC_NUMBER_OFFSET
private static final int FREQ_FIRST_VECTOR_OFFSET
private String energyString
private String energyKey
private int calculationNumber
private int scanPoint
private int equivalentAtomSets
private int stepNumber
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
protected boolean checkLine () throws java.lang.Exception
private void readSCFDone () throws java.lang.Exception
private void setEnergy ()
private void readAtoms () throws java.lang.Exception
void readBasis () throws java.lang.Exception
void readGaussianMolecularOrbitals () throws java.lang.Exception
private void readFrequencies () throws java.lang.Exception java.io.IOException
void readDipoleMoment () throws java.lang.Exception
void readPartialCharges () throws java.lang.Exception
}
org/jmol/adapter/readers/more/GaussianWfnReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.GaussianWfnReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
}
org/jmol/adapter/readers/more/GhemicalMMReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.GhemicalMMReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
void processHeader ()
void processInfo ()
void processAtoms () throws java.lang.Exception
void processBonds () throws java.lang.Exception
void processCoord () throws java.lang.Exception
void processCharges () throws java.lang.Exception
}
org/jmol/adapter/readers/more/GromacsReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.GromacsReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
protected String fileType
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
private int readAtomCount () throws java.lang.Exception
private void readAtomSetName () throws java.lang.Exception
private void readAtoms (int) throws java.lang.Exception
java.lang.String deduceElementSymbol (java.lang.String, java.lang.String)
}
org/jmol/adapter/readers/more/HinReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.HinReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
int atomIndex
int baseAtomIndex
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
void readAtoms () throws java.lang.Exception
void processMol () throws java.lang.Exception
java.lang.String getMolName ()
void processAtom () throws java.lang.Exception
void processEndmol ()
}
org/jmol/adapter/readers/more/JaguarReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.JaguarReader extends org.jmol.adapter.readers.more.MOReader {
int moCount
float lumoEnergy
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
protected boolean checkLine () throws java.lang.Exception
private void readAtoms () throws java.lang.Exception
private void readCharges () throws java.lang.Exception
void readBasis () throws java.lang.Exception
void readBasisNormalized () throws java.lang.Exception
private void readJaguarMolecularOrbitals () throws java.lang.Exception
private void readFrequencies () throws java.lang.Exception
}
org/jmol/adapter/readers/more/JmeReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.JmeReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
java.util.StringTokenizer tokenizer
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
void readAtoms (int) throws java.lang.Exception
void readBonds (int) throws java.lang.Exception
}
org/jmol/adapter/readers/more/MOReader.class
<Unknown>
package org.jmol.adapter.readers.more
abstract org.jmol.adapter.readers.more.MOReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
protected int shellCount
protected int gaussianCount
protected java.util.Hashtable moData
protected java.util.Vector shells
protected float[][] gaussians
protected java.util.Vector orbitals
protected String energyUnits
protected java.util.Vector moTypes
private boolean getNBOs
private boolean getNBOCharges
protected boolean haveNboCharges
private String[] filterTokens
private boolean filterIsNot
protected boolean iHaveAtoms
protected boolean continuing
protected boolean ignoreMOs
protected String alphaBeta
protected final int HEADER_GAMESS_UK_MO
protected final int HEADER_GAMESS_OCCUPANCIES
protected final int HEADER_GAMESS_ORIGINAL
protected final int HEADER_NONE
void <init> ()
public abstract void readAtomSetCollection (java.io.BufferedReader)
protected abstract boolean checkLine () throws java.lang.Exception
public void readAtomSetCollection (java.io.BufferedReader, java.lang.String)
protected void finalizeMoReader ()
private void initializeMoReader (java.io.BufferedReader, java.lang.String)
protected boolean filterMO ()
protected boolean checkNboLine () throws java.lang.Exception
private void getNboCharges () throws java.lang.Exception
protected void getNboTypes () throws java.lang.Exception
protected void readMolecularOrbitals (int) throws java.lang.Exception
protected void getMOHeader (int, java.lang.String[], java.util.Hashtable[], int) throws java.lang.Exception
protected void addMOData (int, java.util.Vector[], java.util.Hashtable[])
protected void setMOData (boolean)
}
org/jmol/adapter/readers/more/MdCrdReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.MdCrdReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
private java.util.Vector trajectorySteps
private int ptFloat
private int lenLine
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
void readCoordinates () throws java.lang.Exception
private float getFloat () throws java.lang.Exception
private javax.vecmath.Point3f getPoint () throws java.lang.Exception
private boolean getTrajectoryStep (javax.vecmath.Point3f[], boolean) throws java.lang.Exception
private boolean skipFloats (int) throws java.lang.Exception
}
org/jmol/adapter/readers/more/MdTopReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.MdTopReader extends org.jmol.adapter.readers.more.FFReader {
private int nAtoms
private int atomCount
String[] group3s
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
private java.lang.String getDataBlock () throws java.lang.Exception
private void getMasses () throws java.lang.Exception
private void getAtomTypes () throws java.lang.Exception
private void getCharges () throws java.lang.Exception
private void getResiduePointers () throws java.lang.Exception
private void getResidueLabels () throws java.lang.Exception
private void getAtomNames () throws java.lang.Exception
private void getPointers () throws java.lang.Exception
}
org/jmol/adapter/readers/more/Mol2Reader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.Mol2Reader extends org.jmol.adapter.readers.more.FFReader {
private int nAtoms
private int atomCount
private boolean isPDB
private int lastSequenceNumber
private char chainID
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
private void processMolecule () throws java.lang.Exception
private void readAtoms (int, boolean) throws java.lang.Exception
private void readBonds (int) throws java.lang.Exception
private void readResInfo (int) throws java.lang.Exception
private void readCrystalInfo () throws java.lang.Exception
}
org/jmol/adapter/readers/more/MoldenReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.MoldenReader extends org.jmol.adapter.readers.more.MopacDataReader {
protected float[] frequencies
protected org.jmol.adapter.smarter.AtomSetCollection freqAtomSet
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
void readAtoms () throws java.lang.Exception
void readGaussianBasis () throws java.lang.Exception
void readMolecularOrbitals () throws java.lang.Exception
void readFreqsAndModes () throws java.lang.Exception
java.lang.String[] splitKeyValue ()
java.lang.String[] splitKeyValue (java.lang.String)
java.lang.String[] splitKeyValue (java.lang.String, java.lang.String) throws java.util.NoSuchElementException
}
org/jmol/adapter/readers/more/MopacData.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.MopacData extends java.lang.Object {
private static final int[] principalQuantumNumber
private static final int[] pnqD
private static final float[] fact
private static final float fourPi
private static final float[] factorDs
public void <init> ()
private static final boolean isNoble (int)
private static final int getNPQ (int)
public static final int getNPQs (int)
public static final int getNPQp (int)
public static final int getNPQd (int)
public static final float getMopacConstS (int, float)
public static final float getMopacConstP (int, float)
public static float getFactorD (int)
public static final float getMopacConstD (int, float)
static void <clinit> ()
}
org/jmol/adapter/readers/more/MopacDataReader.class
<Unknown>
package org.jmol.adapter.readers.more
abstract org.jmol.adapter.readers.more.MopacDataReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
protected static final float MIN_COEF
protected final java.util.Hashtable moData
protected int nOrbitals
protected final java.util.Vector intinfo
protected final java.util.Vector floatinfo
protected final java.util.Vector orbitals
protected static final int[] dValues
void <init> ()
public abstract void readAtomSetCollection (java.io.BufferedReader)
protected final void addSlater (int, int, int, int, int, float, float)
protected final void setSlaters ()
protected final void setMOs (java.lang.String)
static void <clinit> ()
}
org/jmol/adapter/readers/more/MopacGraphfReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.MopacGraphfReader extends org.jmol.adapter.readers.more.MopacDataReader {
int[] atomicNumbers
int atomCount
float[][] invMatrix
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
void readAtoms () throws java.lang.Exception
void readSlaterBasis () throws java.lang.Exception
void readMOs (boolean) throws java.lang.Exception
private boolean readKeywords () throws java.lang.Exception
}
org/jmol/adapter/readers/more/MopacReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.MopacReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
int baseAtomIndex
private boolean chargesFound
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
void processTotalEnergy ()
void processAtomicCharges () throws java.lang.Exception
void processCoordinates () throws java.lang.Exception
private void readFrequencies () throws java.lang.Exception
}
org/jmol/adapter/readers/more/NWChemReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.NWChemReader extends org.jmol.adapter.readers.more.MOReader {
private int taskNumber
private int equivalentAtomSets
private String energyKey
private String energyValue
private boolean converged
private boolean haveEnergy
private boolean haveAt
private boolean inInput
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
protected boolean checkLine () throws java.lang.Exception
private void init ()
private void setEnergies (java.lang.String, java.lang.String, int)
private void setEnergy (java.lang.String, java.lang.String)
private void readSymmetry () throws java.lang.Exception
private void readNWChemLine ()
private void readTotal ()
private void readAtSign () throws java.lang.Exception
private void readAtoms () throws java.lang.Exception
private void readGradients () throws java.lang.Exception
private void readFrequencies () throws java.lang.Exception
void readPartialCharges () throws java.lang.Exception
private java.lang.String fixTag (java.lang.String)
}
org/jmol/adapter/readers/more/OdysseyReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.OdysseyReader extends org.jmol.adapter.readers.more.SpartanInputReader {
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
}
org/jmol/adapter/readers/more/OdysseyXMLReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.OdysseyXMLReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
String modelName
int atomCount
int bondCount
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
void readDescription () throws java.lang.Exception
void readAtoms () throws java.lang.Exception
java.util.Hashtable readXML (java.lang.String) throws java.lang.Exception
void readBonds () throws java.lang.Exception
}
org/jmol/adapter/readers/more/PqrReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.PqrReader extends org.jmol.adapter.readers.cifpdb.PdbReader {
protected String fileType
String[] tokens
public void <init> ()
protected int readOccupancy ()
protected float readBFactor ()
protected float readPartialCharge ()
protected float readRadius ()
}
org/jmol/adapter/readers/more/PsiReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.PsiReader extends org.jmol.adapter.readers.more.MOReader {
java.util.Vector atomNames
java.util.Vector shellsByUniqueAtom
java.util.Hashtable uniqueAtomMap
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
protected boolean checkLine () throws java.lang.Exception
private void readSCFDone () throws java.lang.Exception
private void readAtoms (boolean) throws java.lang.Exception
void readBasis () throws java.lang.Exception
private void readUniqueAtoms () throws java.lang.Exception
void readPsiMolecularOrbitals () throws java.lang.Exception
}
org/jmol/adapter/readers/more/QchemReader$MOInfo.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.QchemReader$MOInfo extends java.lang.Object {
int ne
String label
String symmetry
private final org.jmol.adapter.readers.more.QchemReader this$0
protected void <init> (org.jmol.adapter.readers.more.QchemReader)
}
org/jmol/adapter/readers/more/QchemReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.QchemReader extends org.jmol.adapter.readers.more.MOReader {
private int calculationNumber
org.jmol.adapter.readers.more.QchemReader$MOInfo[] alphas
org.jmol.adapter.readers.more.QchemReader$MOInfo[] betas
int nShell
int nBasis
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
protected boolean checkLine () throws java.lang.Exception
private void readCalculationType ()
void readAtoms () throws java.lang.Exception
private void readFrequencies () throws java.lang.Exception java.io.IOException
void readPartialCharges () throws java.lang.Exception
private void readBasis () throws java.lang.Exception
protected void readESym (boolean) throws java.lang.Exception
private void readQchemMolecularOrbitals () throws java.lang.Exception
private int readMOs (boolean, java.lang.String[], java.util.Vector, org.jmol.adapter.readers.more.QchemReader$MOInfo[]) throws java.lang.Exception
}
org/jmol/adapter/readers/more/ShelxReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.ShelxReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
String[] sfacElementSymbols
boolean isCmdf
boolean iHaveAtomSet
static final String[] supportedRecordTypes
static final String[] unsupportedRecordTypes
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
void processSupportedRecord (int) throws java.lang.Exception
void parseLattRecord () throws java.lang.Exception
void parseSymmRecord () throws java.lang.Exception
void cell () throws java.lang.Exception
void parseSfacRecord ()
void parseSfacElementSymbols (java.lang.String[])
void parseSfacCoefficients (java.lang.String[])
void assumeAtomRecord () throws java.lang.Exception
void processCmdfAtoms () throws java.lang.Exception
java.lang.String getSymbol (java.lang.String)
static void <clinit> ()
}
org/jmol/adapter/readers/more/SpartanArchive.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.SpartanArchive extends java.lang.Object {
private int atomCount
private String bondData
private int moCount
private int coefCount
private int shellCount
private int gaussianCount
private String endCheck
private String calculationType
private String line
private org.jmol.adapter.smarter.AtomSetCollection atomSetCollection
private org.jmol.adapter.smarter.AtomSetCollectionReader r
private java.util.Hashtable moData
private java.util.Vector orbitals
private int modelAtomCount
private java.lang.String[] getTokens ()
void <init> (org.jmol.adapter.smarter.AtomSetCollectionReader, org.jmol.adapter.smarter.AtomSetCollection, java.util.Hashtable)
void <init> (org.jmol.adapter.smarter.AtomSetCollectionReader, org.jmol.adapter.smarter.AtomSetCollection, java.util.Hashtable, java.lang.String, java.lang.String)
private void initialize (org.jmol.adapter.smarter.AtomSetCollectionReader, org.jmol.adapter.smarter.AtomSetCollection, java.util.Hashtable, java.lang.String)
int readArchive (java.lang.String, boolean, int, boolean) throws java.lang.Exception
private static java.lang.String[] getTokens (java.lang.String)
private int parseInt (java.lang.String)
private float parseFloat (java.lang.String)
private int setInfo (java.lang.String) throws java.lang.Exception
void readAtoms (int, boolean) throws java.lang.Exception
void addBonds (java.lang.String, int)
void readBasis () throws java.lang.Exception
void readMolecularOrbital () throws java.lang.Exception
void readProperties () throws java.lang.Exception
void readDipole () throws java.lang.Exception
private void setDipole (java.lang.String[])
private void readProperty () throws java.lang.Exception
void readVibFreqs () throws java.lang.Exception
private void setVibrationsFromProperties () throws java.lang.Exception
private java.lang.String getQuotedString (java.lang.String)
private java.lang.String readLine () throws java.lang.Exception
}
org/jmol/adapter/readers/more/SpartanInputReader.class
<Unknown>
package org.jmol.adapter.readers.more
abstract org.jmol.adapter.readers.more.SpartanInputReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
protected String modelName
protected int atomCount
protected int bondCount
protected String bondData
int modelAtomCount
int atomCount0
void <init> ()
protected void readInputRecords ()
private void readTransform () throws java.lang.Exception
private void readInputHeader () throws java.lang.Exception
private void readInputAtoms () throws java.lang.Exception
private void readAtomNames () throws java.lang.Exception
private void readBonds (int) throws java.lang.Exception
}
org/jmol/adapter/readers/more/SpartanReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.SpartanReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
String modelName
int atomCount
java.util.Hashtable moData
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
boolean isSpartanArchive (java.lang.String) throws java.lang.Exception
void readAtoms () throws java.lang.Exception
void readFrequencies () throws java.lang.Exception
}
org/jmol/adapter/readers/more/SpartanSmolReader$MoleculeRecord.class
<Unknown>
package org.jmol.adapter.readers.more
org.jmol.adapter.readers.more.SpartanSmolReader$MoleculeRecord extends java.lang.Object {
float[] mat
private final org.jmol.adapter.readers.more.SpartanSmolReader this$0
void <init> (org.jmol.adapter.readers.more.SpartanSmolReader, java.lang.String)
private float bytesToDoubleToFloat (byte[], int)
protected void setTrans ()
}
org/jmol/adapter/readers/more/SpartanSmolReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.SpartanSmolReader extends org.jmol.adapter.readers.more.SpartanInputReader {
private String endCheck
private java.util.Hashtable moData
private String title
org.jmol.adapter.readers.more.SpartanArchive spartanArchive
java.util.Hashtable titles
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
private void readOutput () throws java.lang.Exception
private void readArchive () throws java.lang.Exception
private void readProperties () throws java.lang.Exception
private int getModelNumber ()
private void readTransform () throws java.lang.Exception
private boolean readArchiveHeader () throws java.lang.Exception
}
org/jmol/adapter/readers/more/V3000Reader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.V3000Reader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
int headerAtomCount
int headerBondCount
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
void processCtab () throws java.lang.Exception
java.lang.String processAtomBlock () throws java.lang.Exception
void processBondBlock () throws java.lang.Exception
void readLineWithContinuation () throws java.lang.Exception
void flushLines () throws java.lang.Exception
}
org/jmol/adapter/readers/more/WebMOReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.WebMOReader extends org.jmol.adapter.readers.more.MopacDataReader {
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
void readHeader () throws java.lang.Exception
void readAtoms () throws java.lang.Exception
void readBonds () throws java.lang.Exception
void readAtomicOrbitalOrder () throws java.lang.Exception
void readGaussianBasis () throws java.lang.Exception
void readSlaterBasis () throws java.lang.Exception
void readMolecularOrbital () throws java.lang.Exception
}
org/jmol/adapter/readers/more/Wien2kReader.class
<Unknown>
package org.jmol.adapter.readers.more
public org.jmol.adapter.readers.more.Wien2kReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
private boolean isrhombohedral
private char latticeCode
private boolean doSymmetry
private final String cxyz
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
private void readUnitCell () throws java.lang.Exception
private void readAtoms () throws java.lang.Exception
private void addAtom ()
private void readSymmetry () throws java.lang.Exception
private java.lang.String getJones () throws java.lang.Exception
private void readEmbeddedScript () throws java.lang.Exception
}
org/jmol/adapter/readers/xml/XmlArgusReader$ArgusHandler.class
<Unknown>
package org.jmol.adapter.readers.xml
org.jmol.adapter.readers.xml.XmlArgusReader$ArgusHandler extends org.jmol.adapter.readers.xml.XmlReader$JmolXmlHandler {
private final org.jmol.adapter.readers.xml.XmlArgusReader this$0
void <init> (org.jmol.adapter.readers.xml.XmlArgusReader)
void <init> (org.jmol.adapter.readers.xml.XmlArgusReader, org.xml.sax.XMLReader)
}
org/jmol/adapter/readers/xml/XmlArgusReader.class
<Unknown>
package org.jmol.adapter.readers.xml
public org.jmol.adapter.readers.xml.XmlArgusReader extends org.jmol.adapter.readers.xml.XmlReader {
String[] argusImplementedAttributes
String[] keepCharsList
String atomName1
String atomName2
int bondOrder
int elementContext
static final int UNSET
static final int MOLECULE
static final int ATOM
static final int BOND
void <init> ()
protected void processXml (org.jmol.adapter.readers.xml.XmlReader, org.jmol.adapter.smarter.AtomSetCollection, java.io.BufferedReader, org.xml.sax.XMLReader)
protected void processXml (org.jmol.adapter.readers.xml.XmlReader, org.jmol.adapter.smarter.AtomSetCollection, java.io.BufferedReader, netscape.javascript.JSObject)
public void processStartElement (java.lang.String, java.lang.String, java.lang.String, java.util.HashMap)
int parseBondToken (java.lang.String)
public void processEndElement (java.lang.String, java.lang.String, java.lang.String)
}
org/jmol/adapter/readers/xml/XmlChem3dReader$Chem3dHandler.class
<Unknown>
package org.jmol.adapter.readers.xml
org.jmol.adapter.readers.xml.XmlChem3dReader$Chem3dHandler extends org.jmol.adapter.readers.xml.XmlReader$JmolXmlHandler {
private final org.jmol.adapter.readers.xml.XmlChem3dReader this$0
void <init> (org.jmol.adapter.readers.xml.XmlChem3dReader)
void <init> (org.jmol.adapter.readers.xml.XmlChem3dReader, org.xml.sax.XMLReader)
}
org/jmol/adapter/readers/xml/XmlChem3dReader.class
<Unknown>
package org.jmol.adapter.readers.xml
public org.jmol.adapter.readers.xml.XmlChem3dReader extends org.jmol.adapter.readers.xml.XmlReader {
String[] chem3dImplementedAttributes
void <init> ()
protected void processXml (org.jmol.adapter.readers.xml.XmlReader, org.jmol.adapter.smarter.AtomSetCollection, java.io.BufferedReader, org.xml.sax.XMLReader)
protected void processXml (org.jmol.adapter.readers.xml.XmlReader, org.jmol.adapter.smarter.AtomSetCollection, java.io.BufferedReader, netscape.javascript.JSObject)
public void processStartElement (java.lang.String, java.lang.String, java.lang.String, java.util.HashMap)
public void processEndElement (java.lang.String, java.lang.String, java.lang.String)
}
org/jmol/adapter/readers/xml/XmlCmlReader$CmlHandler.class
<Unknown>
package org.jmol.adapter.readers.xml
org.jmol.adapter.readers.xml.XmlCmlReader$CmlHandler extends org.jmol.adapter.readers.xml.XmlReader$JmolXmlHandler {
private final org.jmol.adapter.readers.xml.XmlCmlReader this$0
void <init> (org.jmol.adapter.readers.xml.XmlCmlReader)
void <init> (org.jmol.adapter.readers.xml.XmlCmlReader, org.xml.sax.XMLReader)
}
org/jmol/adapter/readers/xml/XmlCmlReader.class
<Unknown>
package org.jmol.adapter.readers.xml
public org.jmol.adapter.readers.xml.XmlCmlReader extends org.jmol.adapter.readers.xml.XmlReader {
private String[] cmlImplementedAttributes
private int atomCount
private org.jmol.adapter.smarter.Atom[] atomArray
private int bondCount
private org.jmol.adapter.smarter.Bond[] bondArray
private int tokenCount
String[] tokens
private int nModules
private int moduleNestingLevel
private boolean haveMolecule
private String localSpaceGroupName
private boolean processing
protected final int START
protected final int CML
protected final int CRYSTAL
protected final int CRYSTAL_SCALAR
protected final int CRYSTAL_SYMMETRY
protected final int CRYSTAL_SYMMETRY_TRANSFORM3
protected final int MOLECULE
protected final int MOLECULE_ATOM_ARRAY
protected final int MOLECULE_ATOM
protected final int MOLECULE_ATOM_SCALAR
protected final int MOLECULE_BOND_ARRAY
protected final int MOLECULE_BOND
protected final int MOLECULE_FORMULA
protected final int MOLECULE_ATOM_BUILTIN
protected final int MOLECULE_BOND_BUILTIN
protected final int MODULE
protected final int SYMMETRY
protected final int LATTICE_VECTOR
protected int state
private String scalarDictRef
private String scalarDictValue
private String scalarTitle
private String cellParameterType
private int moleculeNesting
private int latticeVectorPtr
private boolean embeddedCrystal
private java.util.Properties atomIdNames
void <init> ()
protected void processXml (org.jmol.adapter.readers.xml.XmlReader, org.jmol.adapter.smarter.AtomSetCollection, java.io.BufferedReader, org.xml.sax.XMLReader)
protected void processXml (org.jmol.adapter.readers.xml.XmlReader, org.jmol.adapter.smarter.AtomSetCollection, java.io.BufferedReader, netscape.javascript.JSObject)
public void processStartElement (java.lang.String, java.lang.String, java.lang.String, java.util.HashMap)
private void getDictRefValue (java.util.HashMap)
public void processEndElement (java.lang.String, java.lang.String, java.lang.String)
int parseBondToken (java.lang.String)
void breakOutTokens (java.lang.String)
void breakOutAtomTokens (java.lang.String)
void checkAtomArrayLength (int)
void breakOutBondTokens (java.lang.String)
void checkBondArrayLength (int)
private void createNewAtomSet (java.util.HashMap)
public void applySymmetryAndSetTrajectory ()
}
org/jmol/adapter/readers/xml/XmlMolproReader$MolproHandler.class
<Unknown>
package org.jmol.adapter.readers.xml
org.jmol.adapter.readers.xml.XmlMolproReader$MolproHandler extends org.jmol.adapter.readers.xml.XmlCmlReader$CmlHandler {
private final org.jmol.adapter.readers.xml.XmlMolproReader this$0
void <init> (org.jmol.adapter.readers.xml.XmlMolproReader)
void <init> (org.jmol.adapter.readers.xml.XmlMolproReader, org.xml.sax.XMLReader)
public void startElement (java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)
public void endElement (java.lang.String, java.lang.String, java.lang.String)
}
org/jmol/adapter/readers/xml/XmlMolproReader.class
<Unknown>
package org.jmol.adapter.readers.xml
public org.jmol.adapter.readers.xml.XmlMolproReader extends org.jmol.adapter.readers.xml.XmlCmlReader {
static String[] molProImplementedAttributes
int frequencyCount
void <init> ()
protected void processXml (org.jmol.adapter.readers.xml.XmlReader, org.jmol.adapter.smarter.AtomSetCollection, java.io.BufferedReader, org.xml.sax.XMLReader)
protected void processXml (org.jmol.adapter.readers.xml.XmlReader, org.jmol.adapter.smarter.AtomSetCollection, java.io.BufferedReader, netscape.javascript.JSObject)
public void processStartElement2 (java.lang.String, java.lang.String, java.lang.String, java.util.HashMap)
public void processEndElement2 (java.lang.String, java.lang.String, java.lang.String)
static void <clinit> ()
}
org/jmol/adapter/readers/xml/XmlOdysseyReader$OdysseyHandler.class
<Unknown>
package org.jmol.adapter.readers.xml
org.jmol.adapter.readers.xml.XmlOdysseyReader$OdysseyHandler extends org.jmol.adapter.readers.xml.XmlReader$JmolXmlHandler {
private final org.jmol.adapter.readers.xml.XmlOdysseyReader this$0
void <init> (org.jmol.adapter.readers.xml.XmlOdysseyReader)
void <init> (org.jmol.adapter.readers.xml.XmlOdysseyReader, org.xml.sax.XMLReader)
}
org/jmol/adapter/readers/xml/XmlOdysseyReader.class
<Unknown>
package org.jmol.adapter.readers.xml
public org.jmol.adapter.readers.xml.XmlOdysseyReader extends org.jmol.adapter.readers.xml.XmlReader {
String[] odysseyImplementedAttributes
String modelName
String formula
String phase
void <init> ()
protected void processXml (org.jmol.adapter.readers.xml.XmlReader, org.jmol.adapter.smarter.AtomSetCollection, java.io.BufferedReader, org.xml.sax.XMLReader)
protected void processXml (org.jmol.adapter.readers.xml.XmlReader, org.jmol.adapter.smarter.AtomSetCollection, java.io.BufferedReader, netscape.javascript.JSObject)
protected void processStartElement (java.lang.String, java.lang.String, java.lang.String, java.util.HashMap)
public void applySymmetryAndSetTrajectory ()
int parseBondToken (java.lang.String)
protected void processEndElement (java.lang.String, java.lang.String, java.lang.String)
}
org/jmol/adapter/readers/xml/XmlReader$DummyResolver.class
<Unknown>
package org.jmol.adapter.readers.xml
public org.jmol.adapter.readers.xml.XmlReader$DummyResolver extends java.lang.Object implements org.xml.sax.EntityResolver {
public void <init> ()
public org.xml.sax.InputSource resolveEntity (java.lang.String, java.lang.String) throws org.xml.sax.SAXException
}
org/jmol/adapter/readers/xml/XmlReader$JmolXmlHandler.class
<Unknown>
package org.jmol.adapter.readers.xml
public org.jmol.adapter.readers.xml.XmlReader$JmolXmlHandler extends org.xml.sax.helpers.DefaultHandler implements org.xml.sax.ErrorHandler {
public java.util.HashMap atts
private final org.jmol.adapter.readers.xml.XmlReader this$0
public void <init> (org.jmol.adapter.readers.xml.XmlReader)
public void <init> (org.jmol.adapter.readers.xml.XmlReader, org.xml.sax.XMLReader)
public void setHandler (org.xml.sax.XMLReader, org.jmol.adapter.readers.xml.XmlReader$JmolXmlHandler)
public void startDocument ()
public void endDocument ()
public void startElement (java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)
private void startElement (java.lang.String, java.lang.String, java.lang.String)
public void endElement (java.lang.String, java.lang.String, java.lang.String)
public void characters (char[], int, int)
public org.xml.sax.InputSource resolveEntity (java.lang.String, java.lang.String, java.lang.String, java.lang.String)
public org.xml.sax.InputSource resolveEntity (java.lang.String, java.lang.String)
public void error (org.xml.sax.SAXParseException)
public void fatalError (org.xml.sax.SAXParseException)
public void warning (org.xml.sax.SAXParseException)
protected void walkDOMTree (netscape.javascript.JSObject)
private void getAttributes (org.xml.sax.Attributes)
private void getAttributes (netscape.javascript.JSObject)
}
org/jmol/adapter/readers/xml/XmlReader.class
<Unknown>
package org.jmol.adapter.readers.xml
public org.jmol.adapter.readers.xml.XmlReader extends org.jmol.adapter.smarter.AtomSetCollectionReader {
protected org.jmol.adapter.readers.xml.XmlReader parent
protected org.jmol.adapter.smarter.Atom atom
String[] implementedAttributes
protected boolean keepChars
protected String chars
public void <init> ()
public void readAtomSetCollection (java.io.BufferedReader)
private org.xml.sax.XMLReader getXMLReader ()
private org.xml.sax.XMLReader allocateXmlReader14 ()
private org.xml.sax.XMLReader allocateXmlReaderAelfred2 ()
private java.lang.Object processXml (org.xml.sax.XMLReader) throws java.lang.Exception
private java.lang.Object getXmlReader ()
protected void processXml (org.jmol.adapter.readers.xml.XmlReader, org.jmol.adapter.smarter.AtomSetCollection, java.io.BufferedReader, org.xml.sax.XMLReader)
protected void parseReaderXML (org.xml.sax.XMLReader)
public void readAtomSetCollectionFromDOM (java.lang.Object)
private java.lang.Object processXml (netscape.javascript.JSObject)
protected void processXml (org.jmol.adapter.readers.xml.XmlReader, org.jmol.adapter.smarter.AtomSetCollection, java.io.BufferedReader, netscape.javascript.JSObject)
protected void processStartElement (java.lang.String, java.lang.String, java.lang.String, java.util.HashMap)
protected void setKeepChars (boolean)
protected void processEndElement (java.lang.String, java.lang.String, java.lang.String)
}
org/jmol/adapter/readers/xml/XmlXsdReader$XsdHandler.class
<Unknown>
package org.jmol.adapter.readers.xml
org.jmol.adapter.readers.xml.XmlXsdReader$XsdHandler extends org.jmol.adapter.readers.xml.XmlReader$JmolXmlHandler {
private final org.jmol.adapter.readers.xml.XmlXsdReader this$0
void <init> (org.jmol.adapter.readers.xml.XmlXsdReader)
void <init> (org.jmol.adapter.readers.xml.XmlXsdReader, org.xml.sax.XMLReader)
}
org/jmol/adapter/readers/xml/XmlXsdReader.class
<Unknown>
package org.jmol.adapter.readers.xml
public org.jmol.adapter.readers.xml.XmlXsdReader extends org.jmol.adapter.readers.xml.XmlReader {
String[] xsdImplementedAttributes
private java.util.BitSet bsBackbone
private int iChain
private int iGroup
private int iAtom
public void <init> ()
protected void processXml (org.jmol.adapter.readers.xml.XmlReader, org.jmol.adapter.smarter.AtomSetCollection, java.io.BufferedReader, org.xml.sax.XMLReader)
protected void processXml (org.jmol.adapter.readers.xml.XmlReader, org.jmol.adapter.smarter.AtomSetCollection, java.io.BufferedReader, netscape.javascript.JSObject)
private void init (org.jmol.adapter.readers.xml.XmlReader, org.jmol.adapter.smarter.AtomSetCollection)
private void fin ()
public void processStartElement (java.lang.String, java.lang.String, java.lang.String, java.util.HashMap)
public void processEndElement (java.lang.String, java.lang.String, java.lang.String)
}
org/jmol/adapter/smarter/Atom.class
<Unknown>
package org.jmol.adapter.smarter
public org.jmol.adapter.smarter.Atom extends javax.vecmath.Point3f implements java.lang.Cloneable {
public int atomSetIndex
public int atomIndex
public java.util.BitSet bsSymmetry
public int atomSite
public String elementSymbol
public short elementNumber
public String atomName
public int formalCharge
public float partialCharge
public float vectorX
public float vectorY
public float vectorZ
public float bfactor
public int occupancy
public float radius
public boolean isHetero
public int atomSerial
public char chainID
public char alternateLocationID
public String group3
public int sequenceNumber
public char insertionCode
public float[] anisoBorU
public Object[] ellipsoid
static final int[] elementCharMasks
public void <init> ()
public org.jmol.adapter.smarter.Atom cloneAtom () throws java.lang.Exception
public java.lang.String getElementSymbol ()
public void addVibrationVector (float, float, float)
public static boolean isValidElementSymbol (char)
public static boolean isValidElementSymbol (char, char)
public static boolean isValidElementSymbolNoCaseSecondChar (char, char)
public static boolean isValidFirstSymbolChar (char)
public static boolean isValidElementSymbolNoCaseSecondChar (java.lang.String)
static void <clinit> ()
}
org/jmol/adapter/smarter/AtomSetCollection.class
<Unknown>
package org.jmol.adapter.smarter
public org.jmol.adapter.smarter.AtomSetCollection extends java.lang.Object {
String fileTypeName
String collectionName
java.util.Properties atomSetCollectionProperties
java.util.Hashtable atomSetCollectionAuxiliaryInfo
static final String[] globalBooleans
static final int GLOBAL_FRACTCOORD
static final int GLOBAL_SYMMETRY
static final int GLOBAL_latticeCells
public static final String[] notionalUnitcellTags
int atomCount
org.jmol.adapter.smarter.Atom[] atoms
int bondCount
org.jmol.adapter.smarter.Bond[] bonds
int structureCount
org.jmol.adapter.smarter.Structure[] structures
int atomSetCount
int currentAtomSetIndex
int[] atomSetNumbers
String[] atomSetNames
int[] atomSetAtomCounts
int[] atomSetBondCounts
java.util.Properties[] atomSetProperties
java.util.Hashtable[] atomSetAuxiliaryInfo
int[] latticeCells
public String errorMessage
boolean coordinatesAreFractional
private boolean isTrajectory
int trajectoryStepCount
javax.vecmath.Point3f[] trajectoryStep
java.util.Vector trajectorySteps
float[] notionalUnitCell
private boolean noAutoBond
java.util.Vector vConnect
int connectNextAtomIndex
int connectNextAtomSet
int[] connectLast
float symmetryRange
org.jmol.api.SymmetryInterface symmetry
boolean doNormalize
boolean doPackUnitCell
boolean isLatticeRange
private float rminx
private float rminy
private float rminz
private float rmaxx
private float rmaxy
private float rmaxz
private final javax.vecmath.Point3f ptOffset
private int minX
private int maxX
private int minY
private int maxY
private int minZ
private int maxZ
javax.vecmath.Point3f[] cartesians
int bondCount0
int bondIndex0
boolean applySymmetryToBonds
boolean checkSpecial
private final javax.vecmath.Point3f ptTemp
private final javax.vecmath.Point3f ptTemp1
private final javax.vecmath.Point3f ptTemp2
java.util.Hashtable atomSymbolicMap
boolean haveMappedSerials
org.jmol.api.VolumeDataInterface vd
public int getAtomCount ()
public org.jmol.adapter.smarter.Atom[] getAtoms ()
public org.jmol.adapter.smarter.Atom getAtom (int)
public int getBondCount ()
public org.jmol.adapter.smarter.Bond[] getBonds ()
public org.jmol.adapter.smarter.Bond getBond (int)
public int getAtomSetCount ()
public int getCurrentAtomSetIndex ()
public boolean isTrajectory ()
public void <init> (java.lang.String)
public void <init> (org.jmol.adapter.smarter.AtomSetCollection[])
public void <init> (java.util.Vector)
private void appendAtomSetCollection (java.util.Vector)
public void setFileTypeName (java.lang.String)
public boolean setTrajectory ()
protected void appendAtomSetCollection (int, org.jmol.adapter.smarter.AtomSetCollection)
void setNoAutoBond ()
void finish ()
void freeze ()
public void discardPreviousAtoms ()
public void removeAtomSet ()
org.jmol.adapter.smarter.Atom newCloneAtom (org.jmol.adapter.smarter.Atom) throws java.lang.Exception
public void cloneFirstAtomSet () throws java.lang.Exception
public void cloneFirstAtomSetWithBonds (int) throws java.lang.Exception
public void cloneLastAtomSet () throws java.lang.Exception
public int getFirstAtomSetAtomCount ()
public int getLastAtomSetAtomCount ()
public int getLastAtomSetAtomIndex ()
public org.jmol.adapter.smarter.Atom addNewAtom ()
public void addAtom (org.jmol.adapter.smarter.Atom)
public void addAtomWithMappedName (org.jmol.adapter.smarter.Atom)
public void addAtomWithMappedSerialNumber (org.jmol.adapter.smarter.Atom)
public org.jmol.adapter.smarter.Bond addNewBond (int, int)
org.jmol.adapter.smarter.Bond addNewBond (java.lang.String, java.lang.String)
public org.jmol.adapter.smarter.Bond addNewBond (int, int, int)
public org.jmol.adapter.smarter.Bond addNewBond (java.lang.String, java.lang.String, int)
public org.jmol.adapter.smarter.Bond addNewBondWithMappedSerialNumbers (int, int, int)
public void addConnection (int[])
public void connectAll (int)
public void addBond (org.jmol.adapter.smarter.Bond)
public void addStructure (org.jmol.adapter.smarter.Structure)
void setAtomSetSpaceGroupName (java.lang.String)
void setCoordinatesAreFractional (boolean)
void setSymmetryRange (float)
void setLatticeCells (int[], boolean, boolean)
private org.jmol.api.SymmetryInterface getSymmetry ()
boolean setNotionalUnitCell (float[])
void setGlobalBoolean (int)
boolean addSpaceGroupOperation (java.lang.String)
public void setLatticeParameter (int)
void applySymmetry () throws java.lang.Exception
void applySymmetry (org.jmol.api.SymmetryInterface) throws java.lang.Exception
void applySymmetry (int, int, int) throws java.lang.Exception
private void setSymmetryMinMax (javax.vecmath.Point3f)
private boolean isInSymmetryRange (javax.vecmath.Point3f)
private static boolean isWithinCell (javax.vecmath.Point3f, int, int, int, int, int, int)
private void applyAllSymmetry (int, int, int) throws java.lang.Exception
public void setCheckSpecial (boolean)
private int symmetryAddAtoms (int, int, int, int, int, int, int, int) throws java.lang.Exception
public void applySymmetry (java.util.Vector, boolean, java.lang.String)
public void setCollectionName (java.lang.String)
void mapMostRecentAtomName ()
public void clearSymbolicMap ()
void mapMostRecentAtomSerialNumber ()
public void createAtomSerialMap ()
void mapAtomName (java.lang.String, int)
public int getAtomNameIndex (java.lang.String)
public int getAtomSerialNumberIndex (int)
public void setAtomSetCollectionProperty (java.lang.String, java.lang.String)
java.lang.String getAtomSetCollectionProperty (java.lang.String)
public void setAtomSetCollectionAuxiliaryInfo (java.lang.String, java.lang.Object)
public boolean setAtomSetCollectionPartialCharges (java.lang.String)
public void mapPartialCharge (java.lang.String, float)
public java.lang.Object getAtomSetCollectionAuxiliaryInfo (java.lang.String)
private void addTrajectoryStep ()
void finalizeTrajectory (java.util.Vector)
private void finalizeTrajectory (boolean)
public void newAtomSet ()
public void setAtomSetName (java.lang.String)
public void setAtomSetName (java.lang.String, int)
public void setAtomSetNames (java.lang.String, int)
public void setAtomSetNumber (int)
public void setAtomSetProperty (java.lang.String, java.lang.String)
public void setAtomSetAuxiliaryInfo (java.lang.String, java.lang.Object)
boolean setAtomSetPartialCharges (java.lang.String)
java.lang.Object getAtomSetAuxiliaryInfo (int, java.lang.String)
public void setAtomSetProperty (java.lang.String, java.lang.String, int)
void setAtomSetAuxiliaryInfo (java.lang.String, java.lang.Object, int)
public void setAtomSetProperties (java.lang.String, java.lang.String, int)
public void cloneLastAtomSetProperties ()
void cloneAtomSetProperties (int)
int getAtomSetNumber (int)
java.lang.String getAtomSetName (int)
java.util.Properties getAtomSetProperties (int)
java.util.Hashtable getAtomSetAuxiliaryInfo (int)
boolean hasAlternateLocations ()
void getAltLocLists ()
boolean hasInsertions ()
void getInsertionLists ()
public void newVolumeData ()
public void setVoxelCounts (int, int, int)
public void setVolumetricVector (int, float, float, float)
public void setVolumetricOrigin (float, float, float)
public void setVoxelData (float[][][])
public java.lang.Object getVolumeData ()
public java.util.Properties setAtomNames (java.util.Properties)
static void <clinit> ()
}
org/jmol/adapter/smarter/AtomSetCollectionReader.class
<Unknown>
package org.jmol.adapter.smarter
public abstract org.jmol.adapter.smarter.AtomSetCollectionReader extends java.lang.Object {
public static final float ANGSTROMS_PER_BOHR
protected org.jmol.adapter.smarter.AtomSetCollection atomSetCollection
protected java.io.BufferedReader reader
protected String readerName
public java.util.Hashtable htParams
public String line
public String prevline
protected int[] next
private long ptLine
public int[] latticeCells
public boolean iHaveUnitCell
public boolean iHaveSymmetryOperators
protected boolean doApplySymmetry
protected boolean ignoreFileSymmetryOperators
protected boolean isTrajectory
protected boolean applySymmetryToBonds
protected boolean needToApplySymmetry
protected boolean getHeader
protected int templateAtomCount
protected int modelNumber
protected java.util.BitSet bsModels
protected java.util.BitSet bsFilter
protected String filter
protected boolean haveAtomFilter
protected String spaceGroup
protected boolean havePartialChargeFilter
public String calculationType
private boolean iHaveFractionalCoordinates
private boolean doPackUnitCell
private boolean doConvertToFractional
private boolean fileCoordinatesAreFractional
protected boolean ignoreFileUnitCell
private boolean ignoreFileSpaceGroupName
private float symmetryRange
private float[] notionalUnitCell
private int[] firstLastStep
private int desiredModelNumber
private int lastModelNumber
private int desiredSpaceGroupIndex
private org.jmol.api.SymmetryInterface symmetry
private boolean haveModel
private int nMatrixElements
private javax.vecmath.Matrix3f matrixRotate
private String previousScript
public void <init> ()
public java.lang.Object readData (java.lang.String, java.util.Hashtable, java.io.BufferedReader) throws java.lang.Exception
protected java.lang.Object readData (java.lang.String, java.util.Hashtable, java.lang.Object)
public abstract void readAtomSetCollection (java.io.BufferedReader)
public void readAtomSetCollectionFromDOM (java.lang.Object)
private java.lang.Object finalize (java.util.Hashtable, java.lang.String)
protected void setError (java.lang.Exception)
void initialize (java.util.Hashtable)
protected boolean doGetModel (int)
protected boolean isLastModel (int)
private void initializeSymmetry ()
protected void newAtomSet (java.lang.String)
public void setSpaceGroupName (java.lang.String)
public void setSymmetryOperator (java.lang.String)
private void initializeCartesianToFractional ()
public void clearLatticeParameters ()
public void setUnitCellItem (int, float)
protected void setUnitCell (float, float, float, float, float, float)
public void addPrimitiveLatticeVector (int, float[])
private boolean checkUnitCell (int)
private org.jmol.api.SymmetryInterface newSymmetry ()
public void setFractionalCoordinates (boolean)
protected boolean filterAtom (org.jmol.adapter.smarter.Atom)
protected boolean filterAtom (org.jmol.adapter.smarter.Atom, int)
public void setAtomCoord (org.jmol.adapter.smarter.Atom, float, float, float)
public void setAtomCoord (org.jmol.adapter.smarter.Atom)
protected void addSites (java.util.Hashtable)
public void applySymmetryAndSetTrajectory () throws java.lang.Exception
public void setMOData (java.util.Hashtable)
public void setTransform (float, float, float, float, float, float, float, float, float)
public static java.lang.String getElementSymbol (int)
protected static java.lang.String deducePdbElementSymbol (boolean, java.lang.String, java.lang.String)
protected void fillDataBlock (java.lang.String[][]) throws java.lang.Exception
protected void discardLines (int) throws java.lang.Exception
protected java.lang.String discardLinesUntilStartsWith (java.lang.String) throws java.lang.Exception
protected java.lang.String discardLinesUntilContains (java.lang.String) throws java.lang.Exception
protected void discardLinesUntilBlank () throws java.lang.Exception
protected java.lang.String discardLinesUntilNonBlank () throws java.lang.Exception
protected void checkLineForScript (java.lang.String)
public void checkLineForScript ()
protected void addJmolScript (java.lang.String)
public java.lang.String readLine () throws java.lang.Exception
protected java.lang.String readLineTrimmed () throws java.lang.Exception
protected static final java.lang.String[] getStrings (java.lang.String, int, int)
protected java.lang.String[] getTokens ()
protected static void getTokensFloat (java.lang.String, float[], int)
public static java.lang.String[] getTokens (java.lang.String)
protected static java.lang.String[] getTokens (java.lang.String, int)
protected float parseFloat ()
public float parseFloat (java.lang.String)
protected float parseFloat (java.lang.String, int, int)
protected int parseInt ()
public int parseInt (java.lang.String)
protected int parseInt (java.lang.String, int)
protected int parseInt (java.lang.String, int, int)
protected java.lang.String parseToken ()
protected java.lang.String parseToken (java.lang.String)
protected java.lang.String parseTokenNext (java.lang.String)
protected java.lang.String parseToken (java.lang.String, int, int)
protected static java.lang.String parseTrimmed (java.lang.String, int)
protected static java.lang.String parseTrimmed (java.lang.String, int, int)
}
org/jmol/adapter/smarter/Bond.class
<Unknown>
package org.jmol.adapter.smarter
public org.jmol.adapter.smarter.Bond extends java.lang.Object {
public int atomIndex1
public int atomIndex2
public int order
public void <init> ()
public void <init> (int, int, int)
}
org/jmol/adapter/smarter/LimitedLineReader.class
<Unknown>
package org.jmol.adapter.smarter
org.jmol.adapter.smarter.LimitedLineReader extends java.lang.Object {
private char[] buf
private int cchBuf
private int ichCurrent
void <init> (java.io.BufferedReader, int) throws java.lang.Exception
java.lang.String getHeader (int)
java.lang.String readLineWithNewline ()
}
org/jmol/adapter/smarter/Resolver.class
<Unknown>
package org.jmol.adapter.smarter
public org.jmol.adapter.smarter.Resolver extends java.lang.Object {
private static final String classBase
private static final String[] readerSets
private static final String CML_NAMESPACE_URI
private static final int SPECIAL_JME
private static final int SPECIAL_MOPACGRAPHF
private static final int SPECIAL_V3000
private static final int SPECIAL_ODYSSEY
private static final int SPECIAL_MOL
private static final int SPECIAL_XYZ
private static final int SPECIAL_FOLDINGXYZ
private static final int SPECIAL_CUBE
private static final int SPECIAL_ALCHEMY
private static final int SPECIAL_WIEN
private static final int SPECIAL_CASTEP
private static final int SPECIAL_AIMS
public static final int SPECIAL_ARGUS_XML
public static final int SPECIAL_CML_XML
public static final int SPECIAL_CHEM3D_XML
public static final int SPECIAL_MOLPRO_XML
public static final int SPECIAL_ODYSSEY_XML
public static final int SPECIAL_XSD_XML
public static final int SPECIAL_ARGUS_DOM
public static final int SPECIAL_CML_DOM
public static final int SPECIAL_CHEM3D_DOM
public static final int SPECIAL_MOLPRO_DOM
public static final int SPECIAL_ODYSSEY_DOM
public static final int SPECIAL_XSD_DOM
public static final String[][] specialTags
private static final int LEADER_CHAR_MAX
private static final String[] cubeFileStartRecords
private static final String[] mol2Records
private static final String[] webmoFileStartRecords
private static final String[] moldenFileStartRecords
private static final String[][] fileStartsWithRecords
private static final String[] pqrLineStartRecords
private static final String[] pdbLineStartRecords
private static final String[] shelxLineStartRecords
private static final String[] cifLineStartRecords
private static final String[] ghemicalMMLineStartRecords
private static final String[] jaguarLineStartRecords
private static final String[] hinLineStartRecords
private static final String[] mdlLineStartRecords
private static final String[] spartanSmolLineStartRecords
private static final String[] csfLineStartRecords
private static final String[] mdTopLineStartRecords
private static final String[][] lineStartsWithRecords
private static final String[] xmlContainsRecords
private static final String[] gaussianContainsRecords
private static final String[] mopacContainsRecords
private static final String[] qchemContainsRecords
private static final String[] gamessUKContainsRecords
private static final String[] gamessUSContainsRecords
private static final String[] spartanBinaryContainsRecords
private static final String[] spartanContainsRecords
private static final String[] adfContainsRecords
private static final String[] psiContainsRecords
private static final String[] nwchemContainsRecords
private static final String[] uicrcifContainsRecords
private static final String[][] containsRecords
public void <init> ()
static java.lang.String getFileType (java.io.BufferedReader)
static java.lang.String[] specialLoad (java.lang.String, java.lang.String)
static java.lang.String[] checkSpecialInZip (java.lang.String[])
static java.lang.StringBuffer checkSpecialData (java.io.InputStream, java.lang.String[])
static java.lang.Object getAtomCollectionAndCloseReader (java.lang.String, java.lang.String, java.io.BufferedReader, java.util.Hashtable, int) throws java.lang.Exception
static java.lang.Object DOMResolve (java.lang.Object) throws java.lang.Exception
public static final java.lang.String getReaderClassBase (java.lang.String)
private static java.lang.String[] getSpartanFileList (java.lang.String, java.lang.String[])
private static java.lang.String[] getSpartanDirs (java.lang.String)
private static java.lang.String getXmlType (netscape.javascript.JSObject)
private static java.lang.String determineAtomSetCollectionReader (java.io.BufferedReader, boolean) throws java.lang.Exception
private static java.lang.String getXmlType (java.lang.String) throws java.lang.Exception
private static final java.lang.String checkSpecial (int, java.lang.String[], boolean)
private static boolean checkGromacs (java.lang.String[])
private static boolean checkWien2k (java.lang.String[])
private static boolean checkCastep (java.lang.String[])
private static boolean checkAims (java.lang.String[])
private static final java.lang.String getReaderFromType (java.lang.String)
private static final java.lang.String checkType (java.lang.String[][], java.lang.String)
private static boolean checkOdyssey (java.lang.String[])
private static boolean checkV3000 (java.lang.String[])
private static boolean checkMol (java.lang.String[])
private static boolean checkAlchemy (java.lang.String)
private static boolean checkXyz (java.lang.String[])
private static boolean checkFoldingXyz (java.lang.String[])
private static boolean checkMopacGraphf (java.lang.String[])
private static boolean checkCube (java.lang.String[])
static void <clinit> ()
}
org/jmol/adapter/smarter/SmarterJmolAdapter$AtomIterator.class
<Unknown>
package org.jmol.adapter.smarter
org.jmol.adapter.smarter.SmarterJmolAdapter$AtomIterator extends org.jmol.api.JmolAdapter$AtomIterator {
org.jmol.adapter.smarter.AtomSetCollection atomSetCollection
int iatom
org.jmol.adapter.smarter.Atom atom
int atomCount
org.jmol.adapter.smarter.Atom[] atoms
private final org.jmol.adapter.smarter.SmarterJmolAdapter this$0
void <init> (org.jmol.adapter.smarter.SmarterJmolAdapter, org.jmol.adapter.smarter.AtomSetCollection)
public boolean hasNext ()
public int getAtomSetIndex ()
public java.util.BitSet getAtomSymmetry ()
public int getAtomSite ()
public java.lang.Object getUniqueID ()
public java.lang.String getElementSymbol ()
public int getElementNumber ()
public java.lang.String getAtomName ()
public int getFormalCharge ()
public float getPartialCharge ()
public java.lang.Object[] getEllipsoid ()
public float getRadius ()
public float getX ()
public float getY ()
public float getZ ()
public float getVectorX ()
public float getVectorY ()
public float getVectorZ ()
public float getBfactor ()
public int getOccupancy ()
public boolean getIsHetero ()
public int getAtomSerial ()
public char getChainID ()
public char getAlternateLocationID ()
public java.lang.String getGroup3 ()
public int getSequenceNumber ()
public char getInsertionCode ()
}
org/jmol/adapter/smarter/SmarterJmolAdapter$BondIterator.class
<Unknown>
package org.jmol.adapter.smarter
org.jmol.adapter.smarter.SmarterJmolAdapter$BondIterator extends org.jmol.api.JmolAdapter$BondIterator {
org.jmol.adapter.smarter.AtomSetCollection atomSetCollection
org.jmol.adapter.smarter.Bond[] bonds
int ibond
org.jmol.adapter.smarter.Bond bond
int bondCount
private final org.jmol.adapter.smarter.SmarterJmolAdapter this$0
void <init> (org.jmol.adapter.smarter.SmarterJmolAdapter, org.jmol.adapter.smarter.AtomSetCollection)
public boolean hasNext ()
public java.lang.Object getAtomUniqueID1 ()
public java.lang.Object getAtomUniqueID2 ()
public int getEncodedOrder ()
}
org/jmol/adapter/smarter/SmarterJmolAdapter$StructureIterator.class
<Unknown>
package org.jmol.adapter.smarter
public org.jmol.adapter.smarter.SmarterJmolAdapter$StructureIterator extends org.jmol.api.JmolAdapter$StructureIterator {
int structureCount
org.jmol.adapter.smarter.Structure[] structures
org.jmol.adapter.smarter.Structure structure
int istructure
private final org.jmol.adapter.smarter.SmarterJmolAdapter this$0
void <init> (org.jmol.adapter.smarter.SmarterJmolAdapter, org.jmol.adapter.smarter.AtomSetCollection)
public boolean hasNext ()
public int getModelIndex ()
public java.lang.String getStructureType ()
public java.lang.String getStructureID ()
public int getSerialID ()
public char getStartChainID ()
public int getStartSequenceNumber ()
public char getStartInsertionCode ()
public char getEndChainID ()
public int getEndSequenceNumber ()
public char getEndInsertionCode ()
public int getStrandCount ()
}
org/jmol/adapter/smarter/SmarterJmolAdapter.class
<Unknown>
package org.jmol.adapter.smarter
public org.jmol.adapter.smarter.SmarterJmolAdapter extends org.jmol.api.JmolAdapter {
public static final String PATH_KEY
public static final String PATH_SEPARATOR
public void <init> ()
public void finish (java.lang.Object)
public java.lang.String[] specialLoad (java.lang.String, java.lang.String)
public java.lang.Object getAtomSetCollectionFromReader (java.lang.String, java.lang.String, java.io.BufferedReader, java.util.Hashtable)
private static java.lang.Object staticGetAtomSetCollectionFromReader (java.lang.String, java.lang.String, java.io.BufferedReader, java.util.Hashtable)
public java.lang.Object getAtomSetCollectionFromReaders (org.jmol.api.JmolFileReaderInterface, java.lang.String[], java.lang.String[], java.util.Hashtable[])
private static java.lang.Object staticGetAtomSetCollectionFromReaders (org.jmol.api.JmolFileReaderInterface, java.lang.String[], java.lang.String[], java.util.Hashtable[])
public java.lang.Object getAtomSetCollectionOrBufferedReaderFromZip (java.io.InputStream, java.lang.String, java.lang.String[], java.util.Hashtable, boolean)
private static java.lang.Object staticGetAtomSetCollectionOrBufferedReaderFromZip (java.io.InputStream, java.lang.String, java.lang.String[], java.util.Hashtable, int, boolean)
public java.lang.Object getAtomSetCollectionFromDOM (java.lang.Object)
private static java.lang.Object staticGetAtomSetCollectionFromDOM (java.lang.Object)
public java.lang.String getFileTypeName (java.lang.Object)
private static java.lang.String staticGetFileTypeName (java.lang.Object)
public java.lang.String getAtomSetCollectionName (java.lang.Object)
public java.util.Properties getAtomSetCollectionProperties (java.lang.Object)
public java.util.Hashtable getAtomSetCollectionAuxiliaryInfo (java.lang.Object)
public int getAtomSetCount (java.lang.Object)
public int getAtomSetNumber (java.lang.Object, int)
public java.lang.String getAtomSetName (java.lang.Object, int)
public java.util.Properties getAtomSetProperties (java.lang.Object, int)
public java.util.Hashtable getAtomSetAuxiliaryInfo (java.lang.Object, int)
public int getEstimatedAtomCount (java.lang.Object)
public boolean coordinatesAreFractional (java.lang.Object)
public float[] getNotionalUnitcell (java.lang.Object)
public float[] getPdbScaleMatrix (java.lang.Object)
public float[] getPdbScaleTranslate (java.lang.Object)
public java.lang.String getClientAtomStringProperty (java.lang.Object, java.lang.String)
public org.jmol.api.JmolAdapter$AtomIterator getAtomIterator (java.lang.Object)
public org.jmol.api.JmolAdapter$BondIterator getBondIterator (java.lang.Object)
public org.jmol.api.JmolAdapter$StructureIterator getStructureIterator (java.lang.Object)
static void <clinit> ()
}
org/jmol/adapter/smarter/Structure.class
<Unknown>
package org.jmol.adapter.smarter
public org.jmol.adapter.smarter.Structure extends java.lang.Object {
public String structureType
public String structureID
public int serialID
public int strandCount
public char startChainID
public int startSequenceNumber
public char startInsertionCode
public char endChainID
public int endSequenceNumber
public char endInsertionCode
public int modelIndex
public void <init> ()
public void <init> (int, java.lang.String, java.lang.String, int, int, char, int, char, char, int, char)
}
org/jmol/api/Interface.class
<Unknown>
package org.jmol.api
public org.jmol.api.Interface extends java.lang.Object {
public void <init> ()
public static java.lang.Object getOptionInterface (java.lang.String)
public static java.lang.Object getApplicationInterface (java.lang.String)
}
org/jmol/api/JmolAdapter$AtomIterator.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.JmolAdapter$AtomIterator extends java.lang.Object {
private final org.jmol.api.JmolAdapter this$0
public void <init> (org.jmol.api.JmolAdapter)
public abstract boolean hasNext ()
public int getAtomSetIndex ()
public java.util.BitSet getAtomSymmetry ()
public int getAtomSite ()
public abstract java.lang.Object getUniqueID ()
public int getElementNumber ()
public java.lang.String getElementSymbol ()
public java.lang.String getAtomName ()
public int getFormalCharge ()
public float getPartialCharge ()
public java.lang.Object[] getEllipsoid ()
public float getRadius ()
public abstract float getX ()
public abstract float getY ()
public abstract float getZ ()
public float getVectorX ()
public float getVectorY ()
public float getVectorZ ()
public float getBfactor ()
public int getOccupancy ()
public boolean getIsHetero ()
public int getAtomSerial ()
public char getChainID ()
public char getAlternateLocationID ()
public java.lang.String getGroup3 ()
public int getSequenceNumber ()
public char getInsertionCode ()
public java.lang.Object getClientAtomReference ()
}
org/jmol/api/JmolAdapter$BondIterator.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.JmolAdapter$BondIterator extends java.lang.Object {
private final org.jmol.api.JmolAdapter this$0
public void <init> (org.jmol.api.JmolAdapter)
public abstract boolean hasNext ()
public abstract java.lang.Object getAtomUniqueID1 ()
public abstract java.lang.Object getAtomUniqueID2 ()
public abstract int getEncodedOrder ()
}
org/jmol/api/JmolAdapter$StructureIterator.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.JmolAdapter$StructureIterator extends java.lang.Object {
private final org.jmol.api.JmolAdapter this$0
public void <init> (org.jmol.api.JmolAdapter)
public abstract boolean hasNext ()
public abstract int getModelIndex ()
public abstract java.lang.String getStructureType ()
public abstract java.lang.String getStructureID ()
public abstract int getSerialID ()
public abstract int getStrandCount ()
public abstract char getStartChainID ()
public abstract int getStartSequenceNumber ()
public abstract char getStartInsertionCode ()
public abstract char getEndChainID ()
public abstract int getEndSequenceNumber ()
public abstract char getEndInsertionCode ()
}
org/jmol/api/JmolAdapter.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.JmolAdapter extends java.lang.Object {
public static final short ORDER_COVALENT_SINGLE
public static final short ORDER_COVALENT_DOUBLE
public static final short ORDER_COVALENT_TRIPLE
public static final short ORDER_AROMATIC
public static final short ORDER_AROMATIC_SINGLE
public static final short ORDER_AROMATIC_DOUBLE
public static final short ORDER_HBOND
public static final short ORDER_STEREO_NEAR
public static final short ORDER_STEREO_FAR
public static final short ORDER_PARTIAL01
public static final short ORDER_PARTIAL12
public static final short ORDER_PARTIAL23
public static final short ORDER_PARTIAL32
public static final short ORDER_UNSPECIFIED
public static final int SHELL_S
public static final int SHELL_P
public static final int SHELL_SP
public static final int SHELL_L
public static final int SHELL_D_CARTESIAN
public static final int SHELL_D_SPHERICAL
public static final int SHELL_F_CARTESIAN
public static final int SHELL_F_SPHERICAL
String adapterName
public static java.lang.String getElementSymbol (int)
public static int getElementNumber (java.lang.String)
public static boolean isHetero (java.lang.String)
public static int getQuantumShellTagID (java.lang.String)
public static int getQuantumShellTagIDSpherical (java.lang.String)
public static final int getQuantumSubshellTagID (int, java.lang.String)
public static final java.lang.String getQuantumSubshellTag (int, int)
public static final java.lang.String canonicalizeQuantumSubshellTag (java.lang.String)
public static final short lookupGroupID (java.lang.String)
public void <init> (java.lang.String)
public java.lang.String getAdapterName ()
public abstract java.lang.Object getAtomSetCollectionFromReader (java.lang.String, java.lang.String, java.io.BufferedReader, java.util.Hashtable)
public abstract java.lang.Object getAtomSetCollectionFromReaders (org.jmol.api.JmolFileReaderInterface, java.lang.String[], java.lang.String[], java.util.Hashtable[])
public abstract java.lang.Object getAtomSetCollectionOrBufferedReaderFromZip (java.io.InputStream, java.lang.String, java.lang.String[], java.util.Hashtable, boolean)
public java.lang.Object openBufferedReader (java.lang.String, java.io.BufferedReader)
public java.lang.Object openBufferedReader (java.lang.String, java.io.BufferedReader, java.util.Hashtable)
public java.lang.Object openBufferedReader (java.lang.String, java.lang.String, java.io.BufferedReader)
public abstract java.lang.Object getAtomSetCollectionFromDOM (java.lang.Object)
public void finish (java.lang.Object)
public abstract java.lang.String getFileTypeName (java.lang.Object)
public abstract java.lang.String getAtomSetCollectionName (java.lang.Object)
public abstract java.util.Properties getAtomSetCollectionProperties (java.lang.Object)
public abstract java.util.Hashtable getAtomSetCollectionAuxiliaryInfo (java.lang.Object)
public abstract int getAtomSetCount (java.lang.Object)
public abstract int getAtomSetNumber (java.lang.Object, int)
public abstract java.lang.String getAtomSetName (java.lang.Object, int)
public abstract java.util.Properties getAtomSetProperties (java.lang.Object, int)
public abstract java.util.Hashtable getAtomSetAuxiliaryInfo (java.lang.Object, int)
public abstract int getEstimatedAtomCount (java.lang.Object)
public abstract boolean coordinatesAreFractional (java.lang.Object)
public abstract float[] getNotionalUnitcell (java.lang.Object)
public abstract float[] getPdbScaleMatrix (java.lang.Object)
public abstract float[] getPdbScaleTranslate (java.lang.Object)
public abstract java.lang.String getClientAtomStringProperty (java.lang.Object, java.lang.String)
public abstract org.jmol.api.JmolAdapter$AtomIterator getAtomIterator (java.lang.Object)
public abstract org.jmol.api.JmolAdapter$BondIterator getBondIterator (java.lang.Object)
public abstract org.jmol.api.JmolAdapter$StructureIterator getStructureIterator (java.lang.Object)
public static final char canonizeAlphaDigit (char)
public static final char canonizeChainID (char)
public static final char canonizeInsertionCode (char)
public static final char canonizeAlternateLocationID (char)
public java.lang.String[] specialLoad (java.lang.String, java.lang.String)
}
org/jmol/api/JmolAppConsoleInterface.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.JmolAppConsoleInterface extends java.lang.Object {
public abstract org.jmol.api.JmolScriptEditorInterface getScriptEditor ()
public abstract org.jmol.api.JmolAppConsoleInterface getAppConsole (org.jmol.viewer.Viewer, java.awt.Component)
public abstract java.lang.String getText ()
public abstract java.lang.Object getMyMenuBar ()
public abstract void setVisible (boolean)
public abstract void sendConsoleEcho (java.lang.String)
public abstract void sendConsoleMessage (java.lang.String)
public abstract void zap ()
public abstract void dispose ()
}
org/jmol/api/JmolAppletInterface.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.JmolAppletInterface extends java.lang.Object {
public abstract java.awt.Graphics setStereoGraphics (boolean)
public abstract java.lang.String getPropertyAsString (java.lang.String)
public abstract java.lang.String getPropertyAsString (java.lang.String, java.lang.String)
public abstract java.lang.String getPropertyAsJSON (java.lang.String)
public abstract java.lang.String getPropertyAsJSON (java.lang.String, java.lang.String)
public abstract java.lang.Object getProperty (java.lang.String)
public abstract java.lang.Object getProperty (java.lang.String, java.lang.String)
public abstract java.lang.String loadInlineString (java.lang.String, java.lang.String, boolean)
public abstract java.lang.String loadInlineArray (java.lang.String[], java.lang.String, boolean)
public abstract java.lang.String loadNodeId (java.lang.String)
public abstract java.lang.String loadDOMNode (netscape.javascript.JSObject)
public abstract void script (java.lang.String)
public abstract java.lang.String scriptNoWait (java.lang.String)
public abstract java.lang.String scriptCheck (java.lang.String)
public abstract java.lang.String scriptWait (java.lang.String)
public abstract java.lang.String scriptWait (java.lang.String, java.lang.String)
public abstract java.lang.String scriptWaitOutput (java.lang.String)
public abstract void syncScript (java.lang.String)
public abstract java.lang.String loadInline (java.lang.String)
public abstract java.lang.String loadInline (java.lang.String[])
public abstract java.lang.String loadInline (java.lang.String, java.lang.String)
public abstract java.lang.String loadInline (java.lang.String[], java.lang.String)
}
org/jmol/api/JmolBioResolver.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.JmolBioResolver extends java.lang.Object {
public abstract org.jmol.modelset.Group distinguishAndPropagateGroup (org.jmol.modelset.Chain, java.lang.String, int, int, int, int, int[], byte[], org.jmol.modelset.Atom[])
public abstract org.jmol.modelset.Polymer buildBioPolymer (org.jmol.modelset.Group, org.jmol.modelset.Group[], int, boolean)
public abstract void clearBioPolymers (org.jmol.modelset.Group[], int, java.util.BitSet)
}
org/jmol/api/JmolCallbackListener.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.JmolCallbackListener extends java.lang.Object {
public abstract void setCallbackFunction (java.lang.String, java.lang.String)
public abstract void notifyCallback (int, java.lang.Object[])
public abstract boolean notifyEnabled (int)
}
org/jmol/api/JmolDialogInterface.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.JmolDialogInterface extends java.lang.Object {
public abstract void setupUI (boolean)
public abstract java.lang.String getType ()
public abstract int getQuality (java.lang.String)
public abstract java.lang.String getOpenFileNameFromDialog (java.lang.String, org.jmol.api.JmolViewer, java.lang.String, java.lang.Object, java.lang.String, boolean)
public abstract java.lang.String getSaveFileNameFromDialog (org.jmol.api.JmolViewer, java.lang.String, java.lang.String)
public abstract java.lang.String getImageFileNameFromDialog (org.jmol.api.JmolViewer, java.lang.String, java.lang.String, java.lang.String[], java.lang.String[], int, int)
}
org/jmol/api/JmolFileReaderInterface.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.JmolFileReaderInterface extends java.lang.Object {
public abstract java.io.BufferedReader getBufferedReader (int)
}
org/jmol/api/JmolImageCreatorInterface.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.JmolImageCreatorInterface extends java.lang.Object {
public abstract void setViewer (org.jmol.api.JmolViewer)
public abstract java.lang.String clipImage (java.lang.String)
public abstract java.lang.String getClipboardText ()
public abstract java.lang.Object createImage (java.lang.String, java.lang.String, java.lang.Object, int)
public abstract java.lang.Object getImageBytes (java.lang.String, int, java.lang.String, java.lang.Object, java.io.OutputStream) throws java.io.IOException
}
org/jmol/api/JmolLineReader.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.JmolLineReader extends java.lang.Object {
public abstract java.lang.String readLine () throws java.lang.Exception
}
org/jmol/api/JmolMovieCreatorInterface.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.JmolMovieCreatorInterface extends java.lang.Object {
public abstract java.lang.String createMovie (org.jmol.viewer.Viewer, java.lang.String[], int, int, int, java.lang.String)
}
org/jmol/api/JmolPdfCreatorInterface.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.JmolPdfCreatorInterface extends java.lang.Object {
public abstract java.lang.String createPdfDocument (java.lang.String, java.awt.Image)
}
org/jmol/api/JmolRendererInterface.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.JmolRendererInterface extends java.lang.Object {
public abstract boolean initializeExporter (java.lang.String, org.jmol.viewer.Viewer, org.jmol.g3d.Graphics3D, java.lang.Object)
public abstract boolean isAntialiased ()
public abstract boolean checkTranslucent (boolean)
public abstract boolean haveTranslucentObjects ()
public abstract int getRenderWidth ()
public abstract int getRenderHeight ()
public abstract int getSlab ()
public abstract void setSlab (int)
public abstract int getDepth ()
public abstract boolean setColix (short)
public abstract void renderBackground ()
public abstract void drawCircleCentered (short, int, int, int, int, boolean)
public abstract void fillScreenedCircleCentered (short, int, int, int, int)
public abstract void fillSphereCentered (int, int, int, int)
public abstract void fillSphereCentered (int, javax.vecmath.Point3i)
public abstract void fillSphereCentered (int, javax.vecmath.Point3f)
public abstract void drawRect (int, int, int, int, int, int)
public abstract void fillRect (int, int, int, int, int, int)
public abstract void drawString (java.lang.String, org.jmol.g3d.Font3D, int, int, int, int)
public abstract void plotPixelClippedNoSlab (int, int, int, int)
public abstract void drawStringNoSlab (java.lang.String, org.jmol.g3d.Font3D, int, int, int)
public abstract void setFont (byte)
public abstract org.jmol.g3d.Font3D getFont3DCurrent ()
public abstract void drawPixel (int, int, int)
public abstract void plotPixelClipped (javax.vecmath.Point3i)
public abstract void drawPoints (int, int[])
public abstract void drawDashedLine (int, int, javax.vecmath.Point3i, javax.vecmath.Point3i)
public abstract void drawDottedLine (javax.vecmath.Point3i, javax.vecmath.Point3i)
public abstract void drawLine (int, int, int, int, int, int)
public abstract void drawLine (javax.vecmath.Point3i, javax.vecmath.Point3i)
public abstract void drawLine (short, short, int, int, int, int, int, int)
public abstract void fillCylinder (short, short, byte, int, int, int, int, int, int, int)
public abstract void fillCylinder (byte, int, int, int, int, int, int, int)
public abstract void fillCylinder (byte, int, javax.vecmath.Point3i, javax.vecmath.Point3i)
public abstract void fillCylinderBits (byte, int, javax.vecmath.Point3f, javax.vecmath.Point3f)
public abstract void fillCone (byte, int, javax.vecmath.Point3i, javax.vecmath.Point3i)
public abstract void fillCone (byte, int, javax.vecmath.Point3f, javax.vecmath.Point3f)
public abstract void drawHermite (int, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i)
public abstract void drawHermite (boolean, boolean, int, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, int)
public abstract void fillHermite (int, int, int, int, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i)
public abstract void drawTriangle (javax.vecmath.Point3i, short, javax.vecmath.Point3i, short, javax.vecmath.Point3i, short, int)
public abstract void drawTriangle (javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, int)
public abstract void drawCylinderTriangle (int, int, int, int, int, int, int, int, int, int)
public abstract void drawfillTriangle (int, int, int, int, int, int, int, int, int)
public abstract void fillTriangle (javax.vecmath.Point3i, short, short, javax.vecmath.Point3i, short, short, javax.vecmath.Point3i, short, short)
public abstract void fillTriangle (short, int, int, int, int, int, int, int, int, int)
public abstract void fillTriangle (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f)
public abstract void fillTriangle (javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i)
public abstract void fillTriangle (javax.vecmath.Point3i, int, javax.vecmath.Point3i, int, javax.vecmath.Point3i, int)
public abstract void fillTriangle (javax.vecmath.Point3i, short, short, javax.vecmath.Point3i, short, short, javax.vecmath.Point3i, short, short, float)
public abstract void drawQuadrilateral (short, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i)
public abstract void fillQuadrilateral (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f)
public abstract void fillQuadrilateral (javax.vecmath.Point3i, short, short, javax.vecmath.Point3i, short, short, javax.vecmath.Point3i, short, short, javax.vecmath.Point3i, short, short)
public abstract void renderIsosurface (javax.vecmath.Point3f[], short, short[], javax.vecmath.Vector3f[], int[][], java.util.BitSet, int, int, short[], int)
public abstract boolean isInDisplayRange (int, int)
public abstract boolean isClippedZ (int)
public abstract boolean isClippedXY (int, int, int)
public abstract int getColixArgb (short)
public abstract java.lang.String getHexColorFromIndex (short)
public abstract int calcSurfaceShade (javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i)
public abstract byte getFontFid (java.lang.String, float)
public abstract short getNormix (javax.vecmath.Vector3f)
public abstract short getInverseNormix (short)
public abstract boolean isDirectedTowardsCamera (short)
public abstract javax.vecmath.Vector3f[] getTransformedVertexVectors ()
public abstract javax.vecmath.Vector3f getNormixVector (short)
public abstract org.jmol.g3d.Font3D getFont3DScaled (org.jmol.g3d.Font3D, float)
public abstract byte getFontFid (float)
public abstract void renderEllipsoid (javax.vecmath.Point3f, javax.vecmath.Point3f[], int, int, int, int, javax.vecmath.Matrix3f, double[], javax.vecmath.Matrix4f, int, javax.vecmath.Point3i[])
public abstract void drawImage (java.awt.Image, int, int, int, int, short, int, int)
public abstract void startShapeBuffer (int)
public abstract void endShapeBuffer ()
public abstract boolean canDoTriangles ()
public abstract boolean isCartesianExport ()
public abstract java.lang.String finalizeOutput ()
public abstract short[] getBgColixes (short[])
}
org/jmol/api/JmolScriptEditorInterface.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.JmolScriptEditorInterface extends java.lang.Object {
public abstract void setVisible (boolean)
public abstract void output (java.lang.String)
public abstract java.lang.String getText ()
public abstract void dispose ()
public abstract boolean isVisible ()
public abstract void notifyContext (org.jmol.viewer.ScriptContext, java.lang.Object[])
public abstract void notifyScriptTermination ()
public abstract void notifyScriptStart ()
public abstract void setFilename (java.lang.String)
}
org/jmol/api/JmolSelectionListener.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.JmolSelectionListener extends java.lang.Object {
public abstract void selectionChanged (java.util.BitSet)
}
org/jmol/api/JmolSimpleViewer.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.JmolSimpleViewer extends java.lang.Object {
public void <init> ()
public static org.jmol.api.JmolSimpleViewer allocateSimpleViewer (java.awt.Component, org.jmol.api.JmolAdapter)
public abstract void renderScreenImage (java.awt.Graphics, java.awt.Dimension, java.awt.Rectangle)
public abstract java.lang.String evalFile (java.lang.String)
public abstract java.lang.String evalString (java.lang.String)
public abstract java.lang.String openStringInline (java.lang.String)
public abstract java.lang.String openDOM (java.lang.Object)
public abstract java.lang.String openFile (java.lang.String)
public abstract java.lang.Object getProperty (java.lang.String, java.lang.String, java.lang.Object)
}
org/jmol/api/JmolStatusListener.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.JmolStatusListener extends java.lang.Object implements org.jmol.api.JmolCallbackListener {
public abstract java.lang.String eval (java.lang.String)
public abstract float[][] functionXY (java.lang.String, int, int)
public abstract float[][][] functionXYZ (java.lang.String, int, int, int)
public abstract java.lang.String createImage (java.lang.String, java.lang.String, java.lang.Object, int)
public abstract java.util.Hashtable getRegistryInfo ()
public abstract void showUrl (java.lang.String)
public abstract java.lang.String dialogAsk (java.lang.String, java.lang.String)
}
org/jmol/api/JmolViewer.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.JmolViewer extends org.jmol.api.JmolSimpleViewer {
public void <init> ()
public static org.jmol.api.JmolViewer allocateViewer (java.awt.Component, org.jmol.api.JmolAdapter, java.lang.String, java.net.URL, java.net.URL, java.lang.String, org.jmol.api.JmolStatusListener)
public abstract void renderScreenImage (java.awt.Graphics, java.awt.Graphics, java.awt.Dimension, java.awt.Rectangle)
public static org.jmol.api.JmolViewer allocateViewer (java.awt.Component, org.jmol.api.JmolAdapter)
public static java.lang.String getJmolVersion ()
public static boolean checkOption (org.jmol.api.JmolViewer, java.lang.String)
public abstract java.lang.String generateOutput (java.lang.String, java.lang.String, int, int)
public abstract void setJmolCallbackListener (org.jmol.api.JmolCallbackListener)
public abstract void setJmolStatusListener (org.jmol.api.JmolStatusListener)
public abstract void setAppletContext (java.lang.String, java.net.URL, java.net.URL, java.lang.String)
public abstract boolean checkHalt (java.lang.String)
public abstract void haltScriptExecution ()
public abstract boolean isJvm12orGreater ()
public abstract java.lang.String getOperatingSystemName ()
public abstract java.lang.String getJavaVersion ()
public abstract java.lang.String getJavaVendor ()
public abstract boolean haveFrame ()
public abstract void pushHoldRepaint ()
public abstract void popHoldRepaint ()
public abstract java.lang.String getData (java.lang.String, java.lang.String)
public abstract void setScreenDimension (java.awt.Dimension)
public abstract int getScreenWidth ()
public abstract int getScreenHeight ()
public abstract java.awt.Image getScreenImage ()
public abstract void releaseScreenImage ()
public abstract void writeTextFile (java.lang.String, java.lang.String)
public abstract java.lang.String clipImage (java.lang.String)
public abstract java.lang.String createImage (java.lang.String, java.lang.String, java.lang.Object, int, int, int)
public abstract java.lang.Object getImageAs (java.lang.String, int, int, int, java.lang.String, java.io.OutputStream)
public abstract boolean handleOldJvm10Event (java.awt.Event)
public abstract int getMotionEventNumber ()
public abstract java.lang.String openReader (java.lang.String, java.lang.String, java.io.Reader)
public abstract void openClientFile (java.lang.String, java.lang.String, java.lang.Object)
public abstract void showUrl (java.lang.String)
public abstract int getMeasurementCount ()
public abstract java.lang.String getMeasurementStringValue (int)
public abstract int[] getMeasurementCountPlusIndices (int)
public abstract java.awt.Component getDisplay ()
public abstract java.util.BitSet getElementsPresentBitSet (int)
public abstract int getAnimationFps ()
public abstract int findNearestAtomIndex (int, int)
public abstract java.lang.String script (java.lang.String)
public abstract java.lang.Object scriptCheck (java.lang.String)
public abstract java.lang.String scriptWait (java.lang.String)
public abstract java.lang.Object scriptWaitStatus (java.lang.String, java.lang.String)
public abstract java.lang.String loadInline (java.lang.String)
public abstract java.lang.String loadInline (java.lang.String, boolean)
public abstract java.lang.String loadInline (java.lang.String, char)
public abstract java.lang.String loadInline (java.lang.String[])
public abstract java.lang.String loadInline (java.lang.String[], boolean)
public abstract java.lang.String evalStringQuiet (java.lang.String)
public abstract boolean isScriptExecuting ()
public abstract java.lang.String getModelSetName ()
public abstract java.lang.String getModelSetFileName ()
public abstract java.lang.String getModelSetPathName ()
public abstract java.lang.String getFileAsString (java.lang.String)
public abstract boolean getFileAsString (java.lang.String[], int, boolean)
public abstract java.util.Properties getModelSetProperties ()
public abstract java.util.Hashtable getModelSetAuxiliaryInfo ()
public abstract int getModelNumber (int)
public abstract java.lang.String getModelName (int)
public abstract java.lang.String getModelNumberDotted (int)
public abstract java.util.Properties getModelProperties (int)
public abstract java.lang.String getModelProperty (int, java.lang.String)
public abstract java.util.Hashtable getModelAuxiliaryInfo (int)
public abstract java.lang.Object getModelAuxiliaryInfo (int, java.lang.String)
public abstract boolean modelHasVibrationVectors (int)
public abstract int getModelCount ()
public abstract int getDisplayModelIndex ()
public abstract int getAtomCount ()
public abstract int getBondCount ()
public abstract int getGroupCount ()
public abstract int getChainCount ()
public abstract int getPolymerCount ()
public abstract int getAtomCountInModel (int)
public abstract int getBondCountInModel (int)
public abstract int getGroupCountInModel (int)
public abstract int getChainCountInModel (int)
public abstract int getPolymerCountInModel (int)
public abstract int getSelectionCount ()
public abstract void addSelectionListener (org.jmol.api.JmolSelectionListener)
public abstract void removeSelectionListener (org.jmol.api.JmolSelectionListener)
public abstract void homePosition ()
public abstract java.util.Hashtable getHeteroList (int)
public abstract boolean getPerspectiveDepth ()
public abstract boolean getShowHydrogens ()
public abstract boolean getShowMeasurements ()
public abstract boolean getShowAxes ()
public abstract boolean getShowBbcage ()
public abstract int getAtomNumber (int)
public abstract java.lang.String getAtomName (int)
public abstract java.lang.String getAtomInfo (int)
public abstract float getRotationRadius ()
public abstract int getZoomPercent ()
public abstract float getZoomPercentFloat ()
public abstract javax.vecmath.Matrix4f getUnscaledTransformMatrix ()
public abstract int getBackgroundArgb ()
public abstract float getAtomRadius (int)
public abstract javax.vecmath.Point3f getAtomPoint3f (int)
public abstract int getAtomArgb (int)
public abstract int getAtomModelIndex (int)
public abstract float getBondRadius (int)
public abstract javax.vecmath.Point3f getBondPoint3f1 (int)
public abstract javax.vecmath.Point3f getBondPoint3f2 (int)
public abstract int getBondArgb1 (int)
public abstract int getBondArgb2 (int)
public abstract short getBondOrder (int)
public abstract int getBondModelIndex (int)
public abstract javax.vecmath.Point3f[] getPolymerLeadMidPoints (int, int)
public abstract boolean getAxesOrientationRasmol ()
public abstract int getPercentVdwAtom ()
public abstract boolean getAutoBond ()
public abstract short getMadBond ()
public abstract float getBondTolerance ()
public abstract void rebond ()
public abstract float getMinBondDistance ()
public abstract void refresh (int, java.lang.String)
public abstract boolean showModelSetDownload ()
public abstract void viewerNotifyRepaintDone ()
public abstract boolean getBooleanProperty (java.lang.String)
public abstract boolean getBooleanProperty (java.lang.String, boolean)
public abstract java.lang.Object getParameter (java.lang.String)
public abstract java.lang.String getSetHistory (int)
public abstract boolean havePartialCharges ()
public abstract boolean isApplet ()
public abstract java.lang.String getAltLocListInModel (int)
public abstract java.lang.String getStateInfo ()
public abstract void syncScript (java.lang.String, java.lang.String)
public abstract void setColorBackground (java.lang.String)
public abstract void setShowAxes (boolean)
public abstract void setShowBbcage (boolean)
public abstract void setJmolDefaults ()
public abstract void setRasmolDefaults ()
public abstract void setBooleanProperty (java.lang.String, boolean)
public abstract void setIntProperty (java.lang.String, int)
public abstract void setFloatProperty (java.lang.String, float)
public abstract void setStringProperty (java.lang.String, java.lang.String)
public abstract void setModeMouse (int)
public abstract void setShowHydrogens (boolean)
public abstract void setShowMeasurements (boolean)
public abstract void setPerspectiveDepth (boolean)
public abstract void setAutoBond (boolean)
public abstract void setMarBond (short)
public abstract void setBondTolerance (float)
public abstract void setMinBondDistance (float)
public abstract void setAxesOrientationRasmol (boolean)
public abstract void setPercentVdwAtom (int)
public abstract void setAnimationFps (int)
public abstract void setFrankOn (boolean)
public abstract void setDebugScript (boolean)
public abstract void deleteMeasurement (int)
public abstract void clearMeasurements ()
public abstract void setVectorScale (float)
public abstract void setVibrationScale (float)
public abstract void setVibrationPeriod (float)
public abstract void selectAll ()
public abstract void clearSelection ()
public abstract void setSelectionSet (java.util.BitSet)
public abstract void setSelectionHalos (boolean)
public abstract void setCenterSelected ()
public abstract void rotateFront ()
public abstract void rotateX (int)
public abstract void rotateY (int)
public abstract void rotateX (float)
public abstract void rotateY (float)
public abstract void rotateZ (float)
public abstract org.jmol.api.JmolAdapter getModelAdapter ()
public abstract void openFileAsynchronously (java.lang.String)
public abstract java.lang.String getErrorMessage ()
public abstract java.lang.String getErrorMessageUntranslated ()
}
org/jmol/api/MOCalculationInterface.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.MOCalculationInterface extends java.lang.Object {
public abstract void calculate (org.jmol.api.VolumeDataInterface, java.util.BitSet, java.lang.String, javax.vecmath.Point3f[], int, java.util.Vector, float[][], java.util.Hashtable, int[][], float[][], float[], float[])
public abstract void calculateElectronDensity (float[])
}
org/jmol/api/MepCalculationInterface.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.MepCalculationInterface extends java.lang.Object {
public abstract void calculate (org.jmol.api.VolumeDataInterface, java.util.BitSet, javax.vecmath.Point3f[], float[])
}
org/jmol/api/MinimizerInterface.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.MinimizerInterface extends java.lang.Object {
public abstract boolean minimize (int, double, java.util.BitSet) throws java.lang.Exception
public abstract void setProperty (java.lang.String, java.lang.Object)
public abstract java.lang.Object getProperty (java.lang.String, int)
}
org/jmol/api/SmilesMatcherInterface.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.SmilesMatcherInterface extends java.lang.Object {
public abstract void setModelSet (org.jmol.modelset.ModelSet)
public abstract java.util.BitSet getSubstructureSet (java.lang.String) throws java.lang.Exception
}
org/jmol/api/SymmetryInterface.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.SymmetryInterface extends java.lang.Object {
public abstract org.jmol.api.SymmetryInterface setPointGroup (org.jmol.api.SymmetryInterface, org.jmol.modelset.Atom[], java.util.BitSet, boolean, float, float)
public abstract java.lang.String getPointGroupName ()
public abstract java.lang.Object getPointGroupInfo (int, boolean, boolean, java.lang.String, int, float)
public abstract void setSpaceGroup (boolean)
public abstract int addSpaceGroupOperation (java.lang.String)
public abstract void setLattice (int)
public abstract java.lang.String getSpaceGroupName ()
public abstract java.lang.Object getSpaceGroup ()
public abstract void setSpaceGroup (org.jmol.api.SymmetryInterface)
public abstract boolean createSpaceGroup (int, java.lang.String, float[], boolean)
public abstract boolean haveSpaceGroup ()
public abstract int determineSpaceGroupIndex (java.lang.String)
public abstract java.lang.String getSpaceGroupInfo (java.lang.String, org.jmol.api.SymmetryInterface)
public abstract java.lang.Object getLatticeDesignation ()
public abstract void setFinalOperations (javax.vecmath.Point3f[], int, int, boolean)
public abstract int getSpaceGroupOperationCount ()
public abstract javax.vecmath.Matrix4f getSpaceGroupOperation (int)
public abstract java.lang.String getSpaceGroupXyz (int, boolean)
public abstract void newSpaceGroupPoint (int, javax.vecmath.Point3f, javax.vecmath.Point3f, int, int, int)
public abstract java.lang.Object rotateEllipsoid (int, javax.vecmath.Point3f, javax.vecmath.Vector3f[], javax.vecmath.Point3f, javax.vecmath.Point3f)
public abstract void setUnitCell (float[])
public abstract void toCartesian (javax.vecmath.Point3f)
public abstract java.lang.Object[] getEllipsoid (float[])
public abstract javax.vecmath.Point3f ijkToPoint3f (int)
public abstract void toFractional (javax.vecmath.Point3f)
public abstract javax.vecmath.Point3f[] getUnitCellVertices ()
public abstract javax.vecmath.Point3f getCartesianOffset ()
public abstract float[] getNotionalUnitCell ()
public abstract void toUnitCell (javax.vecmath.Point3f, javax.vecmath.Point3f)
public abstract void setUnitCellOffset (javax.vecmath.Point3f)
public abstract void setOffset (int)
public abstract javax.vecmath.Point3f getFractionalOffset ()
public abstract float getUnitCellInfo (int)
public abstract int getModelIndex ()
public abstract void setModelIndex (int)
public abstract boolean getCoordinatesAreFractional ()
public abstract int[] getCellRange ()
public abstract java.lang.String getSymmetryInfoString ()
public abstract java.lang.String[] getSymmetryOperations ()
public abstract boolean haveUnitCell ()
public abstract java.lang.String getUnitCellInfo ()
public abstract boolean isPeriodic ()
public abstract void setSymmetryInfo (int, java.util.Hashtable)
public abstract java.lang.Object[] getSymmetryOperationDescription (int, org.jmol.api.SymmetryInterface, javax.vecmath.Point3f, java.lang.String)
}
org/jmol/api/TriangleServer.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.TriangleServer extends java.lang.Object {
public abstract javax.vecmath.Point3i[] getCubeVertexOffsets ()
public abstract java.util.Vector intersectPlane (javax.vecmath.Point4f, javax.vecmath.Point3f[], int)
}
org/jmol/api/VolumeDataInterface.class
<Unknown>
package org.jmol.api
public abstract org.jmol.api.VolumeDataInterface extends java.lang.Object {
public abstract void setVoxelData (float[][][])
public abstract int setVoxelCounts (int, int, int)
public abstract void setVolumetricVector (int, float, float, float)
public abstract void setMatrix ()
public abstract void transform (javax.vecmath.Vector3f, javax.vecmath.Vector3f)
public abstract void setPlaneParameters (javax.vecmath.Point4f)
public abstract float calcVoxelPlaneDistance (int, int, int)
public abstract float distancePointToPlane (javax.vecmath.Point3f)
public abstract void voxelPtToXYZ (int, int, int, javax.vecmath.Point3f)
public abstract void setUnitVectors ()
public abstract void xyzToVoxelPt (float, float, float, javax.vecmath.Point3i)
public abstract float lookupInterpolatedVoxelValue (javax.vecmath.Point3f)
public abstract void setDataDistanceToPlane (javax.vecmath.Point4f)
public abstract void filterData (boolean, float)
public abstract void capData (javax.vecmath.Point4f, float)
public abstract void setVolumetricOrigin (float, float, float)
public abstract float[][][] getVoxelData ()
public abstract int[] getVoxelCounts ()
public abstract float[] getOriginFloat ()
public abstract float[] getVolumetricVectorLengths ()
}
org/jmol/applet/Jmol$MyStatusListener.class
<Unknown>
package org.jmol.applet
org.jmol.applet.Jmol$MyStatusListener extends java.lang.Object implements org.jmol.api.JmolStatusListener {
private boolean haveNotifiedError
private String defaultMessage
private final org.jmol.applet.Jmol this$0
void <init> (org.jmol.applet.Jmol)
public boolean notifyEnabled (int)
public void notifyCallback (int, java.lang.Object[])
private void output (java.lang.String)
private void notifyScriptTermination ()
private java.lang.String notifySync (java.lang.String, java.lang.String)
public void setCallbackFunction (java.lang.String, java.lang.String)
protected void finalize () throws java.lang.Throwable
public java.lang.String eval (java.lang.String)
public java.lang.String createImage (java.lang.String, java.lang.String, java.lang.Object, int)
public float[][] functionXY (java.lang.String, int, int)
public float[][][] functionXYZ (java.lang.String, int, int, int)
public void showUrl (java.lang.String)
private void showStatusAndConsole (java.lang.String, boolean)
private void clearDefaultConsoleMessage ()
private void consoleMessage (java.lang.String)
private java.lang.String sendScript (java.lang.String, java.lang.String, boolean, boolean)
public java.util.Hashtable getRegistryInfo ()
public java.lang.String dialogAsk (java.lang.String, java.lang.String)
}
org/jmol/applet/Jmol.class
<Unknown>
package org.jmol.applet
public org.jmol.applet.Jmol extends java.lang.Object implements org.jmol.appletwrapper.WrappedApplet {
org.jmol.applet.Jvm12 jvm12
boolean mayScript
boolean haveDocumentAccess
boolean loading
String[] callbacks
String language
String htmlName
String fullName
String syncId
String languagePath
org.jmol.appletwrapper.AppletWrapper appletWrapper
protected org.jmol.api.JmolViewer viewer
private static final boolean REQUIRE_PROGRESSBAR
private boolean jvm12orGreater
private boolean hasProgressBar
protected boolean doTranslate
private String statusForm
private String statusText
private String statusTextarea
private int paintCounter
boolean isSigned
public boolean showPaintTime
private boolean isUpdating
protected java.awt.Graphics gRight
protected boolean isStereoSlave
private static final String[] progressbarMsgs
private int timeLast
private int timeCount
private int timeTotal
private long timeBegin
private int lastMotionEventNumber
private static final int SCRIPT_CHECK
private static final int SCRIPT_WAIT
private static final int SCRIPT_NOWAIT
StringBuffer outputBuffer
public void <init> ()
public void setAppletWrapper (org.jmol.appletwrapper.AppletWrapper)
public void init ()
public void destroy ()
java.lang.String getParameter (java.lang.String)
public java.awt.Graphics setStereoGraphics (boolean)
public void initWindows ()
private void setLogging ()
private boolean getBooleanValue (java.lang.String, boolean)
private java.lang.String getValue (java.lang.String, java.lang.String)
private java.lang.String getValueLowerCase (java.lang.String, java.lang.String)
public void initApplication ()
private void setValue (java.lang.String, java.lang.String)
private void setStringProperty (java.lang.String, java.lang.String)
void sendJsTextStatus (java.lang.String)
void sendJsTextareaStatus (java.lang.String)
public void paint (java.awt.Graphics)
public void update (java.awt.Graphics)
private void update (java.awt.Graphics, java.lang.String)
private void printProgressbarMessage (java.awt.Graphics)
public boolean handleEvent (java.awt.Event)
private void startPaintClock ()
private void stopPaintClock ()
private java.lang.String fmt (int)
private void showTimes (int, int, java.awt.Graphics)
private java.lang.String scriptProcessor (java.lang.String, java.lang.String, int)
public void script (java.lang.String)
public java.lang.String scriptCheck (java.lang.String)
public java.lang.String scriptNoWait (java.lang.String)
public java.lang.String scriptWait (java.lang.String)
public java.lang.String scriptWait (java.lang.String, java.lang.String)
public java.lang.String scriptWaitOutput (java.lang.String)
public synchronized void syncScript (java.lang.String)
public java.lang.String getAppletInfo ()
public java.lang.Object getProperty (java.lang.String)
public java.lang.Object getProperty (java.lang.String, java.lang.String)
public java.lang.String getPropertyAsString (java.lang.String)
public java.lang.String getPropertyAsString (java.lang.String, java.lang.String)
public java.lang.String getPropertyAsJSON (java.lang.String)
public java.lang.String getPropertyAsJSON (java.lang.String, java.lang.String)
public java.lang.String loadInlineString (java.lang.String, java.lang.String, boolean)
public java.lang.String loadInlineArray (java.lang.String[], java.lang.String, boolean)
public java.lang.String loadInline (java.lang.String)
public java.lang.String loadInline (java.lang.String, java.lang.String)
public java.lang.String loadInline (java.lang.String[])
public java.lang.String loadInline (java.lang.String[], java.lang.String)
private java.lang.String loadInlineSeparated (java.lang.String, java.lang.String)
public java.lang.String loadDOMNode (netscape.javascript.JSObject)
public java.lang.String loadNodeId (java.lang.String)
static void <clinit> ()
}
org/jmol/applet/JmolAppletRegistry.class
<Unknown>
package org.jmol.applet
final org.jmol.applet.JmolAppletRegistry extends java.lang.Object {
static java.util.Hashtable htRegistry
void <init> ()
static synchronized void checkIn (java.lang.String, java.applet.Applet)
static synchronized void checkOut (java.lang.String)
private static synchronized void cleanRegistry ()
public static synchronized void findApplets (java.lang.String, java.lang.String, java.lang.String, java.util.Vector)
static void <clinit> ()
}
org/jmol/applet/Jvm12$1.class
<Unknown>
package org.jmol.applet
final org.jmol.applet.Jvm12$1 extends java.lang.Object implements java.lang.Runnable {
private final org.jmol.applet.Jvm12 this$0
void <init> (org.jmol.applet.Jvm12)
public void run ()
}
org/jmol/applet/Jvm12.class
<Unknown>
package org.jmol.applet
public org.jmol.applet.Jvm12 extends java.lang.Object {
protected org.jmol.api.JmolViewer viewer
public java.awt.Component awtComponent
protected String appletContext
private final java.awt.Rectangle rectClip
private final java.awt.Dimension dimSize
protected static final String[] imageChoices
protected static final String[] imageExtensions
String inputFileName
String outputFileName
String dialogType
int qualityJPG
int qualityPNG
String imageType
int imageQuality
void <init> (java.awt.Component, org.jmol.api.JmolViewer, java.lang.String)
java.awt.Rectangle getClipBounds (java.awt.Graphics)
public java.awt.Dimension getSize ()
static org.jmol.api.JmolDialogInterface newDialog (boolean)
public java.lang.String dialogAsk (java.lang.String, java.lang.String)
java.lang.String createImage (java.lang.String, java.lang.String, java.lang.Object, int)
java.lang.String getClipboardText ()
static void <clinit> ()
}
org/jmol/appletwrapper/AppletWrapper.class
<Unknown>
package org.jmol.appletwrapper
public org.jmol.appletwrapper.AppletWrapper extends java.applet.Applet {
private String wrappedAppletClassName
private String preloadImageName
private String preloadTextMessage
private int preloadThreadCount
private String[] preloadClassNames
private int preloadClassIndex
private String previousClassName
private boolean needToCompleteInitialization
private boolean preloadImageReadyForDisplay
private boolean preloadImagePainted
private java.awt.Image preloadImage
private java.awt.MediaTracker mediaTracker
private java.awt.Color bgcolor
private java.awt.Color textColor
public org.jmol.appletwrapper.WrappedApplet wrappedApplet
private long startTime
private int clockX
private int clockBaseline
private int clockWidth
private static int MINIMUM_ELAPSED_SECONDS
private static String fontFace
private static int fontSizeDivisor
private int fontSize
private java.awt.Font font
private java.awt.FontMetrics fontMetrics
private int fontAscent
private int fontHeight
private boolean isSigned
private static final String[] colorNames
private static final java.awt.Color[] colors
public void destroy ()
public void <init> (java.lang.String, java.lang.String, int, java.lang.String[])
public boolean isSigned ()
public java.lang.String getAppletInfo ()
public void init ()
public void update (java.awt.Graphics)
public void paint (java.awt.Graphics)
void repaintClock ()
private boolean completeInitialization (java.awt.Graphics, java.awt.Dimension)
private java.awt.Color getColorFromName (java.lang.String)
private java.awt.Color getContrastingBlackOrWhite (java.awt.Color)
public boolean handleEvent (java.awt.Event)
synchronized java.lang.String getNextPreloadClassName ()
static void <clinit> ()
}
org/jmol/appletwrapper/ClassPreloader.class
<Unknown>
package org.jmol.appletwrapper
org.jmol.appletwrapper.ClassPreloader extends java.lang.Thread {
org.jmol.appletwrapper.AppletWrapper appletWrapper
void <init> (org.jmol.appletwrapper.AppletWrapper)
public void run ()
}
org/jmol/appletwrapper/TickerThread.class
<Unknown>
package org.jmol.appletwrapper
org.jmol.appletwrapper.TickerThread extends java.lang.Thread {
org.jmol.appletwrapper.AppletWrapper appletWrapper
boolean keepRunning
void <init> (org.jmol.appletwrapper.AppletWrapper)
public void run ()
}
org/jmol/appletwrapper/WrappedApplet.class
<Unknown>
package org.jmol.appletwrapper
public abstract org.jmol.appletwrapper.WrappedApplet extends java.lang.Object implements org.jmol.api.JmolAppletInterface {
public abstract java.lang.String getAppletInfo ()
public abstract void setAppletWrapper (org.jmol.appletwrapper.AppletWrapper)
public abstract void init ()
public abstract void update (java.awt.Graphics)
public abstract void paint (java.awt.Graphics)
public abstract boolean handleEvent (java.awt.Event)
public abstract void destroy ()
}
org/jmol/appletwrapper/WrappedAppletLoader.class
<Unknown>
package org.jmol.appletwrapper
org.jmol.appletwrapper.WrappedAppletLoader extends java.lang.Thread {
org.jmol.appletwrapper.AppletWrapper appletWrapper
String wrappedAppletClassName
private static final int minimumLoadSeconds
void <init> (org.jmol.appletwrapper.AppletWrapper, java.lang.String)
public void run ()
}
org/jmol/atomdata/AtomData.class
<Unknown>
package org.jmol.atomdata
public org.jmol.atomdata.AtomData extends java.lang.Object {
public static final int MODE_FILL_COORDS
public static final int MODE_FILL_COORDS_AND_RADII
public static final int MODE_GET_ATTACHED_HYDROGENS
public String programInfo
public String fileName
public String modelName
public int modelIndex
public java.util.BitSet bsSelected
public java.util.BitSet bsIgnored
public boolean useIonic
public int firstAtomIndex
public int firstModelIndex
public int lastModelIndex
public float hAtomRadius
public javax.vecmath.Point3f[] atomXyz
public float[] atomRadius
public int[] atomicNumber
public javax.vecmath.Point3f[][] hAtoms
public int atomCount
public int hydrogenAtomCount
public int adpMode
public void <init> ()
}
org/jmol/atomdata/AtomDataServer.class
<Unknown>
package org.jmol.atomdata
public abstract org.jmol.atomdata.AtomDataServer extends java.lang.Object {
public abstract org.jmol.modelset.AtomIndexIterator getWithinAtomSetIterator (int, float, java.util.BitSet, boolean, boolean)
public abstract void fillAtomData (org.jmol.atomdata.AtomData, int)
public abstract java.io.BufferedInputStream getBufferedInputStream (java.lang.String)
}
org/jmol/bspt/Bspf.class
<Unknown>
package org.jmol.bspt
public final org.jmol.bspt.Bspf extends java.lang.Object {
int dimMax
org.jmol.bspt.Bspt[] bspts
org.jmol.bspt.CubeIterator[] cubeIterators
public void <init> (int)
public int getBsptCount ()
public void clearBspt (int)
public boolean isInitialized (int)
public void addTuple (int, javax.vecmath.Point3f)
public void stats ()
public org.jmol.bspt.CubeIterator getCubeIterator (int)
public void initialize (int, javax.vecmath.Point3f[], java.util.BitSet)
}
org/jmol/bspt/Bspt.class
<Unknown>
package org.jmol.bspt
public final org.jmol.bspt.Bspt extends java.lang.Object {
static final int leafCountMax
static final int MAX_TREE_DEPTH
int treeDepth
int dimMax
org.jmol.bspt.Element eleRoot
public void <init> (int)
public void addTuple (javax.vecmath.Point3f)
public void stats ()
public org.jmol.bspt.CubeIterator allocateCubeIterator ()
}
org/jmol/bspt/CubeIterator.class
<Unknown>
package org.jmol.bspt
public org.jmol.bspt.CubeIterator extends java.lang.Object {
org.jmol.bspt.Bspt bspt
org.jmol.bspt.Element[] stack
int sp
int leafIndex
org.jmol.bspt.Leaf leaf
float radius
float[] centerValues
private float cx
private float cy
private float cz
protected float dx
protected float dy
protected float dz
boolean tHemisphere
void <init> (org.jmol.bspt.Bspt)
public void initialize (javax.vecmath.Point3f, float)
public void initializeHemisphere (javax.vecmath.Point3f, float)
public void release ()
public boolean hasMoreElements ()
public javax.vecmath.Point3f nextElement ()
public float foundDistance2 ()
private void findLeftLeaf ()
protected boolean isWithinRadius (javax.vecmath.Point3f)
}
org/jmol/bspt/Element.class
<Unknown>
package org.jmol.bspt
abstract org.jmol.bspt.Element extends java.lang.Object {
org.jmol.bspt.Bspt bspt
int count
void <init> ()
abstract org.jmol.bspt.Element addTuple (int, javax.vecmath.Point3f)
}
org/jmol/bspt/Leaf.class
<Unknown>
package org.jmol.bspt
org.jmol.bspt.Leaf extends org.jmol.bspt.Element {
javax.vecmath.Point3f[] tuples
void <init> (org.jmol.bspt.Bspt)
void <init> (org.jmol.bspt.Bspt, org.jmol.bspt.Leaf, int)
void sort (int)
org.jmol.bspt.Element addTuple (int, javax.vecmath.Point3f)
}
org/jmol/bspt/Node.class
<Unknown>
package org.jmol.bspt
org.jmol.bspt.Node extends org.jmol.bspt.Element {
int dim
float minLeft
float maxLeft
org.jmol.bspt.Element eleLeft
float minRight
float maxRight
org.jmol.bspt.Element eleRight
void <init> (org.jmol.bspt.Bspt, int, org.jmol.bspt.Leaf)
org.jmol.bspt.Element addTuple (int, javax.vecmath.Point3f)
static float getDimensionValue (javax.vecmath.Point3f, int)
}
org/jmol/console/AppletConsole$ControlEnterTextArea.class
<Unknown>
package org.jmol.console
org.jmol.console.AppletConsole$ControlEnterTextArea extends javax.swing.JTextArea {
private final org.jmol.console.AppletConsole this$0
void <init> (org.jmol.console.AppletConsole)
public void processComponentKeyEvent (java.awt.event.KeyEvent)
private void recallCommand (boolean)
}
org/jmol/console/AppletConsole$GetKey.class
<Unknown>
package org.jmol.console
abstract org.jmol.console.AppletConsole$GetKey extends java.lang.Object {
public abstract java.lang.String getKey ()
}
org/jmol/console/AppletConsole$KeyJMenu.class
<Unknown>
package org.jmol.console
org.jmol.console.AppletConsole$KeyJMenu extends javax.swing.JMenu implements org.jmol.console.AppletConsole$GetKey {
String key
private final org.jmol.console.AppletConsole this$0
void <init> (org.jmol.console.AppletConsole, java.lang.String, java.lang.String, char)
public java.lang.String getKey ()
}
org/jmol/console/AppletConsole$KeyJMenuItem.class
<Unknown>
package org.jmol.console
org.jmol.console.AppletConsole$KeyJMenuItem extends javax.swing.JMenuItem implements org.jmol.console.AppletConsole$GetKey {
String key
private final org.jmol.console.AppletConsole this$0
void <init> (org.jmol.console.AppletConsole, java.lang.String, java.lang.String, char)
public java.lang.String getKey ()
}
org/jmol/console/AppletConsole.class
<Unknown>
package org.jmol.console
public org.jmol.console.AppletConsole extends org.jmol.console.JmolConsole implements org.jmol.api.JmolAppConsoleInterface {
private final javax.swing.JTextArea input
private final javax.swing.JTextPane output
private final javax.swing.text.Document outputDocument
private javax.swing.JFrame jf
private final javax.swing.text.SimpleAttributeSet attributesCommand
private javax.swing.JMenuBar menubar
private javax.swing.JButton clearOutButton
private javax.swing.JButton clearInButton
private javax.swing.JButton loadButton
protected java.util.Hashtable map
protected java.util.Hashtable labels
public java.lang.Object getMyMenuBar ()
public void dispose ()
public void <init> ()
public org.jmol.api.JmolAppConsoleInterface getAppConsole (org.jmol.viewer.Viewer, java.awt.Component)
private void <init> (org.jmol.viewer.Viewer, java.awt.Component)
public void sendConsoleEcho (java.lang.String)
public void sendConsoleMessage (java.lang.String)
public void zap ()
private void set (org.jmol.api.JmolViewer)
protected javax.swing.JMenuBar createMenubar ()
protected void addHelpMenuBar (javax.swing.JMenuBar)
private void addHelpItems (javax.swing.JMenu, java.lang.String, java.lang.String)
protected javax.swing.JMenuItem createMenuItem (java.lang.String)
private void setupInput ()
private void setupOutput ()
public void setVisible (boolean)
private void output (java.lang.String)
private void output (java.lang.String, javax.swing.text.AttributeSet)
public java.lang.String getText ()
protected void clearContent (java.lang.String)
public void actionPerformed (java.awt.event.ActionEvent)
protected void execute (java.lang.String)
public void windowClosed (java.awt.event.WindowEvent)
private void destroyConsole ()
public void windowClosing (java.awt.event.WindowEvent)
private java.util.Hashtable setupLabels ()
private java.lang.String getLabel (java.lang.String)
private javax.swing.JMenu newJMenu (java.lang.String)
private javax.swing.JMenuItem newJMenuItem (java.lang.String)
private static java.lang.String getLabelWithoutMnemonic (java.lang.String)
private static char getMnemonic (java.lang.String)
}
org/jmol/console/JmolConsole.class
<Unknown>
package org.jmol.console
public abstract org.jmol.console.JmolConsole extends javax.swing.JDialog implements java.awt.event.ActionListener java.awt.event.WindowListener {
public org.jmol.api.JmolViewer viewer
protected java.awt.Component display
protected org.jmol.console.ScriptEditor scriptEditor
protected javax.swing.JButton editButton
protected javax.swing.JButton runButton
protected javax.swing.JButton historyButton
protected javax.swing.JButton stateButton
void setScriptEditor (org.jmol.console.ScriptEditor)
public org.jmol.api.JmolScriptEditorInterface getScriptEditor ()
org.jmol.api.JmolViewer getViewer ()
public void <init> ()
public void <init> (org.jmol.api.JmolViewer, javax.swing.JFrame, java.lang.String, boolean)
protected abstract void clearContent (java.lang.String)
protected abstract void execute (java.lang.String)
public void actionPerformed (java.awt.event.ActionEvent)
public void windowActivated (java.awt.event.WindowEvent)
public void windowClosed (java.awt.event.WindowEvent)
public void windowClosing (java.awt.event.WindowEvent)
public void windowDeactivated (java.awt.event.WindowEvent)
public void windowDeiconified (java.awt.event.WindowEvent)
public void windowIconified (java.awt.event.WindowEvent)
public void windowOpened (java.awt.event.WindowEvent)
}
org/jmol/console/ScriptEditor$EditorDocument$MyUndoableEditListener.class
<Unknown>
package org.jmol.console
public org.jmol.console.ScriptEditor$EditorDocument$MyUndoableEditListener extends java.lang.Object implements javax.swing.event.UndoableEditListener {
private final org.jmol.console.ScriptEditor$EditorDocument this$1
protected void <init> (org.jmol.console.ScriptEditor$EditorDocument)
public void undoableEditHappened (javax.swing.event.UndoableEditEvent)
}
org/jmol/console/ScriptEditor$EditorDocument.class
<Unknown>
package org.jmol.console
org.jmol.console.ScriptEditor$EditorDocument extends javax.swing.text.DefaultStyledDocument {
org.jmol.console.ScriptEditor$EditorTextPane EditorTextPane
protected javax.swing.undo.UndoManager undo
private final org.jmol.console.ScriptEditor this$0
void <init> (org.jmol.console.ScriptEditor)
void setEditorTextPane (org.jmol.console.ScriptEditor$EditorTextPane)
void doHighlight (int, int, javax.swing.text.SimpleAttributeSet)
void clearHighlight ()
protected void undo ()
protected void redo ()
void clearContent ()
java.lang.String outputEcho (java.lang.String)
}
org/jmol/console/ScriptEditor$EditorTextPane.class
<Unknown>
package org.jmol.console
org.jmol.console.ScriptEditor$EditorTextPane extends javax.swing.JTextPane {
org.jmol.console.ScriptEditor$EditorDocument editorDoc
boolean checking
private final org.jmol.console.ScriptEditor this$0
void <init> (org.jmol.console.ScriptEditor, org.jmol.console.ScriptEditor)
public void clearContent ()
public synchronized void clearContent (java.lang.String)
protected void processKeyEvent (java.awt.event.KeyEvent)
}
org/jmol/console/ScriptEditor.class
<Unknown>
package org.jmol.console
public final org.jmol.console.ScriptEditor extends javax.swing.JDialog implements org.jmol.api.JmolScriptEditorInterface java.awt.event.ActionListener {
protected org.jmol.console.ScriptEditor$EditorTextPane editor
private javax.swing.JButton openButton
private javax.swing.JButton closeButton
private javax.swing.JButton loadButton
private javax.swing.JButton topButton
private javax.swing.JButton checkButton
private javax.swing.JButton runButton
private javax.swing.JButton pauseButton
private javax.swing.JButton haltButton
private javax.swing.JButton clearButton
private javax.swing.JButton stateButton
private javax.swing.JButton consoleButton
protected javax.swing.JButton stepButton
protected javax.swing.JButton resumeButton
private org.jmol.api.JmolViewer viewer
private org.jmol.console.JmolConsole jmolConsole
protected String title
protected String parsedData
protected org.jmol.viewer.ScriptContext parsedContext
protected javax.swing.text.SimpleAttributeSet attHighlight
protected javax.swing.text.SimpleAttributeSet attEcho
protected javax.swing.text.SimpleAttributeSet attError
private javax.swing.JPanel buttonPanel
protected String filename
private static String[] lastOpened
public void <init> ()
void <init> (org.jmol.api.JmolViewer, javax.swing.JFrame, org.jmol.console.JmolConsole)
private void setAttributes ()
void layoutWindow (java.awt.Container)
private javax.swing.JButton setButton (java.lang.String)
public void notifyScriptStart ()
public void notifyScriptTermination ()
public void setVisible (boolean)
public java.lang.Object getMyMenuBar ()
public java.lang.String getText ()
public void output (java.lang.String)
public void dispose ()
public void notifyContext (org.jmol.viewer.ScriptContext, java.lang.Object[])
private synchronized void setContext (org.jmol.viewer.ScriptContext)
private void gotoCommand (int, boolean, javax.swing.text.SimpleAttributeSet)
public void actionPerformed (java.awt.event.ActionEvent)
private synchronized void checkAction (java.awt.event.ActionEvent)
private void doOpen ()
public void gotoTop ()
public void checkScript ()
protected void parseScript (java.lang.String)
private void gotoParsedLine ()
public void doStep ()
protected void doResume ()
private void gotoPosition (int, int)
public void setFilename (java.lang.String)
static void <clinit> ()
}
org/jmol/g3d/Awt3D.class
<Unknown>
package org.jmol.g3d
final org.jmol.g3d.Awt3D extends org.jmol.g3d.Platform3D implements java.awt.image.ImageProducer {
java.awt.Component component
java.awt.image.ColorModel colorModelRGB
java.awt.image.ImageConsumer ic
void <init> (java.awt.Component)
java.awt.Image allocateImage ()
void notifyEndOfRendering ()
java.awt.Image allocateOffscreenImage (int, int)
java.awt.Graphics getGraphics (java.awt.Image)
public synchronized void addConsumer (java.awt.image.ImageConsumer)
public boolean isConsumer (java.awt.image.ImageConsumer)
public void removeConsumer (java.awt.image.ImageConsumer)
public void requestTopDownLeftRightResend (java.awt.image.ImageConsumer)
public void startProduction (java.awt.image.ImageConsumer)
}
org/jmol/g3d/Circle3D.class
<Unknown>
package org.jmol.g3d
final org.jmol.g3d.Circle3D extends java.lang.Object {
org.jmol.g3d.Graphics3D g3d
int xCenter
int yCenter
int zCenter
int sizeCorrection
void <init> (org.jmol.g3d.Graphics3D)
void plotCircleCenteredClipped (int, int, int, int)
void plotCircleCenteredUnclipped (int, int, int, int)
private void plot8CircleCenteredClipped (int, int)
private void plot8CircleCenteredUnclipped (int, int)
private void plot8FilledCircleCenteredClipped (int, int)
private void plot8FilledCircleCenteredUnclipped (int, int)
void plotFilledCircleCenteredClipped (int, int, int, int)
void plotFilledCircleCenteredUnclipped (int, int, int, int)
}
org/jmol/g3d/Colix3D.class
<Unknown>
package org.jmol.g3d
org.jmol.g3d.Colix3D extends java.lang.Object {
private static int colixMax
private static int[] argbs
private static int[] argbsGreyscale
private static int[][] ashades
private static int[][] ashadesGreyscale
private static final org.jmol.util.Int2IntHash colixHash
static final int[] predefinedArgbs
void <init> ()
static short getColix (int)
private static synchronized int allocateColix (int)
private static synchronized void calcArgbsGreyscale ()
static final int getArgb (short)
static final int getArgbGreyscale (short)
static final int[] getShades (short)
static final int[] getShadesGreyscale (short)
static final synchronized void flushShades ()
static void <clinit> ()
}
org/jmol/g3d/Cylinder3D.class
<Unknown>
package org.jmol.g3d
org.jmol.g3d.Cylinder3D extends java.lang.Object {
final org.jmol.g3d.Graphics3D g3d
final org.jmol.g3d.Line3D line3d
private short colixA
private short colixB
private int[] shadesA
private boolean isScreenedA
private int[] shadesB
private boolean isScreenedB
private int xA
private int yA
private int zA
private int dxB
private int dyB
private int dzB
private float xAf
private float yAf
private float zAf
private float dxBf
private float dyBf
private float dzBf
private boolean tEvenDiameter
private int diameter
private byte endcaps
private boolean tEndcapOpen
private int xEndcap
private int yEndcap
private int zEndcap
private int argbEndcap
private short colixEndcap
private int intensityEndcap
private float radius
private float radius2
private float cosTheta
private float cosPhi
private float sinPhi
boolean clipped
private boolean drawBackside
float xTip
float yTip
float zTip
int rasterCount
float[] tRaster
float[] txRaster
float[] tyRaster
float[] tzRaster
int[] xRaster
int[] yRaster
int[] zRaster
int[] fp8IntensityUp
int yMin
int yMax
int xMin
int xMax
int zXMin
int zXMax
void <init> (org.jmol.g3d.Graphics3D)
void render (short, short, boolean, boolean, byte, int, int, int, int, int, int, int)
void renderBits (short, short, boolean, boolean, byte, int, float, float, float, float, float, float)
private void plotRasterBits (int)
void renderCone (short, boolean, byte, int, float, float, float, float, float, float, boolean)
private void generateBaseEllipse ()
private void generateBaseEllipsePrecisely ()
private void calcRotatedPoint (float, int, boolean)
private void interpolate (int, int)
private void interpolatePrecisely (int, int)
private void plotRaster (int)
private int[] realloc (int[])
private float[] realloc (float[])
private int allocRaster (boolean)
private void findMinMaxY ()
private void findMinMaxX (int)
private void renderFlatEndcap (boolean)
private void renderFlatEndcapPrecisely (boolean)
private void renderSphericalEndcaps ()
private void plotRasterCone (int, boolean)
private void calcArgbEndcap (boolean, boolean)
}
org/jmol/g3d/Font3D.class
<Unknown>
package org.jmol.g3d
public final org.jmol.g3d.Font3D extends java.lang.Object {
public final byte fid
public final String fontFace
public final String fontStyle
public final float fontSizeNominal
public final int idFontFace
public final int idFontStyle
public final float fontSize
public final java.awt.Font font
public final java.awt.FontMetrics fontMetrics
private static final int FONT_ALLOCATION_UNIT
private static int fontkeyCount
private static int[] fontkeys
private static org.jmol.g3d.Font3D[] font3ds
public static final int FONT_FACE_SANS
public static final int FONT_FACE_SERIF
public static final int FONT_FACE_MONO
private static final String[] fontFaces
public static final int FONT_STYLE_PLAIN
public static final int FONT_STYLE_BOLD
public static final int FONT_STYLE_ITALIC
public static final int FONT_STYLE_BOLDITALIC
private static final String[] fontStyles
private void <init> (byte, int, int, float, float, java.awt.Font, java.awt.FontMetrics)
static synchronized org.jmol.g3d.Font3D getFont3D (int, int, float, float, org.jmol.g3d.Platform3D)
private static java.util.Hashtable getFontMap (java.lang.String, int, float)
public static int getFontFaceID (java.lang.String)
public static int getFontStyleID (java.lang.String)
public static org.jmol.g3d.Font3D getFont3D (byte)
static void <clinit> ()
}
org/jmol/g3d/Graphics3D$Pixel.class
<Unknown>
package org.jmol.g3d
org.jmol.g3d.Graphics3D$Pixel extends java.lang.Object {
private final org.jmol.g3d.Graphics3D this$0
void <init> (org.jmol.g3d.Graphics3D)
void addPixel (int, int, int)
}
org/jmol/g3d/Graphics3D$ShadePixel.class
<Unknown>
package org.jmol.g3d
org.jmol.g3d.Graphics3D$ShadePixel extends org.jmol.g3d.Graphics3D$Pixel {
private final org.jmol.g3d.Graphics3D this$0
void <init> (org.jmol.g3d.Graphics3D)
void addPixel (int, int, int)
}
org/jmol/g3d/Graphics3D.class
<Unknown>
package org.jmol.g3d
public final org.jmol.g3d.Graphics3D extends java.lang.Object implements org.jmol.api.JmolRendererInterface {
org.jmol.g3d.Platform3D platform
org.jmol.g3d.Line3D line3d
org.jmol.g3d.Circle3D circle3d
org.jmol.g3d.Sphere3D sphere3d
org.jmol.g3d.Triangle3D triangle3d
org.jmol.g3d.Cylinder3D cylinder3d
org.jmol.g3d.Hermite3D hermite3d
org.jmol.g3d.Normix3D normix3d
boolean isFullSceneAntialiasingEnabled
private boolean antialiasThisFrame
private boolean antialias2
private boolean antialiasEnabled
boolean inGreyscaleMode
byte[] anaglyphChannelBytes
boolean twoPass
boolean isPass2
boolean addAllPixels
boolean haveTranslucentObjects
int windowWidth
int windowHeight
int width
int height
int displayMinX
int displayMaxX
int displayMinY
int displayMaxY
int slab
int depth
int zSlab
int zDepth
boolean zShade
int xLast
int yLast
int[] pbuf
int[] pbufT
int[] zbuf
int[] zbufT
int bufferSize
short colixCurrent
int[] shadesCurrent
int argbCurrent
boolean isTranslucent
boolean isScreened
int translucencyMask
int argbNoisyUp
int argbNoisyDn
org.jmol.g3d.Font3D font3dCurrent
public static final byte ENDCAPS_NONE
public static final byte ENDCAPS_OPEN
public static final byte ENDCAPS_FLAT
public static final byte ENDCAPS_SPHERICAL
public static final byte ENDCAPS_OPENEND
public static final byte shadeMax
public static final byte shadeLast
public static final byte shadeNormal
public static final byte intensitySpecularSurfaceLimit
public static final short INHERIT_ALL
public static final short USE_PALETTE
public static final short BLACK
public static final short ORANGE
public static final short PINK
public static final short BLUE
public static final short WHITE
public static final short CYAN
public static final short RED
public static final short GREEN
public static final short GRAY
public static final short SILVER
public static final short LIME
public static final short MAROON
public static final short NAVY
public static final short OLIVE
public static final short PURPLE
public static final short TEAL
public static final short MAGENTA
public static final short YELLOW
public static final short HOTPINK
public static final short GOLD
int newWindowWidth
int newWindowHeight
boolean newAntialiasing
public double random
int anaglyphLength
public java.awt.Image backgroundImage
public int bgcolor
org.jmol.g3d.Graphics3D$Pixel pixel
int zShadeR
int zShadeG
int zShadeB
private int currentIntensity
int zMargin
boolean currentlyRendering
static final int yGT
static final int yLT
static final int xGT
static final int xLT
static final int zGT
static final int zLT
private static final short CHANGEABLE_MASK
private static final short UNMASK_CHANGEABLE_TRANSLUCENT
private static final int TRANSLUCENT_SHIFT
private static final int ALPHA_SHIFT
private static final int TRANSLUCENT_MASK
private static final int TRANSLUCENT_SCREENED
private static final int TRANSPARENT
static final int TRANSLUCENT_50
public static final short OPAQUE_MASK
private static final short INHERIT_COLOR
static final short UNUSED_OPTION3
static final short SPECIAL_COLIX_MAX
private short[] changeableColixMap
static final float[] lighting
private final javax.vecmath.Vector3f vectorAB
private final javax.vecmath.Vector3f vectorAC
private final javax.vecmath.Vector3f vectorNormal
private static final String[] colorNames
private static final int[] colorArgbs
private static final java.util.Hashtable mapJavaScriptColors
public static final short NORMIX_NULL
public void destroy ()
public boolean isDisplayAntialiased ()
public boolean isAntialiased ()
public void <init> (java.awt.Component)
public boolean currentlyRendering ()
public void setWindowParameters (int, int, boolean)
public void setNewWindowParametersForExport ()
private void setWidthHeight (boolean)
public boolean checkTranslucent (boolean)
public void beginRendering (javax.vecmath.Matrix3f)
private void releaseBuffers ()
public boolean setPass2 (boolean)
public void endRendering ()
public void snapshotAnaglyphChannelBytes ()
public void applyCustomAnaglyph (int[])
public void applyGreenAnaglyph ()
public void applyBlueAnaglyph ()
public void applyCyanAnaglyph ()
public java.awt.Image getScreenImage ()
public void releaseScreenImage ()
public boolean haveTranslucentObjects ()
public int getRenderWidth ()
public int getRenderHeight ()
public int getSlab ()
public int getDepth ()
public void setBackgroundTransparent (boolean)
public void setBackgroundArgb (int)
public void setBackgroundImage (java.awt.Image)
public void setGreyscaleMode (boolean)
public void setSlabAndDepthValues (int, int, boolean, int, int)
public void setSlab (int)
void addPixel (int, int, int)
private void downsampleFullSceneAntialiasing (boolean)
void mergeOpaqueAndTranslucentBuffers ()
static void averageBufferPixel (int[], int[], int, int)
static void mergeBufferPixel (int[], int, int, int)
public boolean hasContent ()
private void setColixAndIntensity (short, int)
public boolean setColix (short)
void setColorNoisy (int)
void setZMargin (int)
public void drawCircleCentered (short, int, int, int, int, boolean)
public void fillScreenedCircleCentered (short, int, int, int, int)
public void fillSphereCentered (int, int, int, int)
public void fillSphereCentered (int, javax.vecmath.Point3i)
public void fillSphereCentered (int, javax.vecmath.Point3f)
public void renderEllipsoid (javax.vecmath.Point3f, javax.vecmath.Point3f[], int, int, int, int, javax.vecmath.Matrix3f, double[], javax.vecmath.Matrix4f, int, javax.vecmath.Point3i[])
public void drawRect (int, int, int, int, int, int)
private void drawHLine (int, int, int, int)
private void drawVLine (int, int, int, int)
public void fillRect (int, int, int, int, int, int)
public void drawString (java.lang.String, org.jmol.g3d.Font3D, int, int, int, int)
public void drawStringNoSlab (java.lang.String, org.jmol.g3d.Font3D, int, int, int)
public void plotText (int, int, int, int, java.lang.String, org.jmol.g3d.Font3D, org.jmol.api.JmolRendererInterface)
public void drawImage (java.awt.Image, int, int, int, int, short, int, int)
public void plotImage (int, int, int, java.awt.Image, org.jmol.api.JmolRendererInterface, short, int, int)
public void setFont (byte)
public void setFont (org.jmol.g3d.Font3D)
public org.jmol.g3d.Font3D getFont3DCurrent ()
public void drawPixel (int, int, int)
public void drawPoints (int, int[])
public void drawDashedLine (int, int, javax.vecmath.Point3i, javax.vecmath.Point3i)
public void drawDottedLine (javax.vecmath.Point3i, javax.vecmath.Point3i)
public void drawLine (int, int, int, int, int, int)
public void drawLine (short, short, int, int, int, int, int, int)
public void drawLine (javax.vecmath.Point3i, javax.vecmath.Point3i)
public void fillCylinder (short, short, byte, int, int, int, int, int, int, int)
public void fillCylinder (byte, int, int, int, int, int, int, int)
public void fillCylinder (byte, int, javax.vecmath.Point3i, javax.vecmath.Point3i)
public void fillCylinderBits (byte, int, javax.vecmath.Point3f, javax.vecmath.Point3f)
public void fillCone (byte, int, javax.vecmath.Point3i, javax.vecmath.Point3i)
public void fillCone (byte, int, javax.vecmath.Point3f, javax.vecmath.Point3f)
public void drawHermite (int, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i)
public void drawHermite (boolean, boolean, int, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, int)
public void fillHermite (int, int, int, int, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i)
public static void getHermiteList (int, javax.vecmath.Tuple3f, javax.vecmath.Tuple3f, javax.vecmath.Tuple3f, javax.vecmath.Tuple3f, javax.vecmath.Tuple3f, javax.vecmath.Tuple3f[], int, int)
public void drawTriangle (javax.vecmath.Point3i, short, javax.vecmath.Point3i, short, javax.vecmath.Point3i, short, int)
public void drawTriangle (javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, int)
public void drawCylinderTriangle (int, int, int, int, int, int, int, int, int, int)
public void drawfillTriangle (int, int, int, int, int, int, int, int, int)
public void fillTriangle (javax.vecmath.Point3i, int, javax.vecmath.Point3i, int, javax.vecmath.Point3i, int)
public void fillTriangle (javax.vecmath.Point3i, short, short, javax.vecmath.Point3i, short, short, javax.vecmath.Point3i, short, short)
public void fillTriangle (short, int, int, int, int, int, int, int, int, int)
public void fillTriangle (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f)
public void fillTriangle (javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i)
public void fillTriangle (javax.vecmath.Point3i, short, short, javax.vecmath.Point3i, short, short, javax.vecmath.Point3i, short, short, float)
public void drawQuadrilateral (short, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i)
public void fillQuadrilateral (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f)
public void fillQuadrilateral (javax.vecmath.Point3i, short, short, javax.vecmath.Point3i, short, short, javax.vecmath.Point3i, short, short, javax.vecmath.Point3i, short, short)
public void renderIsosurface (javax.vecmath.Point3f[], short, short[], javax.vecmath.Vector3f[], int[][], java.util.BitSet, int, int, short[], int)
public boolean isClipped (int, int, int)
public boolean isClipped (int, int)
public boolean isInDisplayRange (int, int)
public boolean isClippedXY (int, int, int)
public boolean isClippedZ (int)
public int clipCode (int, int, int)
public int clipCode (int)
void plotPixelClipped (int, int, int)
public void plotPixelClipped (javax.vecmath.Point3i)
void plotPixelClipped (int, int, int, int)
public void plotPixelClippedNoSlab (int, int, int, int)
void plotPixelClipped (int, boolean, int, int, int)
void plotPixelUnclipped (int, int, int)
void plotPixelUnclipped (int, int, int, int)
void plotPixelsClipped (int, int, int, int)
void plotPixelsClipped (int, int, int, int, int, org.jmol.g3d.Rgb16, org.jmol.g3d.Rgb16)
void plotPixelsUnclipped (int, int, int, int, int, org.jmol.g3d.Rgb16, org.jmol.g3d.Rgb16)
void plotPixelsUnclipped (int, int, int, int)
private void plotPoints (int, int[])
public static int calcGreyscaleRgbFromRgb (int)
public static short getColix (int)
public static final javax.vecmath.Point3f colorPointFromInt (int, javax.vecmath.Point3f)
public static final javax.vecmath.Point3f colorPointFromInt2 (int)
public static final javax.vecmath.Point3f colorPointFromString (java.lang.String, javax.vecmath.Point3f)
public static short getColix (java.lang.String)
private static final short applyColorTranslucencyLevel (short, float)
public static final int getColixTranslucencyLevel (short)
public static short getColix (java.lang.Object)
public static final short getColixTranslucent (short, boolean, float)
public int getColixArgb (short)
int[] getShades (short)
public static final short getChangeableColixIndex (short)
public static final boolean isColixTranslucent (short)
public static final short getColixInherited (short, short)
public static final boolean isColixColorInherited (short)
public java.lang.String getHexColorFromIndex (short)
public static java.lang.String getHexColorFromRGB (int)
public short getChangeableColix (short, int)
public void changeColixArgb (short, int)
public static void flushShadesAndSphereCaches ()
public static synchronized void setSpecular (boolean)
public static boolean getSpecular ()
public static synchronized void setSpecularPower (int)
public static int getSpecularPower ()
public static synchronized void setSpecularPercent (int)
public static int getSpecularPercent ()
public static synchronized void setSpecularExponent (int)
public static int getSpecularExponent ()
public static synchronized void setDiffusePercent (int)
public static int getDiffusePercent ()
public static synchronized void setAmbientPercent (int)
public static int getAmbientPercent ()
public static javax.vecmath.Point3f getLightSource ()
public int calcSurfaceShade (javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i)
private int calcIntensityScreen (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f)
public org.jmol.g3d.Font3D getFont3D (float)
public org.jmol.g3d.Font3D getFont3D (java.lang.String, float)
public org.jmol.g3d.Font3D getFont3D (java.lang.String, java.lang.String, float)
public org.jmol.g3d.Font3D getFont3DScaled (org.jmol.g3d.Font3D, float)
public byte getFontFid (float)
public byte getFontFid (java.lang.String, float)
public static int getColorArgb (int)
public static int getArgbFromString (java.lang.String)
public short getNormix (javax.vecmath.Vector3f)
public short getInverseNormix (short)
public short get2SidedNormix (javax.vecmath.Vector3f)
public boolean isDirectedTowardsCamera (short)
public javax.vecmath.Vector3f[] getTransformedVertexVectors ()
public javax.vecmath.Vector3f getNormixVector (short)
public void renderBackground ()
public void renderBackground (org.jmol.api.JmolRendererInterface)
public void endShapeBuffer ()
public void startShapeBuffer (int)
public boolean canDoTriangles ()
public boolean isCartesianExport ()
public boolean initializeExporter (java.lang.String, org.jmol.viewer.Viewer, org.jmol.g3d.Graphics3D, java.lang.Object)
public java.lang.String finalizeOutput ()
public short[] getBgColixes (short[])
static void <clinit> ()
}
org/jmol/g3d/Hermite3D.class
<Unknown>
package org.jmol.g3d
public org.jmol.g3d.Hermite3D extends java.lang.Object {
private org.jmol.api.JmolRendererInterface g3d
private final javax.vecmath.Point3i[] pLeft
private final javax.vecmath.Point3i[] pRight
private final float[] sLeft
private final float[] sRight
int sp
private final javax.vecmath.Point3f[] pTopLeft
private final javax.vecmath.Point3f[] pTopRight
private final javax.vecmath.Point3f[] pBotLeft
private final javax.vecmath.Point3f[] pBotRight
private final boolean[] needToFill
private final javax.vecmath.Point3f a1
private final javax.vecmath.Point3f a2
private final javax.vecmath.Point3f b1
private final javax.vecmath.Point3f b2
private final javax.vecmath.Point3f c1
private final javax.vecmath.Point3f c2
private final javax.vecmath.Point3f d1
private final javax.vecmath.Point3f d2
private final javax.vecmath.Vector3f depth1
private final javax.vecmath.Vector3f T1
private final javax.vecmath.Vector3f T2
public void <init> (org.jmol.api.JmolRendererInterface)
public void render (boolean, int, int, int, int, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i)
private void render2x (boolean, int, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i)
private static void set (javax.vecmath.Point3f, javax.vecmath.Point3i)
public void render2 (boolean, boolean, int, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, int)
private void setDepth (javax.vecmath.Vector3f, javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f, float)
private void setPoint (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Vector3f, int)
static void getHermiteList (int, javax.vecmath.Tuple3f, javax.vecmath.Tuple3f, javax.vecmath.Tuple3f, javax.vecmath.Tuple3f, javax.vecmath.Tuple3f, javax.vecmath.Tuple3f[], int, int)
}
org/jmol/g3d/Line3D.class
<Unknown>
package org.jmol.g3d
final org.jmol.g3d.Line3D extends java.lang.Object {
org.jmol.g3d.Graphics3D g3d
java.util.BitSet lineBits
float slope
boolean lineTypeX
int nBits
int nCached
int nFound
java.util.Hashtable lineCache
Float slopeKey
static final int VISIBILITY_UNCLIPPED
static final int VISIBILITY_CLIPPED
static final int VISIBILITY_OFFSCREEN
int x1t
int y1t
int z1t
int x2t
int y2t
int z2t
int cc1
int cc2
void <init> (org.jmol.g3d.Graphics3D)
void setLineBits (float, float)
boolean getCachedLine ()
int getTrimmedLine ()
void plotLine (int, boolean, int, boolean, int, int, int, int, int, int, boolean)
void plotLineDelta (int, boolean, int, boolean, int, int, int, int, int, int, boolean)
void plotLineDelta (int[], boolean, int[], boolean, int, int, int, int, int, int, int, boolean)
void plotLineDeltaBits (int[], boolean, int[], boolean, int, int, int, int, int, int, int, boolean)
void plotDashedLine (int, boolean, int, int, int, int, int, int, int, int, boolean)
private void plotLineClipped (int, boolean, int, boolean, int, int, int, int, int, int, boolean, int, int)
private void plotLineClipped (int[], boolean, int[], boolean, int, int, int, int, int, int, int, boolean, int, int)
private void plotLineClippedBits (int[], boolean, int[], boolean, int, int, int, int, int, int, int, int, int)
}
org/jmol/g3d/Normix3D.class
<Unknown>
package org.jmol.g3d
org.jmol.g3d.Normix3D extends java.lang.Object {
static final int NORMIX_GEODESIC_LEVEL
private static final int normixCount
private static final javax.vecmath.Vector3f[] vertexVectors
private static final short[][] faceVertexesArrays
private static final short[][] neighborVertexesArrays
private final javax.vecmath.Vector3f[] transformedVectors
private final byte[] intensities
private final byte[] intensities2Sided
private static short[][] faceNormixesArrays
private static final boolean TIMINGS
private static final boolean DEBUG_WITH_SEQUENTIAL_SEARCH
private final javax.vecmath.Matrix3f rotationMatrix
final java.util.BitSet bsConsidered
short[] inverseNormixes
private static byte nullIntensity
private static final boolean DEBUG_FACE_VECTORS
void <init> ()
short getNormix (javax.vecmath.Vector3f)
javax.vecmath.Vector3f getVector (short)
short getNormix (double, double, double, int)
void calculateInverseNormixes ()
byte getIntensity (short)
void setRotationMatrix (javax.vecmath.Matrix3f)
javax.vecmath.Vector3f[] getTransformedVectors ()
short[] getFaceNormixes (int)
static double dist2 (javax.vecmath.Vector3f, javax.vecmath.Vector3f)
static double dist2 (javax.vecmath.Vector3f, double, double, double)
private synchronized short[] calcFaceNormixes (int)
boolean isDirectedTowardsCamera (short)
static void <clinit> ()
}
org/jmol/g3d/Platform3D$ClearingThread.class
<Unknown>
package org.jmol.g3d
org.jmol.g3d.Platform3D$ClearingThread extends java.lang.Thread implements java.lang.Runnable {
boolean bufferHasBeenCleared
boolean clientHasBuffer
private final org.jmol.g3d.Platform3D this$0
void <init> (org.jmol.g3d.Platform3D)
synchronized void notifyBackgroundChange (int)
synchronized void obtainBufferForClient ()
synchronized void releaseBufferForClearing ()
synchronized void waitForClientRelease ()
synchronized void notifyBufferReady ()
public void run ()
}
org/jmol/g3d/Platform3D.class
<Unknown>
package org.jmol.g3d
abstract org.jmol.g3d.Platform3D extends java.lang.Object {
int windowWidth
int windowHeight
int windowSize
int bufferWidth
int bufferHeight
int bufferSize
int bufferSizeT
java.awt.Image imagePixelBuffer
int[] pBuffer
int[] pBufferT
int[] zBuffer
int[] zBufferT
int widthOffscreen
int heightOffscreen
java.awt.Image imageOffscreen
java.awt.Graphics gOffscreen
static final boolean forcePlatformAWT
static final boolean desireClearingThread
boolean useClearingThread
org.jmol.g3d.Platform3D$ClearingThread clearingThread
java.awt.Graphics graphicsOffscreen
void <init> ()
static org.jmol.g3d.Platform3D createInstance (java.awt.Component)
private static org.jmol.g3d.Platform3D allocateSwing3D ()
final void initialize (boolean)
abstract java.awt.Image allocateImage ()
void allocateTBuffers (boolean)
void allocateBuffers (int, int, boolean)
void releaseBuffers ()
boolean hasContent ()
void clearScreenBuffer ()
void setBackgroundColor (int)
void clearTBuffer ()
final void obtainScreenBuffer ()
final void clearScreenBufferThreaded ()
void notifyEndOfRendering ()
abstract java.awt.Image allocateOffscreenImage (int, int)
abstract java.awt.Graphics getGraphics (java.awt.Image)
boolean checkOffscreenSize (int, int)
void setBackgroundTransparent (boolean)
}
org/jmol/g3d/Rgb16.class
<Unknown>
package org.jmol.g3d
final org.jmol.g3d.Rgb16 extends java.lang.Object {
int rScaled
int gScaled
int bScaled
void <init> ()
void <init> (int)
void set (int)
void set (org.jmol.g3d.Rgb16)
void diffDiv (org.jmol.g3d.Rgb16, org.jmol.g3d.Rgb16, int)
void setAndIncrement (org.jmol.g3d.Rgb16, org.jmol.g3d.Rgb16)
int getArgb ()
public java.lang.String toString ()
}
org/jmol/g3d/Shade3D.class
<Unknown>
package org.jmol.g3d
final org.jmol.g3d.Shade3D extends java.lang.Object {
static final int shadeMax
static final int shadeLast
static byte shadeNormal
private static final float xLightsource
private static final float yLightsource
private static final float zLightsource
private static final float magnitudeLight
static final float xLight
static final float yLight
static final float zLight
static int SPECULAR_ON
static int SPECULAR_PERCENT
static int SPECULAR_EXPONENT
static int SPECULAR_POWER
static int DIFFUSE_PERCENT
static int AMBIENT_PERCENT
static int INTENSITY_SPECULAR
static int INTENSE_FRACTION
static int INTENSITY_DIFFUSE
static int AMBIENT_FRACTION
static final float[] lighting
static final byte intensitySpecularSurfaceLimit
static boolean sphereShadingCalculated
static final byte[] sphereIntensities
private static int seed
void <init> ()
static int[] getShades (int, boolean)
private static final int rgb (int, int, int)
static byte calcIntensity (float, float, float)
static byte calcIntensityNormalized (float, float, float)
static int calcFp8Intensity (float, float, float)
private static float calcFloatIntensityNormalized (float, float, float)
static byte calcDitheredNoisyIntensity (float, float, float, float)
static synchronized void calcSphereShading ()
static int nextRandom8Bit ()
static void <clinit> ()
}
org/jmol/g3d/Sphere3D.class
<Unknown>
package org.jmol.g3d
public org.jmol.g3d.Sphere3D extends java.lang.Object {
org.jmol.g3d.Graphics3D g3d
private static final int maxSphereCache
private static final int maxOddSizeSphere
static final int maxSphereDiameter
static final int maxSphereDiameter2
private static final int[][] sphereShapeCache
private double[] zroot
private static int nOut
private static int nIn
private javax.vecmath.Matrix3f mat
private double[] coef
private javax.vecmath.Matrix4f mDeriv
private int selectedOctant
private javax.vecmath.Point3i[] octantPoints
private int planeShade
private int[] zbuf
private int width
private int height
private int depth
private int slab
private int offsetPbufBeginLine
private boolean addAllPixels
private int minX
private int maxX
private int minY
private int maxY
private int minZ
private int maxZ
private int x
private int y
private int z
private int diameter
private boolean tScreened
private int[] shades
private static final int SHADE_SLAB_CLIPPED
private final javax.vecmath.Point3f ptTemp
private final int[] planeShades
private final float[][] dxyz
private static byte[][][] ellipsoidShades
private static final int SLIM
private static final int SDIM
void <init> (org.jmol.g3d.Graphics3D)
static synchronized void flushSphereCache ()
private static int[] getSphereShape (int)
private static synchronized int[] createSphereShape (int)
void render (int[], boolean, int, int, int, int, javax.vecmath.Matrix3f, double[], javax.vecmath.Matrix4f, int, javax.vecmath.Point3i[])
private void renderShapeUnclipped (int[])
private void renderShapeClipped (int[])
private void renderLarge ()
private void renderQuadrant (int, int)
private void renderQuadrantUnclipped (int, int, int)
private void renderQuadrantClipped (int, int, int)
private void setPlaneDerivatives ()
private int getPlaneShade (int, int, double[])
private static void createEllipsoidShades ()
private static int getEllipsoidShade (float, float, float, int, javax.vecmath.Matrix4f)
static void <clinit> ()
}
org/jmol/g3d/Swing3D.class
<Unknown>
package org.jmol.g3d
final org.jmol.g3d.Swing3D extends org.jmol.g3d.Platform3D {
private static final java.awt.image.DirectColorModel rgbColorModel
private static final int[] sampleModelBitMasks
private static final java.awt.image.DirectColorModel rgbColorModelT
private static final int[] sampleModelBitMasksT
private static boolean backgroundTransparent
void <init> ()
java.awt.Image allocateImage ()
void setBackgroundTransparent (boolean)
java.awt.Image allocateOffscreenImage (int, int)
java.awt.Graphics getGraphics (java.awt.Image)
static java.awt.Graphics getStaticGraphics (java.awt.Image)
static void <clinit> ()
}
org/jmol/g3d/Text3D.class
<Unknown>
package org.jmol.g3d
public org.jmol.g3d.Text3D extends java.lang.Object {
private int height
private int ascent
private int width
private int mapWidth
private int size
private int[] bitmap
private boolean isInvalid
private static final java.util.Hashtable htFont3d
private static final java.util.Hashtable htFont3dAntialias
private static boolean working
public int getWidth ()
public static int plot (int, int, int, int, java.lang.String, org.jmol.g3d.Font3D, org.jmol.g3d.Graphics3D, org.jmol.api.JmolRendererInterface, boolean)
public static void plotImage (int, int, int, java.awt.Image, org.jmol.g3d.Graphics3D, org.jmol.api.JmolRendererInterface, boolean, int, int, int)
private static void plotImageClipped (int, int, int, org.jmol.g3d.Graphics3D, org.jmol.api.JmolRendererInterface, int, int, int[], int)
private static void plotImageUnClipped (int, int, int, org.jmol.g3d.Graphics3D, int, int, int[], int)
private static int plotByCharacter (int, int, int, int, java.lang.String, org.jmol.g3d.Font3D, org.jmol.g3d.Graphics3D, org.jmol.api.JmolRendererInterface, boolean)
private static void plotUnclipped (int, int, int, int, org.jmol.g3d.Graphics3D, int, int, int[])
private static void plotClipped (int, int, int, int, org.jmol.g3d.Graphics3D, org.jmol.api.JmolRendererInterface, int, int, int[])
private void <init> (java.lang.String, org.jmol.g3d.Font3D, boolean)
private void renderOffscreen (java.lang.String, org.jmol.g3d.Font3D, org.jmol.g3d.Platform3D, boolean)
private void rasterize (org.jmol.g3d.Platform3D, boolean)
public static synchronized void clearFontCache ()
private static synchronized org.jmol.g3d.Text3D getText3D (int, int, org.jmol.g3d.Graphics3D, java.lang.String, org.jmol.g3d.Font3D, boolean)
private void setBitmap (java.lang.String, org.jmol.g3d.Font3D, org.jmol.g3d.Platform3D, boolean)
static void <clinit> ()
}
org/jmol/g3d/Triangle3D.class
<Unknown>
package org.jmol.g3d
org.jmol.g3d.Triangle3D extends java.lang.Object {
final org.jmol.g3d.Graphics3D g3d
final org.jmol.g3d.Line3D line3d
int[] ax
int[] ay
int[] az
org.jmol.g3d.Rgb16[] rgb16sGouraud
private static final boolean VERIFY
final org.jmol.g3d.Rgb16 rgb16t1
final org.jmol.g3d.Rgb16 rgb16t2
private static final int DEFAULT
int[] axW
int[] azW
int[] axE
int[] azE
org.jmol.g3d.Rgb16[] rgb16sW
org.jmol.g3d.Rgb16[] rgb16sE
void <init> (org.jmol.g3d.Graphics3D)
org.jmol.g3d.Rgb16[] reallocRgb16s (org.jmol.g3d.Rgb16[], int)
void setGouraud (int, int, int)
void drawfillTriangle (int, int, int, int, int, int, int, int, int, boolean)
void fillTriangle (int, int, int, int, int, int, int, int, int, boolean)
void fillTriangle (javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, boolean)
void fillTriangle (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f, boolean)
void fillTriangle (javax.vecmath.Point3i, javax.vecmath.Point3i, javax.vecmath.Point3i, float, boolean)
private void adjustVertex (int[], float)
private void fillTriangle (boolean)
private void reallocRasterArrays (int)
private void generateRaster (int, int, int, int[], int[], int, org.jmol.g3d.Rgb16[])
private void fillRaster (int, int, boolean, boolean, int)
}
org/jmol/geodesic/EnvelopeCalculation.class
<Unknown>
package org.jmol.geodesic
public final org.jmol.geodesic.EnvelopeCalculation extends java.lang.Object {
private short[] mads
private org.jmol.atomdata.AtomData atomData
private org.jmol.atomdata.AtomDataServer viewer
private int atomCount
public static final float SURFACE_DISTANCE_FOR_CALCULATION
public static final int MAX_LEVEL
private float maxRadius
private float scale
private float setRadius
private float addRadius
private boolean modelZeroBased
private int[][] dotsConvexMaps
private int dotsConvexMax
private int geodesicCount
private int[] geodesicMap
private int[] mapT
private static final int[] mapNull
private java.util.BitSet bsSurface
private boolean disregardNeighbors
private java.util.BitSet bsMySelected
private float radiusP
private float diameterP
private javax.vecmath.Point3f[] currentPoints
private int indexI
private javax.vecmath.Point3f centerI
private float radiusI
private float radiiIP2
private final javax.vecmath.Point3f pointT
private javax.vecmath.Point3f centerT
private final javax.vecmath.Point3f[] vertexTest
private static int[] power4
private int neighborCount
private int[] neighborIndices
private javax.vecmath.Point3f[] neighborCenters
private float[] neighborPlusProbeRadii2
private float[] neighborRadii2
public void <init> (org.jmol.atomdata.AtomDataServer, int, short[])
public int[][] getDotsConvexMaps ()
public int getDotsConvexMax ()
public void allocDotsConvexMaps (int)
public java.util.BitSet getBsSurfaceClone ()
public void setMads (short[])
public void setFromBits (int, java.util.BitSet)
public float getRadius ()
public void newSet ()
public void calculate (float, float, float, float, java.util.BitSet, java.util.BitSet, boolean, boolean, boolean, boolean, boolean)
private void setRadii (boolean)
public javax.vecmath.Point3f[] getPoints ()
public static final boolean getBit (int[], int)
private int getPointCount (int[], int)
private void setDotsConvexMax ()
public float getAppropriateRadius (int)
private void setAtomI (int)
private void calcConvexMap (boolean)
private int getMapStorageCount (int[])
private void addIncompleteFaces (int[])
private void calcConvexBits ()
private void getNeighbors ()
private static final int[] allocateBitmap (int)
private static final void setBit (int[], int)
private static final void clearBit (int[], int)
private static final void setAllBits (int[], int)
private static final void clearBitmap (int[])
public void deleteAtoms (int, int, java.util.BitSet)
static void <clinit> ()
}
org/jmol/geodesic/Geodesic.class
<Unknown>
package org.jmol.geodesic
public org.jmol.geodesic.Geodesic extends java.lang.Object {
private static final float halfRoot5
private static final float oneFifth
private static final float oneTenth
private static final short[] faceVertexesIcosahedron
private static final short[] neighborVertexesIcosahedron
public static final int standardLevel
private static final int maxLevel
private static short[] vertexCounts
private static javax.vecmath.Vector3f[] vertexVectors
private static short[][] faceVertexesArrays
private static short[][] neighborVertexesArrays
private static short vertexNext
private static java.util.Hashtable htVertex
private static final boolean VALIDATE
public void <init> ()
public static short[][] getFaceVertexesArrays ()
public static short[][] getNeighborVertexesArrays ()
public static int getVertexCount (int)
public static javax.vecmath.Vector3f[] getVertexVectors ()
public static int getVertexVectorsCount ()
public static javax.vecmath.Vector3f getVertexVector (int)
public static short[] getFaceVertexes (int)
private static synchronized void createGeodesic ()
private static void quadruple (int, short[])
private static void addNeighboringVertexes (short[], short, short)
private static short getVertex (short, short)
static void <clinit> ()
}
org/jmol/i18n/GT$Language.class
<Unknown>
package org.jmol.i18n
public org.jmol.i18n.GT$Language extends java.lang.Object {
public final String code
public final String language
public final boolean display
public void <init> (java.lang.String, java.lang.String, boolean)
}
org/jmol/i18n/GT.class
<Unknown>
package org.jmol.i18n
public org.jmol.i18n.GT extends java.lang.Object {
private static boolean ignoreApplicationBundle
private static org.jmol.i18n.GT getTextWrapper
private java.util.ResourceBundle[] translationResources
private int translationResourcesCount
private boolean doTranslate
private String language
private static org.jmol.i18n.GT$Language[] languageList
static Class class$java$util$ResourceBundle
public void <init> (java.lang.String)
private void <init> ()
public static org.jmol.i18n.GT$Language[] getLanguageList ()
private synchronized org.jmol.i18n.GT$Language[] createLanguageList ()
private java.lang.String getSupported (java.lang.String, boolean)
private java.lang.String findClosest (java.lang.String)
public static java.lang.String getLanguage ()
private synchronized void getTranslation (java.lang.String)
private void addBundles (java.lang.String, java.lang.String, java.lang.String, java.lang.String)
private void addBundle (java.lang.String, java.lang.String)
private static org.jmol.i18n.GT getTextWrapper ()
public static void ignoreApplicationBundle ()
public static void setDoTranslate (boolean)
public static boolean getDoTranslate ()
public static java.lang.String _ (java.lang.String)
public static java.lang.String _ (java.lang.String, java.lang.String)
public static java.lang.String _ (java.lang.String, int)
public static java.lang.String _ (java.lang.String, java.lang.Object[])
public static java.lang.String _ (java.lang.String, boolean)
public static java.lang.String _ (java.lang.String, java.lang.String, boolean)
public static java.lang.String _ (java.lang.String, int, boolean)
public static synchronized java.lang.String _ (java.lang.String, java.lang.Object[], boolean)
private java.lang.String getString (java.lang.String)
private java.lang.String getString (java.lang.String, java.lang.Object[])
public static java.lang.String escapeHTML (java.lang.String)
public static void setLanguagePath (java.lang.String)
static java.lang.Class class$ (java.lang.String)
static void <clinit> ()
}
org/jmol/jvxl/api/MeshDataServer.class
<Unknown>
package org.jmol.jvxl.api
public abstract org.jmol.jvxl.api.MeshDataServer extends java.lang.Object implements org.jmol.jvxl.api.VertexDataServer {
public abstract void invalidateTriangles ()
public abstract void fillMeshData (org.jmol.jvxl.data.MeshData, int)
public abstract void notifySurfaceGenerationCompleted ()
public abstract void notifySurfaceMappingCompleted ()
public abstract javax.vecmath.Point3f[] calculateGeodesicSurface (java.util.BitSet, float)
public abstract int getColixArgb (short)
}
org/jmol/jvxl/api/VertexDataServer.class
<Unknown>
package org.jmol.jvxl.api
public abstract org.jmol.jvxl.api.VertexDataServer extends java.lang.Object {
public abstract int getSurfacePointIndexAndFraction (float, boolean, int, int, int, javax.vecmath.Point3i, int, int, float, float, javax.vecmath.Point3f, javax.vecmath.Vector3f, boolean, float[])
public abstract int addVertexCopy (javax.vecmath.Point3f, float, int)
public abstract void addTriangleCheck (int, int, int, int, boolean, int)
public abstract float getValue (int, int, int)
}
org/jmol/jvxl/calc/MarchingCubes.class
<Unknown>
package org.jmol.jvxl.calc
public org.jmol.jvxl.calc.MarchingCubes extends org.jmol.jvxl.calc.TriangleData {
private org.jmol.jvxl.api.VertexDataServer surfaceReader
private org.jmol.jvxl.data.VolumeData volumeData
private int contourType
private boolean isContoured
private float cutoff
private boolean isCutoffAbsolute
private boolean isSquared
private boolean isXLowToHigh
private int cubeCountX
private int cubeCountY
private int cubeCountZ
private int nY
private int nZ
private int yzCount
private float fractionOutside
private boolean integrateSquared
private java.util.BitSet bsVoxels
private StringBuffer edgeData
private int mode
private static final int MODE_CUBE
private static final int MODE_BITSET
private static final int MODE_GETXYZ
private final float[] vertexValues
int edgeCount
private final javax.vecmath.Vector3f[] voxelVertexVectors
private final javax.vecmath.Vector3f[] edgeVectors
private static int[] yzPlanePts
private final int[] edgePointIndexes
private int[][][] isoPointIndexPlanes
private float[][] yzPlanes
javax.vecmath.Vector3f vTemp
private java.util.BitSet bsValues
private final javax.vecmath.Point3f pt0
private final javax.vecmath.Point3f pointA
private static final int[] edgeVertexPointersLowToHigh
private static final int[] edgeVertexPointersHighToLow
private int[] edgeVertexPointers
private static final int[] edgeVertexPlanesLowToHigh
private static final int[] edgeVertexPlanesHighToLow
private int[] edgeVertexPlanes
private float[] fReturn
private static final javax.vecmath.Vector3f[] cubeVertexVectors
private static final int[] edgeTypeTable
private final int[] linearOffsets
private static final short[] insideMaskTable
public java.util.BitSet getBsVoxels ()
public void <init> ()
public void <init> (org.jmol.jvxl.api.VertexDataServer, org.jmol.jvxl.data.VolumeData, java.util.BitSet, boolean, int, float, boolean, boolean, boolean)
private void calcVoxelVertexVectors ()
private int[][] resetIndexPlane (int[][])
public java.lang.String getEdgeData ()
private void addTriangle (int, int, int, int)
private float getValue (int, int, int, int, int, float[])
public static boolean isInside (float, float, boolean)
private boolean processOneCubical (int, int, int, int, int)
public void calcVertexPoint (int, int, int, int, javax.vecmath.Point3f)
private void setLinearOffsets ()
public int getLinearOffset (int, int, int, int)
static void <clinit> ()
}
org/jmol/jvxl/calc/MarchingSquares$ContourVertex.class
<Unknown>
package org.jmol.jvxl.calc
org.jmol.jvxl.calc.MarchingSquares$ContourVertex extends java.lang.Object {
javax.vecmath.Point3f vertexXYZ
javax.vecmath.Point3i voxelLocation
int[] pixelLocation
float value
int vertexIndex
void <init> (int, int, int, javax.vecmath.Point3f, int)
void setValue (float, org.jmol.jvxl.data.VolumeData)
void setPixelLocation (javax.vecmath.Point3i)
}
org/jmol/jvxl/calc/MarchingSquares$PlanarSquare.class
<Unknown>
package org.jmol.jvxl.calc
org.jmol.jvxl.calc.MarchingSquares$PlanarSquare extends java.lang.Object {
int[] edgeMask12
int edgeMask12All
int nInside
int nOutside
int nThrough
int contourBits
final int[] vertexes
float[][] fractions
int[][] intersectionPoints
void <init> (int)
void setIntersectionPoints (int, int[], float[])
void setVertex (int, int)
void addEdgeMask (int, int, int)
}
org/jmol/jvxl/calc/MarchingSquares.class
<Unknown>
package org.jmol.jvxl.calc
public org.jmol.jvxl.calc.MarchingSquares extends java.lang.Object {
public static final int CONTOUR_POINT
public static final int VERTEX_POINT
public static final int EDGE_POINT
private boolean logMessages
private org.jmol.jvxl.api.VertexDataServer surfaceReader
private org.jmol.jvxl.data.VolumeData volumeData
private static final int nContourMax
public static final int defaultContourCount
private int nContourSegments
private int nContoursSpecified
private int contourType
private javax.vecmath.Point4f thePlane
private boolean is3DContour
private int thisContour
private float valueMin
private float valueMax
private int nVertices
private final javax.vecmath.Vector3f pointVector
private final javax.vecmath.Point3f pointA
private final javax.vecmath.Point3f pointB
private final javax.vecmath.Vector3f edgeVector
private final javax.vecmath.Point3f planarOrigin
private final javax.vecmath.Vector3f[] planarVectors
private final javax.vecmath.Vector3f[] unitPlanarVectors
private final float[] planarVectorLengths
private final javax.vecmath.Matrix3f matXyzToPlane
private boolean contourFromZero
private static final javax.vecmath.Point3i[] squareVertexOffsets
private static final javax.vecmath.Vector3f[] squareVertexVectors
private static final byte[] edgeVertexes2d
private static final byte[] insideMaskTable2d
private int contourVertexCount
private org.jmol.jvxl.calc.MarchingSquares$ContourVertex[] contourVertexes
private final int[] pixelCounts
private final javax.vecmath.Matrix3f planarMatrix
private float[][] pixelData
private final float[] vertexValues2d
private final javax.vecmath.Point3f[] contourPoints
private int squareCountX
private int squareCountY
private org.jmol.jvxl.calc.MarchingSquares$PlanarSquare[] planarSquares
private int nSquares
private float contourPlaneMinimumValue
private float contourPlaneMaximumValue
private int contourIndex
private float[] squareFractions
private final javax.vecmath.Point3f pixelOrigin
private javax.vecmath.Vector3f[] pixelVertexVectors
private final int[] triangleVertexList
private final javax.vecmath.Point3i ptiTemp
public void <init> (org.jmol.jvxl.api.VertexDataServer, org.jmol.jvxl.data.VolumeData, javax.vecmath.Point4f, int, int, boolean)
public int getContourType ()
public void setMinMax (float, float)
private void setContourType ()
private static int getContourType (javax.vecmath.Point4f, javax.vecmath.Vector3f[])
public int generateContourData (boolean)
private void getPlanarVectors ()
private void setPlanarTransform ()
private void getPlanarOrigin ()
public int addContourVertex (int, int, int, javax.vecmath.Point3i, javax.vecmath.Point3f, float)
public int getContourVertexCount ()
public void setContourData (int, float)
private void loadPixelData (boolean)
public float getInterpolatedPixelValue (javax.vecmath.Point3f)
private void getPixelCounts ()
private void createPlanarSquares ()
public boolean createContours (float, float)
private int generateContourData (float)
private boolean isInside2d (float, float)
private int[] propagateNeighborPointIndexes2d (int, int, int[][], float[][])
private void processOneQuadrilateral (int, float, int[], int, int)
private void calcVertexPoints2d (int, int, int, int)
private void calcVertexPoints3d (int, int, int, int)
private void contourLocateXYZ (int, int, javax.vecmath.Point3f)
private int findContourVertex (int, int)
private float calcContourPoint (float, float, float, javax.vecmath.Point3f)
private void calcPixelVertexVectors ()
private void triangulateContours (boolean)
private void fillSquare (org.jmol.jvxl.calc.MarchingSquares$PlanarSquare, int, int, boolean, int)
private void createTriangleSet (int, int, int)
private static void setupMatrix (javax.vecmath.Matrix3f, javax.vecmath.Vector3f[])
private void xyzToPixelVector (javax.vecmath.Vector3f)
private javax.vecmath.Point3f pixelPtToXYZ (int, int)
private javax.vecmath.Point3i locatePixel (javax.vecmath.Point3f)
static void <clinit> ()
}
org/jmol/jvxl/calc/TriangleData.class
<Unknown>
package org.jmol.jvxl.calc
public org.jmol.jvxl.calc.TriangleData extends java.lang.Object implements org.jmol.api.TriangleServer {
protected static final int[] Pwr2
protected static final javax.vecmath.Point3i[] cubeVertexOffsets
protected static final byte[] edgeVertexes
protected static final byte[][] triangleTable2
public void <init> ()
public javax.vecmath.Point3i[] getCubeVertexOffsets ()
public java.util.Vector intersectPlane (javax.vecmath.Point4f, javax.vecmath.Point3f[], int)
static void <clinit> ()
}
org/jmol/jvxl/data/JvxlData.class
<Unknown>
package org.jmol.jvxl.data
public org.jmol.jvxl.data.JvxlData extends java.lang.Object {
public boolean wasJvxl
public boolean wasCubic
public String jvxlFileTitle
public String jvxlFileMessage
public String jvxlFileHeader
public String jvxlExtraLine
public String jvxlDefinitionLine
public String jvxlSurfaceData
public String jvxlEdgeData
public String jvxlColorData
public String jvxlInfoLine
public javax.vecmath.Point4f jvxlPlane
public int jvxlCompressionRatio
public boolean isJvxlPrecisionColor
public boolean jvxlDataIsColorMapped
public boolean jvxlDataIs2dContour
public boolean isColorReversed
public int edgeFractionBase
public int edgeFractionRange
public int colorFractionBase
public int colorFractionRange
public boolean insideOut
public boolean isXLowToHigh
public boolean isContoured
public boolean isBicolorMap
public boolean isTruncated
public boolean vertexDataOnly
public float mappedDataMin
public float mappedDataMax
public float valueMappedToRed
public float valueMappedToBlue
public float cutoff
public float pointsPerAngstrom
public int nPointsX
public int nPointsY
public int nPointsZ
public int nBytes
public int nContours
public int nEdges
public int nSurfaceInts
public int vertexCount
public java.util.Vector[] vContours
public int[] contourColors
public short minColorIndex
public short maxColorIndex
public String[] title
public String version
public void <init> ()
}
org/jmol/jvxl/data/MeshData.class
<Unknown>
package org.jmol.jvxl.data
public org.jmol.jvxl.data.MeshData extends java.lang.Object {
private static final int SEED_COUNT
public static final int MODE_GET_VERTICES
public static final int MODE_GET_COLOR_INDEXES
public static final int MODE_PUT_SETS
public static final int MODE_PUT_VERTICES
public int polygonCount
public javax.vecmath.Point3f[] vertices
public short[] vertexColixes
public int vertexCount
public float[] vertexValues
public int[][] polygonIndexes
public short[] polygonColixes
public java.util.BitSet[] surfaceSet
public int[] vertexSets
public int nSets
public javax.vecmath.Point3f[] dots
private boolean setsSuccessful
public int vertexIncrement
private int lastColor
private short lastColix
public void <init> ()
public int addVertexCopy (javax.vecmath.Point3f, float, int)
private int addVertexCopy (javax.vecmath.Point3f)
public void addTriangleCheck (int, int, int, int, int)
public java.util.BitSet[] getSurfaceSet ()
public java.util.BitSet[] getSurfaceSet (int)
private int findSet (int)
private void createSet (int, int, int)
private void mergeSets (int, int)
public void invalidateSurfaceSet (int)
public static boolean checkCutoff (int, int, int, float[])
private boolean setABC (int)
public void invalidateTriangles ()
}
org/jmol/jvxl/data/VolumeData.class
<Unknown>
package org.jmol.jvxl.data
public org.jmol.jvxl.data.VolumeData extends java.lang.Object implements org.jmol.api.VolumeDataInterface {
public final javax.vecmath.Point3f volumetricOrigin
public final float[] origin
public final javax.vecmath.Vector3f[] volumetricVectors
public final int[] voxelCounts
public int nPoints
public float[][][] voxelData
public final float[] volumetricVectorLengths
public final javax.vecmath.Vector3f[] unitVolumetricVectors
private final javax.vecmath.Matrix3f volumetricMatrix
private javax.vecmath.Point4f thePlane
private float thePlaneNormalMag
private final javax.vecmath.Point3f ptXyzTemp
private final javax.vecmath.Vector3f pointVector
public void <init> ()
public void setVolumetricOrigin (float, float, float)
public float[] getOriginFloat ()
public float[] getVolumetricVectorLengths ()
public void setVolumetricVector (int, float, float, float)
public int[] getVoxelCounts ()
public int setVoxelCounts (int, int, int)
public float[][][] getVoxelData ()
public void setVoxelData (float[][][])
public void setMatrix ()
public void transform (javax.vecmath.Vector3f, javax.vecmath.Vector3f)
public void setPlaneParameters (javax.vecmath.Point4f)
public float calcVoxelPlaneDistance (int, int, int)
public float distancePointToPlane (javax.vecmath.Point3f)
public void voxelPtToXYZ (int, int, int, javax.vecmath.Point3f)
public void setUnitVectors ()
private float scaleByVoxelVector (javax.vecmath.Vector3f, int)
public void xyzToVoxelPt (float, float, float, javax.vecmath.Point3i)
private void setVoxelPoint ()
public float lookupInterpolatedVoxelValue (javax.vecmath.Point3f)
private float getInterpolatedVoxelValue (javax.vecmath.Point3f)
public static float getFractional2DValue (float, float, float, float, float, float)
private static int indexDown (float, int)
void offsetCenter (javax.vecmath.Point3f)
public void setDataDistanceToPlane (javax.vecmath.Point4f)
public void filterData (boolean, float)
public void capData (javax.vecmath.Point4f, float)
}
org/jmol/jvxl/readers/ApbsReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.ApbsReader extends org.jmol.jvxl.readers.VolumeFileReader {
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader)
protected void readTitleLines () throws java.lang.Exception
protected void readAtomCountAndOrigin () throws java.lang.Exception
protected void readVoxelVector (int) throws java.lang.Exception
}
org/jmol/jvxl/readers/AtomDataReader.class
<Unknown>
package org.jmol.jvxl.readers
abstract org.jmol.jvxl.readers.AtomDataReader extends org.jmol.jvxl.readers.VolumeDataReader {
protected org.jmol.atomdata.AtomDataServer atomDataServer
protected String fileName
protected String fileDotModel
protected int modelIndex
protected org.jmol.atomdata.AtomData atomData
protected javax.vecmath.Point3f[] atomXyz
protected float[] atomRadius
protected float[] atomProp
protected int[] atomNo
protected int[] atomIndex
protected int[] myIndex
protected int atomCount
protected int myAtomCount
protected int nearbyAtomCount
protected int firstNearbyAtom
protected java.util.BitSet bsMySelected
protected java.util.BitSet bsMyIgnored
private javax.vecmath.Point3f xyzMin
private javax.vecmath.Point3f xyzMax
protected boolean doAddHydrogens
protected boolean doUsePlane
protected boolean doUseIterator
void <init> (org.jmol.jvxl.readers.SurfaceGenerator)
protected void setup ()
protected void getAtoms (float, boolean, boolean)
private float getWorkingRadius (int, float)
protected void setHeader (java.lang.String, java.lang.String)
protected void setRangesAndAddAtoms (float, int, int)
protected boolean fixTitleLine (int)
}
org/jmol/jvxl/readers/CubeReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.CubeReader extends org.jmol.jvxl.readers.VolumeFileReader {
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader)
protected void readTitleLines () throws java.lang.Exception
protected void readAtomCountAndOrigin () throws java.lang.Exception
}
org/jmol/jvxl/readers/EfvetReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.EfvetReader extends org.jmol.jvxl.readers.PolygonFileReader {
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader)
void getSurfaceData () throws java.lang.Exception
private void getHeader () throws java.lang.Exception
private void getVertices () throws java.lang.Exception
private void getTriangles () throws java.lang.Exception
}
org/jmol/jvxl/readers/IsoFxyReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.IsoFxyReader extends org.jmol.jvxl.readers.VolumeDataReader {
private String functionName
private float[][] data
private boolean isPlanarMapping
void <init> (org.jmol.jvxl.readers.SurfaceGenerator)
protected void setup ()
public float getValue (int, int, int)
}
org/jmol/jvxl/readers/IsoFxyzReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.IsoFxyzReader extends org.jmol.jvxl.readers.VolumeDataReader {
private String functionName
private float[][][] data
void <init> (org.jmol.jvxl.readers.SurfaceGenerator)
protected void setup ()
public float getValue (int, int, int)
}
org/jmol/jvxl/readers/IsoMOReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.IsoMOReader extends org.jmol.jvxl.readers.AtomDataReader {
void <init> (org.jmol.jvxl.readers.SurfaceGenerator)
protected void setup ()
private void fixTitleLine (int, java.util.Hashtable)
protected void generateCube ()
private void getData (org.jmol.api.MOCalculationInterface, java.util.Hashtable, float[], float[])
}
org/jmol/jvxl/readers/IsoMepReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.IsoMepReader extends org.jmol.jvxl.readers.AtomDataReader {
void <init> (org.jmol.jvxl.readers.SurfaceGenerator)
protected void setup ()
protected void generateCube ()
}
org/jmol/jvxl/readers/IsoPlaneReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.IsoPlaneReader extends org.jmol.jvxl.readers.AtomDataReader {
void <init> (org.jmol.jvxl.readers.SurfaceGenerator)
protected void setup ()
public float getValue (int, int, int)
}
org/jmol/jvxl/readers/IsoShapeReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.IsoShapeReader extends org.jmol.jvxl.readers.VolumeDataReader {
private int psi_n
private int psi_l
private int psi_m
private float psi_Znuc
private float sphere_radiusAngstroms
private boolean allowNegative
private double[] rfactor
private double[] pfactor
private static final double A0
private static final double ROOT2
private float radius
private float ppa
private int maxGrid
private static final float[] fact
private final javax.vecmath.Point3f ptPsi
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, float)
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, int, int, int, float)
protected void setup ()
public float getValue (int, int, int)
private void setHeader (java.lang.String)
private float autoScaleOrbital ()
private void calcFactors (int, int, int)
private double hydrogenAtomPsiAt (javax.vecmath.Point3f, int, int, int)
protected void readSurfaceData (boolean) throws java.lang.Exception
static void <clinit> ()
}
org/jmol/jvxl/readers/IsoSolventReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.IsoSolventReader extends org.jmol.jvxl.readers.AtomDataReader {
private float cavityRadius
private float envelopeRadius
private boolean doCalculateTroughs
private boolean isCavity
private boolean isPocket
private float solventRadius
private boolean isProperty
private boolean doSmoothProperty
final javax.vecmath.Point3f ptXyzTemp
final javax.vecmath.Point3f ptS
void <init> (org.jmol.jvxl.readers.SurfaceGenerator)
protected void setup ()
public void selectPocket (boolean)
protected void generateCube ()
private void generateSolventCavity ()
void generateSolventCube (boolean)
void setGridLimitsForAtom (javax.vecmath.Point3f, float, javax.vecmath.Point3i, javax.vecmath.Point3i)
float checkSpecialVoxel (javax.vecmath.Point3f, float, javax.vecmath.Point3f, float, float, javax.vecmath.Point3f)
boolean voxelIsInTrough (float, float, float, float, float, float)
float solventDistance (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f, float, float, float, float, float)
}
org/jmol/jvxl/readers/JaguarReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.JaguarReader extends org.jmol.jvxl.readers.VolumeFileReader {
private float[] extents
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader)
protected void readTitleLines () throws java.lang.Exception
protected void readAtomCountAndOrigin () throws java.lang.Exception
protected void readVoxelVector (int) throws java.lang.Exception
protected float nextVoxel () throws java.lang.Exception
}
org/jmol/jvxl/readers/JvxlReader.class
<Unknown>
package org.jmol.jvxl.readers
public org.jmol.jvxl.readers.JvxlReader extends org.jmol.jvxl.readers.VolumeFileReader {
private static final String JVXL_VERSION
public static final int defaultEdgeFractionBase
public static final int defaultEdgeFractionRange
public static final int defaultColorFractionBase
public static final int defaultColorFractionRange
private int surfaceDataCount
private int edgeDataCount
private int colorDataCount
private boolean haveContourData
private int nThisValue
private boolean thisInside
private int fractionPtr
private String strFractionTemp
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader)
protected static void jvxlUpdateInfo (org.jmol.jvxl.data.JvxlData, java.lang.String[], int)
public static void jvxlUpdateInfoLines (org.jmol.jvxl.data.JvxlData)
protected boolean readVolumeData (boolean)
protected boolean gotoAndReadVoxelData (boolean)
protected void initializeVoxelData ()
protected void readSurfaceData (boolean) throws java.lang.Exception
protected void readTitleLines () throws java.lang.Exception
protected static boolean jvxlCheckAtomLine (boolean, boolean, java.lang.String, java.lang.String, java.lang.StringBuffer)
protected void readAtomCountAndOrigin () throws java.lang.Exception
protected static void jvxlReadAtoms (java.io.BufferedReader, java.lang.StringBuffer, int, org.jmol.jvxl.data.VolumeData) throws java.lang.Exception
protected int readExtraLine () throws java.lang.Exception
private void jvxlReadDefinitionLine (boolean) throws java.lang.Exception
private java.lang.String jvxlReadData (java.lang.String, int)
public static java.lang.String jvxlCompressString (java.lang.String)
private static java.lang.String jvxlUncompressString (java.lang.String)
protected java.util.BitSet getVoxelBitSet (int) throws java.lang.Exception
protected float getNextVoxelValue (java.lang.StringBuffer) throws java.lang.Exception
public static void setSurfaceInfoFromBitSet (org.jmol.jvxl.data.JvxlData, java.util.BitSet, javax.vecmath.Point4f)
private static int jvxlEncodeBitSet (java.util.BitSet, int, java.lang.StringBuffer)
private static java.util.BitSet jvxlDecodeBitSet (java.lang.String)
protected static void setSurfaceInfo (org.jmol.jvxl.data.JvxlData, javax.vecmath.Point4f, int, java.lang.StringBuffer)
protected float getSurfacePointAndFraction (float, boolean, float, float, javax.vecmath.Point3f, javax.vecmath.Vector3f, float[], javax.vecmath.Point3f)
private float jvxlGetNextFraction (int, int, float)
protected java.lang.String readColorData ()
protected void gotoData (int, int) throws java.lang.Exception
private void jvxlSkipData (int, boolean) throws java.lang.Exception
private void jvxlSkipDataBlock (int, boolean) throws java.lang.Exception
private int countData (java.lang.String)
protected static void jvxlCreateHeaderWithoutTitleOrAtoms (org.jmol.jvxl.data.VolumeData, java.lang.StringBuffer)
protected static void jvxlCreateHeader (org.jmol.jvxl.data.VolumeData, int, javax.vecmath.Point3f[], int[], java.lang.StringBuffer)
private static void jvxlAddDummyAtomList (org.jmol.jvxl.data.VolumeData, java.lang.StringBuffer)
public static java.lang.String jvxlGetDefinitionLine (org.jmol.jvxl.data.JvxlData, boolean)
protected static java.lang.String jvxlExtraLine (org.jmol.jvxl.data.JvxlData, int)
public static java.lang.String jvxlGetFile (org.jmol.jvxl.api.MeshDataServer, org.jmol.jvxl.data.JvxlData, org.jmol.jvxl.data.MeshData, java.lang.String[], java.lang.String, boolean, int, java.lang.String, java.lang.String)
private static void jvxlEncodeContourData (java.util.Vector[], java.lang.StringBuffer)
protected static float jvxlFractionFromCharacter (int, int, int, float)
protected static float jvxlValueFromCharacter2 (int, int, float, float, int, int)
protected static float jvxlFractionFromCharacter2 (int, int, int, int)
protected static char jvxlValueAsCharacter (float, float, float, int, int)
public static char jvxlFractionAsCharacter (float)
protected static char jvxlFractionAsCharacter (float, int, int)
private static void jvxlAppendCharacter2 (float, float, float, int, int, java.lang.StringBuffer, java.lang.StringBuffer)
public static void jvxlUpdateSurfaceData (org.jmol.jvxl.data.JvxlData, float[], int, int, char)
public static void jvxlCreateColorData (org.jmol.jvxl.data.JvxlData, float[])
public static java.lang.String jvxlEncodeTriangleData (int[][], int, int[])
public static java.lang.String jvxlEncodeVertexData (org.jmol.jvxl.api.MeshDataServer, org.jmol.jvxl.data.JvxlData, int[], javax.vecmath.Point3f[], float[], int, short[], int, boolean)
private void getEncodedVertexData () throws java.lang.Exception
private void jvxlDecodeContourData (java.lang.String) throws java.lang.Exception
public static void set3dContourVector (java.util.Vector, int[][], javax.vecmath.Point3f[])
private java.lang.String getXmlData (java.lang.String, java.lang.String, boolean) throws java.lang.Exception
public javax.vecmath.Point3f[] jvxlDecodeVertexData (java.lang.String, boolean)
int[][] jvxlDecodeTriangleData (java.lang.String, java.lang.String, boolean)
private static java.lang.String getXmlAttrib (java.lang.String, java.lang.String)
private static int setNext (java.lang.String, java.lang.String, int[], int)
}
org/jmol/jvxl/readers/LimitedLineReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.LimitedLineReader extends java.lang.Object {
private char[] buf
private int cchBuf
private int ichCurrent
private int iLine
void <init> (java.io.BufferedReader, int)
java.lang.String info ()
int iLine ()
java.lang.String readNonCommentLine ()
}
org/jmol/jvxl/readers/MapFileReader.class
<Unknown>
package org.jmol.jvxl.readers
abstract org.jmol.jvxl.readers.MapFileReader extends org.jmol.jvxl.readers.VolumeFileReader {
protected int mapc
protected int mapr
protected int maps
protected int nx
protected int ny
protected int nz
protected int mode
protected int[] nxyzStart
protected int na
protected int nb
protected int nc
protected float a
protected float b
protected float c
protected float alpha
protected float beta
protected float gamma
protected javax.vecmath.Point3f origin
protected javax.vecmath.Point3f adjustment
protected javax.vecmath.Point3f[] vectors
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader)
protected abstract void readParameters () throws java.lang.Exception
protected int readVolumetricHeader ()
protected void getVectorsAndOrigin ()
}
org/jmol/jvxl/readers/MrcBinaryReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.MrcBinaryReader extends org.jmol.jvxl.readers.MapFileReader {
protected String[] labels
private static byte[] b8
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.lang.String, boolean)
protected void readParameters () throws java.lang.Exception
protected float nextVoxel () throws java.lang.Exception
protected void skipData (int) throws java.lang.Exception
static void <clinit> ()
}
org/jmol/jvxl/readers/ObjReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.ObjReader extends org.jmol.jvxl.readers.PolygonFileReader {
private int nPolygons
String pmeshError
javax.vecmath.Point3f pt
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.lang.String, java.io.BufferedReader)
void getSurfaceData () throws java.lang.Exception
private boolean readPmesh ()
private boolean readVertices () throws java.lang.Exception
private boolean readPolygons ()
}
org/jmol/jvxl/readers/Parameters.class
<Unknown>
package org.jmol.jvxl.readers
public org.jmol.jvxl.readers.Parameters extends java.lang.Object {
public static final int STATE_UNINITIALIZED
public static final int STATE_INITIALIZED
public static final int STATE_DATA_READ
public static final int STATE_DATA_COLORED
int state
boolean logMessages
boolean logCompression
boolean logCube
boolean isSilent
float assocCutoff
static final int NO_ANISOTROPY
static final int IS_SILENT
public static final int IS_SOLVENTTYPE
static final int HAS_MAXGRID
static final int CAN_CONTOUR
public int dataType
int surfaceType
static final int SURFACE_NONE
static final int SURFACE_SPHERE
static final int SURFACE_ELLIPSOID2
static final int SURFACE_ELLIPSOID3
static final int SURFACE_LOBE
static final int SURFACE_LCAOCARTOON
public static final int SURFACE_LONEPAIR
public static final int SURFACE_RADICAL
static final int SURFACE_FUNCTIONXY
static final int SURFACE_FUNCTIONXYZ
static final int SURFACE_SOLVENT
static final int SURFACE_SASURFACE
static final int SURFACE_MOLECULARORBITAL
static final int SURFACE_ATOMICORBITAL
static final int SURFACE_MEP
static final int SURFACE_FILE
static final int SURFACE_INFO
static final int SURFACE_MOLECULAR
static final int SURFACE_NOMAP
static final int SURFACE_PROPERTY
String calculationType
boolean addHydrogens
float solventRadius
float solventExtendedAtomRadius
float solventAtomRadiusFactor
float solventAtomRadiusAbsolute
float solventAtomRadiusOffset
boolean propertySmoothing
boolean useIonic
float envelopeRadius
float cavityRadius
boolean isCavity
Boolean pocket
int minSet
javax.vecmath.Point4f cappingPlane
boolean doCapIsosurface
float[] theProperty
float solvent_ptsPerAngstrom
int solvent_gridMax
static final float ANGSTROMS_PER_BOHR
static final int defaultEdgeFractionBase
static final int defaultEdgeFractionRange
static final int defaultColorFractionBase
static final int defaultColorFractionRange
static final float defaultMappedDataMin
static final float defaultMappedDataMax
static final float defaultCutoff
static final float defaultOrbitalCutoff
public static final float defaultQMOrbitalCutoff
static final float defaultQMElectronDensityCutoff
static final int defaultContourCount
static final int nContourMax
static final int defaultColorNegative
static final int defaultColorPositive
static final int defaultColorNegativeLCAO
static final int defaultColorPositiveLCAO
static final float defaultSolventRadius
static final float defaultMepCutoff
static final float defaultMepMin
static final float defaultMepMax
boolean colorBySign
boolean colorByPhase
boolean colorBySets
int colorNeg
int colorPos
int colorPosLCAO
int colorNegLCAO
int colorPhase
boolean iAddGridPoints
boolean remappable
int atomIndex
boolean isAngstroms
float scale
float[] anisotropy
boolean isAnisotropic
javax.vecmath.Matrix3f eccentricityMatrix
javax.vecmath.Matrix3f eccentricityMatrixInverse
boolean isEccentric
float eccentricityScale
float eccentricityRatio
float[] aniosU
float[] anisoB
String lcaoType
public java.util.Vector functionXYinfo
int psi_n
int psi_l
int psi_m
float psi_Znuc
float psi_ptsPerAngstrom
public static final int MEP_MAX_GRID
int mep_gridMax
float mep_ptsPerAngstrom
float mep_marginAngstroms
int qmOrbitalType
int qmOrbitalCount
static final int QM_TYPE_UNKNOWN
static final int QM_TYPE_GAUSSIAN
static final int QM_TYPE_SLATER
java.util.Hashtable moData
java.util.Hashtable mo
float[] moCoefficients
public static final int MO_MAX_GRID
int qm_gridMax
float qm_ptsPerAngstrom
float qm_marginAngstroms
int qm_nAtoms
int qm_moNumber
javax.vecmath.Point3f center
javax.vecmath.Point3f point
float distance
String script
java.util.BitSet bsSelected
java.util.BitSet bsIgnore
java.util.BitSet bsSolvent
boolean iUseBitSets
String[] title
boolean blockCubeData
boolean readAllData
int fileIndex
String fileName
int modelIndex
boolean isXLowToHigh
boolean insideOut
float cutoff
boolean isCutoffAbsolute
boolean isPositiveOnly
boolean rangeAll
public boolean rangeDefined
float valueMappedToRed
float valueMappedToBlue
float mappedDataMin
float mappedDataMax
boolean isColorReversed
boolean isBicolorMap
boolean isSquared
javax.vecmath.Point4f thePlane
boolean isContoured
int nContours
int thisContour
boolean contourFromZero
float resolution
int downsampleFactor
int maxSet
public void <init> ()
void initialize ()
void setAnisotropy (javax.vecmath.Point3f)
void setEccentricity (javax.vecmath.Point4f)
void setPlane (javax.vecmath.Point4f)
void setSphere (float)
void setEllipsoid (javax.vecmath.Point4f)
public void setEllipsoid (float[])
void setLobe (javax.vecmath.Point4f)
void setLp (javax.vecmath.Point4f)
void setRadical (javax.vecmath.Point4f)
void setLcao (java.lang.String, int)
void setRadius (boolean, float)
void setSolvent (java.lang.String, float)
void setFunctionXY (java.util.Vector)
void setFunctionXYZ (java.util.Vector)
boolean setAtomicOrbital (float[])
void setMep (float[], boolean)
void setMO (int, boolean)
void setMapRanges (org.jmol.jvxl.readers.SurfaceReader)
}
org/jmol/jvxl/readers/PltFormattedReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.PltFormattedReader extends org.jmol.jvxl.readers.VolumeFileReader {
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader)
protected int readVolumetricHeader ()
protected void readTitleLines () throws java.lang.Exception
protected void readAtomCountAndOrigin () throws java.lang.Exception
protected void readVoxelVectors () throws java.lang.Exception
private java.lang.String getLine () throws java.io.IOException
}
org/jmol/jvxl/readers/PmeshReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.PmeshReader extends org.jmol.jvxl.readers.PolygonFileReader {
private int nPolygons
private boolean isBinary
static final String PMESH_BINARY_MAGIC_NUMBER
String pmeshError
private String[] tokens
private int iToken
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.lang.String, java.io.BufferedReader)
private boolean checkBinary (java.lang.String)
void getSurfaceData () throws java.lang.Exception
private boolean readPmesh ()
boolean readBinaryHeader ()
private boolean readVertices () throws java.lang.Exception
private boolean readPolygons () throws java.lang.Exception
private java.lang.String nextToken () throws java.lang.Exception
private int getInt () throws java.lang.Exception
private float getFloat () throws java.lang.Exception
}
org/jmol/jvxl/readers/PolygonFileReader.class
<Unknown>
package org.jmol.jvxl.readers
abstract org.jmol.jvxl.readers.PolygonFileReader extends org.jmol.jvxl.readers.SurfaceFileReader {
protected int nVertices
protected int nTriangles
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader)
void discardTempData (boolean)
boolean readVolumeParameters ()
boolean readVolumeData (boolean)
protected void readSurfaceData (boolean) throws java.lang.Exception
abstract void getSurfaceData () throws java.lang.Exception
}
org/jmol/jvxl/readers/SurfaceFileReader.class
<Unknown>
package org.jmol.jvxl.readers
abstract org.jmol.jvxl.readers.SurfaceFileReader extends org.jmol.jvxl.readers.SurfaceReader {
protected java.io.BufferedReader br
protected org.jmol.util.BinaryDocument binarydoc
String line
int[] next
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader)
static java.lang.String determineFileType (java.io.BufferedReader)
void discardTempData (boolean)
java.lang.String[] getTokens ()
float parseFloat ()
float parseFloat (java.lang.String)
int parseInt ()
int parseInt (java.lang.String)
int parseIntNext (java.lang.String)
protected void skipTo (java.lang.String, java.lang.String) throws java.lang.Exception
}
org/jmol/jvxl/readers/SurfaceGenerator.class
<Unknown>
package org.jmol.jvxl.readers
public org.jmol.jvxl.readers.SurfaceGenerator extends java.lang.Object {
private org.jmol.util.ColorEncoder colorEncoder
private org.jmol.jvxl.data.JvxlData jvxlData
private org.jmol.jvxl.data.MeshData meshData
private org.jmol.jvxl.readers.Parameters params
private org.jmol.jvxl.data.VolumeData volumeData
private org.jmol.jvxl.api.MeshDataServer meshDataServer
private org.jmol.atomdata.AtomDataServer atomDataServer
private org.jmol.jvxl.calc.MarchingSquares marchingSquares
private String version
private String fileType
org.jmol.jvxl.readers.SurfaceReader surfaceReader
int colorPtr
private boolean rangeDefined
final javax.vecmath.Vector3f vAC
final javax.vecmath.Vector3f vAB
final javax.vecmath.Vector3f vNorm
final javax.vecmath.Point3f ptRef
public void setVersion (java.lang.String)
public void <init> ()
public void <init> (org.jmol.atomdata.AtomDataServer, org.jmol.jvxl.api.MeshDataServer, org.jmol.util.ColorEncoder, org.jmol.jvxl.data.MeshData, org.jmol.jvxl.data.JvxlData)
private void setup (org.jmol.atomdata.AtomDataServer, org.jmol.jvxl.api.MeshDataServer, org.jmol.util.ColorEncoder, org.jmol.jvxl.data.MeshData, org.jmol.jvxl.data.JvxlData)
public boolean isStateDataRead ()
public int getDataType ()
org.jmol.jvxl.api.MeshDataServer getMeshDataServer ()
org.jmol.atomdata.AtomDataServer getAtomDataServer ()
org.jmol.util.ColorEncoder getColorEncoder ()
public void setJvxlData (org.jmol.jvxl.data.JvxlData)
public org.jmol.jvxl.data.JvxlData getJvxlData ()
org.jmol.jvxl.data.MeshData getMeshData ()
void setMarchingSquares (org.jmol.jvxl.calc.MarchingSquares)
org.jmol.jvxl.calc.MarchingSquares getMarchingSquares ()
public org.jmol.jvxl.readers.Parameters getParams ()
public java.lang.String getScript ()
public java.lang.String[] getTitle ()
public java.util.BitSet getBsSelected ()
public java.util.BitSet getBsIgnore ()
public java.util.Vector getFunctionXYinfo ()
org.jmol.jvxl.data.VolumeData getVolumeData ()
public javax.vecmath.Point4f getPlane ()
public int getColor (int)
public void setModelIndex (int)
public boolean getIUseBitSets ()
public boolean getIAddGridPoints ()
public boolean getIsPositiveOnly ()
public boolean isInsideOut ()
public float getCutoff ()
public java.util.Hashtable getMoData ()
public boolean isCubeData ()
public boolean setParameter (java.lang.String, java.lang.Object)
public boolean setParameter (java.lang.String, java.lang.Object, java.util.BitSet)
private void getSurfaceSets ()
private void processState ()
private boolean setReader ()
private void generateSurface ()
private void mapSurface (java.lang.Object)
void colorIsosurface ()
public java.lang.Object getProperty (java.lang.String, int)
private org.jmol.jvxl.readers.SurfaceReader setFileData (java.lang.Object)
void initializeIsosurface ()
public void initState ()
public java.lang.String setLcao ()
private void getFunctionZfromXY ()
private float distanceVerticalToPlane (float, float, javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f)
private static float findNearestThreePoints (float, float, float[][], int[])
}
org/jmol/jvxl/readers/SurfaceReader.class
<Unknown>
package org.jmol.jvxl.readers
public abstract org.jmol.jvxl.readers.SurfaceReader extends java.lang.Object implements org.jmol.jvxl.api.VertexDataServer {
protected org.jmol.jvxl.readers.SurfaceGenerator sg
protected org.jmol.jvxl.api.MeshDataServer meshDataServer
protected org.jmol.util.ColorEncoder colorEncoder
protected org.jmol.jvxl.readers.Parameters params
protected org.jmol.jvxl.data.MeshData meshData
protected org.jmol.jvxl.data.JvxlData jvxlData
protected org.jmol.jvxl.data.VolumeData volumeData
private String edgeData
protected boolean isProgressive
protected boolean isXLowToHigh
private float assocCutoff
boolean vertexDataOnly
boolean hasColorData
static final float ANGSTROMS_PER_BOHR
static final float defaultMappedDataMin
static final float defaultMappedDataMax
static final float defaultCutoff
private int edgeCount
protected javax.vecmath.Point3f volumetricOrigin
protected javax.vecmath.Vector3f[] volumetricVectors
protected int[] voxelCounts
protected float[][][] voxelData
protected long nBytes
protected int nDataPoints
protected int nPointsX
protected int nPointsY
protected int nPointsZ
protected boolean isJvxl
protected boolean isApbsDx
protected int edgeFractionBase
protected int edgeFractionRange
protected int colorFractionBase
protected int colorFractionRange
protected StringBuffer jvxlFileHeaderBuffer
protected StringBuffer fractionData
protected String jvxlEdgeDataRead
protected String jvxlColorDataRead
protected java.util.BitSet jvxlVoxelBitSet
protected java.util.Vector[] vContours
protected boolean jvxlDataIsColorMapped
protected boolean jvxlDataIsPrecisionColor
protected boolean jvxlDataIs2dContour
protected float jvxlCutoff
protected int jvxlNSurfaceInts
protected char cJvxlEdgeNaN
protected int contourVertexCount
protected org.jmol.jvxl.calc.MarchingSquares marchingSquares
private org.jmol.jvxl.calc.MarchingCubes marchingCubes
protected final javax.vecmath.Point3f ptTemp
private static final String[] colorPhases
void <init> (org.jmol.jvxl.readers.SurfaceGenerator)
void setVolumeData (org.jmol.jvxl.data.VolumeData)
abstract boolean readVolumeParameters ()
abstract boolean readVolumeData (boolean)
void jvxlUpdateInfo ()
boolean createIsosurface (boolean)
void resetIsosurface ()
void discardTempData (boolean)
protected void initializeVolumetricData ()
protected abstract void readSurfaceData (boolean) throws java.lang.Exception
protected boolean gotoAndReadVoxelData (boolean)
protected void gotoData (int, int) throws java.lang.Exception
protected java.lang.String readColorData ()
public float getValue (int, int, int)
private void generateSurfaceData ()
public int getSurfacePointIndexAndFraction (float, boolean, int, int, int, javax.vecmath.Point3i, int, int, float, float, javax.vecmath.Point3f, javax.vecmath.Vector3f, boolean, float[])
protected float getSurfacePointAndFraction (float, boolean, float, float, javax.vecmath.Point3f, javax.vecmath.Vector3f, float[], javax.vecmath.Point3f)
public int addVertexCopy (javax.vecmath.Point3f, float, int)
public void addTriangleCheck (int, int, int, int, boolean, int)
void colorIsosurface ()
void applyColorScale ()
private void colorData ()
static int getColorPhaseIndex (java.lang.String)
private float getPhase (javax.vecmath.Point3f)
float getMinMappedValue ()
float getMaxMappedValue ()
protected short getColorIndexFromPalette (float)
protected int getArgbFromPalette (float)
void updateTriangles ()
void updateSurfaceData ()
public void selectPocket (boolean)
void excludeMinimumSet ()
void excludeMaximumSet ()
static void <clinit> ()
}
org/jmol/jvxl/readers/VolumeDataReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.VolumeDataReader extends org.jmol.jvxl.readers.SurfaceReader {
protected int dataType
protected boolean precalculateVoxelData
protected boolean allowMapData
protected javax.vecmath.Point3f center
protected javax.vecmath.Point3f point
protected float[] anisotropy
protected boolean isAnisotropic
protected javax.vecmath.Matrix3f eccentricityMatrix
protected javax.vecmath.Matrix3f eccentricityMatrixInverse
protected boolean isEccentric
protected float eccentricityScale
protected float eccentricityRatio
void <init> (org.jmol.jvxl.readers.SurfaceGenerator)
void setup ()
boolean readVolumeParameters ()
boolean readVolumeData (boolean)
protected void readVoxelDataIndividually (boolean) throws java.lang.Exception
protected int setVoxelRange (int, float, float, float, int)
protected void readSurfaceData (boolean) throws java.lang.Exception
protected void generateCube ()
}
org/jmol/jvxl/readers/VolumeFileReader.class
<Unknown>
package org.jmol.jvxl.readers
abstract org.jmol.jvxl.readers.VolumeFileReader extends org.jmol.jvxl.readers.SurfaceFileReader {
protected boolean endOfData
protected boolean negativeAtomCount
protected int atomCount
private int nSurfaces
protected boolean isAngstroms
protected boolean canDownsample
protected int[] downsampleRemainders
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader)
boolean readVolumeParameters ()
boolean readVolumeData (boolean)
protected int readVolumetricHeader ()
protected void readTitleLines () throws java.lang.Exception
protected java.lang.String skipComments (boolean) throws java.lang.Exception
protected void readAtomCountAndOrigin () throws java.lang.Exception
protected void readVoxelVector (int) throws java.lang.Exception
protected int readExtraLine () throws java.lang.Exception
protected void readSurfaceData (boolean) throws java.lang.Exception
private void skipVoxels (int) throws java.lang.Exception
protected java.util.BitSet getVoxelBitSet (int) throws java.lang.Exception
protected float getNextVoxelValue () throws java.lang.Exception
protected float nextVoxel () throws java.lang.Exception
protected void gotoData (int, int) throws java.lang.Exception
protected void skipData (int) throws java.lang.Exception
private int countData (java.lang.String)
}
org/jmol/jvxl/readers/XplorReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.XplorReader extends org.jmol.jvxl.readers.MapFileReader {
private int nBlock
private int linePt
private int nRead
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader)
protected void readParameters () throws java.lang.Exception
private java.lang.String getLine () throws java.io.IOException
protected float nextVoxel () throws java.lang.Exception
}
org/jmol/minimize/MinAtom.class
<Unknown>
package org.jmol.minimize
public org.jmol.minimize.MinAtom extends java.lang.Object {
int index
public org.jmol.modelset.Atom atom
public double[] coord
public double[] force
public java.util.Vector bonds
public int nBonds
public String type
int[] bondedAtoms
void <init> (int, org.jmol.modelset.Atom, double[], java.lang.String)
void set ()
public org.jmol.minimize.MinBond getBondTo (int)
public int[] getBondedAtomIndexes ()
public java.lang.String getIdentity ()
}
org/jmol/minimize/MinBond.class
<Unknown>
package org.jmol.minimize
public org.jmol.minimize.MinBond extends java.lang.Object {
public int[] atomIndexes
public boolean isAromatic
public boolean isAmide
void <init> (int[], boolean, boolean)
public int getOtherAtom (int)
}
org/jmol/minimize/Minimizer$MinimizationThread.class
<Unknown>
package org.jmol.minimize
org.jmol.minimize.Minimizer$MinimizationThread extends java.lang.Thread implements java.lang.Runnable {
private final org.jmol.minimize.Minimizer this$0
void <init> (org.jmol.minimize.Minimizer)
public void run ()
}
org/jmol/minimize/Minimizer.class
<Unknown>
package org.jmol.minimize
public org.jmol.minimize.Minimizer extends java.lang.Object implements org.jmol.api.MinimizerInterface {
public org.jmol.viewer.Viewer viewer
public org.jmol.modelset.Atom[] atoms
public org.jmol.minimize.MinAtom[] minAtoms
public org.jmol.minimize.MinBond[] minBonds
public java.util.BitSet bsMinFixed
private int atomCount
private int bondCount
private int atomCountFull
private int[] atomMap
public int[][] angles
public int[][] torsions
public double[] partialCharges
private int steps
private double crit
private static java.util.Vector atomTypes
private org.jmol.minimize.forcefield.ForceField pFF
private String ff
private java.util.BitSet bsTaint
private java.util.BitSet bsSelected
private java.util.BitSet bsAtoms
private java.util.BitSet bsFixed
public java.util.Vector constraints
java.util.Hashtable constraintMap
static final int TOKEN_ELEMENT_ONLY
static final int TOKEN_ELEMENT_CHARGED
static final int TOKEN_ELEMENT_CONNECTED
static final int TOKEN_ELEMENT_AROMATIC
static final int TOKEN_ELEMENT_SP
static final int TOKEN_ELEMENT_SP2
static final int PT_ELEMENT
static final int PT_CHARGE
static final int PT_CONNECT
static final org.jmol.viewer.Token[][] tokenTypes
boolean minimizationOn
private org.jmol.minimize.Minimizer$MinimizationThread minimizationThread
double[][] coordSaved
public void <init> ()
public void setProperty (java.lang.String, java.lang.Object)
public java.lang.Object getProperty (java.lang.String, int)
private void addConstraint (java.lang.Object[])
private void clear ()
public boolean minimize (int, double, java.util.BitSet)
private boolean setupMinimization ()
private void setAtomPositions ()
private java.util.BitSet getSearch (java.lang.String, int, java.util.BitSet)
public void getAngles ()
public void getTorsions ()
public org.jmol.minimize.forcefield.ForceField getForceField ()
public java.util.Vector getAtomTypes ()
private void setMinimizationOn (boolean)
private void getEnergyOnly ()
public boolean startMinimization ()
boolean stepMinimization ()
void endMinimization ()
private void saveCoordinates ()
private void restoreCoordinates ()
private void stopMinimization (boolean)
void updateAtomXYZ ()
private void minimizeWithoutThread ()
static void <clinit> ()
}
org/jmol/minimize/Util.class
<Unknown>
package org.jmol.minimize
public org.jmol.minimize.Util extends java.lang.Object {
public static final double RAD_TO_DEG
public static final double DEG_TO_RAD
static final double max_squarable_double
static final double min_squarable_double
public void <init> ()
public static void sub (double[], double[], javax.vecmath.Vector3d)
public static void putCoord (javax.vecmath.Vector3d, double[])
public static double distance2 (double[], double[])
public static double distance2 (javax.vecmath.Vector3d, javax.vecmath.Vector3d)
public static double getAngleRadiansABC (double[], double[], double[])
public static boolean isApprox (javax.vecmath.Vector3d, javax.vecmath.Vector3d, double)
public static boolean canBeSquared (double)
public static boolean isNegligible (double, double)
public static boolean isFinite (double)
public static boolean isNegligible (double, double, double)
public static boolean isNear (double, double)
public static boolean isNear (double, double, double)
public static boolean isNearZero (double)
public static boolean isNearZero (double, double)
public static boolean canBeNormalized (javax.vecmath.Vector3d)
public static double pointPlaneAngleRadians (javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d)
private static double vectorAngleRadians (javax.vecmath.Vector3d, javax.vecmath.Vector3d)
public static double getTorsionAngleRadians (double[], double[], double[], double[], javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d)
public static double restorativeForceAndDistance (javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d)
private static void randomizeUnitVector (javax.vecmath.Vector3d)
public static double restorativeForceAndAngleRadians (javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d)
public static double restorativeForceAndOutOfPlaneAngleRadians (javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d)
public static double restorativeForceAndTorsionAngleRadians (javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d)
}
org/jmol/minimize/forcefield/Calculation.class
<Unknown>
package org.jmol.minimize.forcefield
abstract org.jmol.minimize.forcefield.Calculation extends java.lang.Object {
double dE
org.jmol.minimize.forcefield.FFParam parA
org.jmol.minimize.forcefield.FFParam parB
org.jmol.minimize.forcefield.FFParam parC
org.jmol.minimize.MinAtom a
org.jmol.minimize.MinAtom b
org.jmol.minimize.MinAtom c
org.jmol.minimize.MinAtom d
int ia
int ib
int ic
int id
int[] iData
double[] dData
double delta
double rab
double theta
double energy
void <init> ()
abstract double compute (java.lang.Object[])
double getEnergy ()
void getPointers (java.lang.Object[])
}
org/jmol/minimize/forcefield/Calculations.class
<Unknown>
package org.jmol.minimize.forcefield
abstract org.jmol.minimize.forcefield.Calculations extends java.lang.Object {
public static final double RAD_TO_DEG
public static final double DEG_TO_RAD
static final double KCAL_TO_KJ
static final int CALC_DISTANCE
static final int CALC_ANGLE
static final int CALC_TORSION
static final int CALC_OOP
static final int CALC_VDW
static final int CALC_ES
static final int CALC_MAX
org.jmol.minimize.forcefield.ForceField ff
java.util.Vector[] calculations
public java.util.Hashtable ffParams
int atomCount
int bondCount
org.jmol.minimize.MinAtom[] atoms
org.jmol.minimize.MinBond[] bonds
int[][] angles
int[][] torsions
double[] partialCharges
boolean havePartialCharges
java.util.Vector constraints
boolean isPreliminary
boolean gradients
boolean silent
StringBuffer logData
boolean logging
boolean loggingEnabled
final javax.vecmath.Vector3d da
final javax.vecmath.Vector3d db
final javax.vecmath.Vector3d dc
final javax.vecmath.Vector3d dd
int ia
int ib
int ic
int id
final javax.vecmath.Vector3d v1
final javax.vecmath.Vector3d v2
final javax.vecmath.Vector3d v3
private static final double PI_OVER_2
private static final double TWO_PI
public void setConstraints (java.util.Vector)
void <init> (org.jmol.minimize.forcefield.ForceField, org.jmol.minimize.MinAtom[], org.jmol.minimize.MinBond[], int[][], int[][], double[], java.util.Vector)
boolean haveParams ()
void setParams (java.util.Hashtable)
static org.jmol.minimize.forcefield.FFParam getParameter (java.lang.String, java.util.Hashtable)
abstract boolean setupCalculations ()
abstract java.lang.String getAtomList (java.lang.String)
abstract boolean setupElectrostatics ()
abstract java.lang.String getDebugHeader (int)
abstract java.lang.String getDebugFooter (int, double)
abstract java.lang.String getUnit ()
abstract double compute (int, java.lang.Object[])
void addForce (javax.vecmath.Vector3d, int, double)
public void setSilent (boolean)
public java.lang.String getLogData ()
void appendLogData (java.lang.String)
void setLoggingEnabled (boolean)
void setPreliminary (boolean)
private double calc (int, boolean)
double energyStrBnd (boolean)
double energyBond (boolean)
double energyAngle (boolean)
double energyTorsion (boolean)
double energyOOP (boolean)
double energyVDW (boolean)
double energyES (boolean)
private double constraintEnergy (int)
private double constrainQuadratic (double, double, double, int)
}
org/jmol/minimize/forcefield/CalculationsUFF$AngleCalc.class
<Unknown>
package org.jmol.minimize.forcefield
org.jmol.minimize.forcefield.CalculationsUFF$AngleCalc extends org.jmol.minimize.forcefield.Calculation {
private final org.jmol.minimize.forcefield.CalculationsUFF this$0
void <init> (org.jmol.minimize.forcefield.CalculationsUFF)
void setData (java.util.Vector, int)
double compute (java.lang.Object[])
}
org/jmol/minimize/forcefield/CalculationsUFF$DistanceCalc.class
<Unknown>
package org.jmol.minimize.forcefield
org.jmol.minimize.forcefield.CalculationsUFF$DistanceCalc extends org.jmol.minimize.forcefield.Calculation {
double r0
double kb
private final org.jmol.minimize.forcefield.CalculationsUFF this$0
void <init> (org.jmol.minimize.forcefield.CalculationsUFF)
void setData (java.util.Vector, int, int, double)
double compute (java.lang.Object[])
}
org/jmol/minimize/forcefield/CalculationsUFF$ESCalc.class
<Unknown>
package org.jmol.minimize.forcefield
org.jmol.minimize.forcefield.CalculationsUFF$ESCalc extends org.jmol.minimize.forcefield.CalculationsUFF$PairCalc {
private final org.jmol.minimize.forcefield.CalculationsUFF this$0
void <init> (org.jmol.minimize.forcefield.CalculationsUFF)
void setData (java.util.Vector, int, int)
double compute (java.lang.Object[])
}
org/jmol/minimize/forcefield/CalculationsUFF$OOPCalc.class
<Unknown>
package org.jmol.minimize.forcefield
org.jmol.minimize.forcefield.CalculationsUFF$OOPCalc extends org.jmol.minimize.forcefield.Calculation {
private final org.jmol.minimize.forcefield.CalculationsUFF this$0
void <init> (org.jmol.minimize.forcefield.CalculationsUFF)
void setData (java.util.Vector, int, int)
double compute (java.lang.Object[])
}
org/jmol/minimize/forcefield/CalculationsUFF$PairCalc.class
<Unknown>
package org.jmol.minimize.forcefield
abstract org.jmol.minimize.forcefield.CalculationsUFF$PairCalc extends org.jmol.minimize.forcefield.Calculation {
private final org.jmol.minimize.forcefield.CalculationsUFF this$0
void <init> (org.jmol.minimize.forcefield.CalculationsUFF)
abstract void setData (java.util.Vector, int, int)
}
org/jmol/minimize/forcefield/CalculationsUFF$TorsionCalc.class
<Unknown>
package org.jmol.minimize.forcefield
org.jmol.minimize.forcefield.CalculationsUFF$TorsionCalc extends org.jmol.minimize.forcefield.Calculation {
private final org.jmol.minimize.forcefield.CalculationsUFF this$0
void <init> (org.jmol.minimize.forcefield.CalculationsUFF)
void setData (java.util.Vector, int)
double compute (java.lang.Object[])
}
org/jmol/minimize/forcefield/CalculationsUFF$VDWCalc.class
<Unknown>
package org.jmol.minimize.forcefield
org.jmol.minimize.forcefield.CalculationsUFF$VDWCalc extends org.jmol.minimize.forcefield.CalculationsUFF$PairCalc {
private final org.jmol.minimize.forcefield.CalculationsUFF this$0
void <init> (org.jmol.minimize.forcefield.CalculationsUFF)
void setData (java.util.Vector, int, int)
double compute (java.lang.Object[])
}
org/jmol/minimize/forcefield/CalculationsUFF.class
<Unknown>
package org.jmol.minimize.forcefield
org.jmol.minimize.forcefield.CalculationsUFF extends org.jmol.minimize.forcefield.Calculations {
public static final int PAR_R
public static final int PAR_THETA
public static final int PAR_X
public static final int PAR_D
public static final int PAR_ZETA
public static final int PAR_Z
public static final int PAR_V
public static final int PAR_U
public static final int PAR_XI
public static final int PAR_HARD
public static final int PAR_RADIUS
org.jmol.minimize.forcefield.CalculationsUFF$DistanceCalc bondCalc
org.jmol.minimize.forcefield.CalculationsUFF$AngleCalc angleCalc
org.jmol.minimize.forcefield.CalculationsUFF$TorsionCalc torsionCalc
org.jmol.minimize.forcefield.CalculationsUFF$OOPCalc oopCalc
org.jmol.minimize.forcefield.CalculationsUFF$VDWCalc vdwCalc
org.jmol.minimize.forcefield.CalculationsUFF$ESCalc esCalc
static final double KCAL644
static final double KCAL6
static final double KCAL22
static final double KCAL44
static final double KCAL332
void <init> (org.jmol.minimize.forcefield.ForceField, org.jmol.minimize.MinAtom[], org.jmol.minimize.MinBond[], int[][], int[][], double[], java.util.Vector)
java.lang.String getUnit ()
boolean setupCalculations ()
private boolean isInvertible (int)
private void pairSearch (java.util.Vector, org.jmol.minimize.forcefield.CalculationsUFF$PairCalc)
boolean setupElectrostatics ()
static double calculateR0 (double, double, double, double, double)
double compute (int, java.lang.Object[])
java.lang.String getAtomList (java.lang.String)
java.lang.String getDebugHeader (int)
java.lang.String getDebugLine (int, org.jmol.minimize.forcefield.Calculation)
java.lang.String getDebugFooter (int, double)
}
org/jmol/minimize/forcefield/FFParam.class
<Unknown>
package org.jmol.minimize.forcefield
public org.jmol.minimize.forcefield.FFParam extends java.lang.Object {
int[] iVal
double[] dVal
String[] sVal
public void <init> ()
}
org/jmol/minimize/forcefield/ForceField.class
<Unknown>
package org.jmol.minimize.forcefield
public abstract org.jmol.minimize.forcefield.ForceField extends java.lang.Object {
static final int ENERGY
static final int EBOND
static final int EANGLE
static final int ESTRBND
static final int ETORSION
static final int EOOP
static final int EVDW
static final int EELECTROSTATIC
org.jmol.minimize.forcefield.Calculations calc
private double criterion
private double e0
private double dE
private int currentStep
private int stepMax
private double[][] coordSaved
int atomCount
int bondCount
org.jmol.viewer.Viewer viewer
org.jmol.minimize.MinAtom[] atoms
org.jmol.minimize.MinBond[] bonds
java.util.BitSet bsFixed
private java.lang.String getUnits ()
public abstract java.util.Vector getAtomTypes ()
protected abstract java.util.Hashtable getFFParameters ()
public void <init> ()
public void setModel (org.jmol.minimize.Minimizer)
public void setConstraints (org.jmol.minimize.Minimizer)
public boolean setup ()
public void steepestDescentInitialize (int, double)
private void clearForces ()
public boolean steepestDescentTakeNSteps (int)
private double getEnergy (int, boolean)
private void setForcesUsingNumericalDerivative (org.jmol.minimize.MinAtom, int)
private double getDE (org.jmol.minimize.MinAtom, int, int, double)
public double energyFull (boolean, boolean)
double energyStrBnd (boolean)
double energyBond (boolean)
double energyAngle (boolean)
double energyTorsion (boolean)
double energyOOP (boolean)
double energyVDW (boolean)
double energyES (boolean)
private void linearSearch ()
private void saveCoordinates ()
private void restoreCoordinates ()
public boolean detectExplosion ()
public int getCurrentStep ()
public double getEnergy ()
public java.lang.String getAtomList (java.lang.String)
public double getEnergyDiff ()
public java.lang.String getLogData ()
double getNormalizedDE ()
}
org/jmol/minimize/forcefield/ForceFieldUFF.class
<Unknown>
package org.jmol.minimize.forcefield
public org.jmol.minimize.forcefield.ForceFieldUFF extends org.jmol.minimize.forcefield.ForceField {
public void <init> ()
public void setModel (org.jmol.minimize.Minimizer)
protected java.util.Hashtable getFFParameters ()
public java.util.Vector getAtomTypes ()
}
org/jmol/minimize/forcefield/UFF.txt
org/jmol/modelset/Atom.class
<Unknown>
package org.jmol.modelset
public final org.jmol.modelset.Atom extends org.jmol.util.Point3fi {
private static final byte VIBRATION_VECTOR_FLAG
private static final byte IS_HETERO_FLAG
private static final byte FLAG_MASK
public static final int RADIUS_MAX
private static final int MAD_MAX
org.jmol.modelset.Group group
int atomIndex
java.util.BitSet atomSymmetry
int atomSite
private float userDefinedVanDerWaalRadius
private short atomicAndIsotopeNumber
private byte formalChargeAndFlags
private byte valence
char alternateLocationID
short madAtom
short colixAtom
byte paletteID
org.jmol.modelset.Bond[] bonds
int nBondsDisplayed
int nBackbonesDisplayed
int clickabilityFlags
int shapeVisibilityFlags
boolean isSimple
public int getScreenRadius ()
public short getMadAtom ()
public int getNBackbonesDisplayed ()
public boolean isSimple ()
public void <init> (javax.vecmath.Point3f)
void <init> (org.jmol.viewer.Viewer, int, int, java.util.BitSet, int, short, int, int, float, float, float, boolean, char, char, float)
public final void setShapeVisibilityFlags (int)
public final void setShapeVisibility (int, boolean)
public boolean isBonded (org.jmol.modelset.Atom)
public org.jmol.modelset.Bond getBond (org.jmol.modelset.Atom)
void addDisplayedBond (int, boolean)
public void addDisplayedBackbone (int, boolean)
void deleteBond (org.jmol.modelset.Bond)
private void deleteBond (int)
void clearBonds ()
int getBondedAtomIndex (int)
public void setMadAtom (org.jmol.viewer.Viewer, int, float)
public short convertEncodedMad (org.jmol.viewer.Viewer, int, float)
public float getADPMinMax (boolean)
public int getRasMolRadius ()
public int getCovalentBondCount ()
int getCovalentHydrogenCount ()
public org.jmol.modelset.Bond[] getBonds ()
public void setColixAtom (short)
public void setPaletteID (byte)
public void setTranslucent (boolean, float)
public boolean isTranslucent ()
public short getElementNumber ()
public short getIsotopeNumber ()
public short getAtomicAndIsotopeNumber ()
public void setAtomicAndIsotopeNumber (int)
public java.lang.String getElementSymbol (boolean)
public java.lang.String getElementSymbol ()
public char getAlternateLocationID ()
boolean isAlternateLocationMatch (java.lang.String)
public boolean isHetero ()
void setFormalCharge (int)
void setVibrationVector ()
public int getFormalCharge ()
public int getOccupancy100 ()
public int getBfactor100 ()
public boolean setRadius (float)
public void setValence (int)
public int getValence ()
public float getDimensionValue (int)
private int getVanderwaalsMad (org.jmol.viewer.Viewer)
short getBondingMar ()
public float getVanderwaalsRadiusFloat ()
public float getCovalentRadiusFloat ()
public float getBondingRadiusFloat ()
int getCurrentBondCount ()
public short getColix ()
public byte getPaletteID ()
public float getRadius ()
public int getAtomIndex ()
public int getAtomSite ()
public java.util.BitSet getAtomSymmetry ()
void setGroup (org.jmol.modelset.Group)
public org.jmol.modelset.Group getGroup ()
public void transform (org.jmol.viewer.Viewer)
public java.lang.String getAtomName ()
public java.lang.String getAtomType ()
public int getAtomNumber ()
public boolean isInFrame ()
public int getShapeVisibilityFlags ()
public boolean isShapeVisible (int)
public float getPartialCharge ()
public float getStraightness ()
public java.lang.Object[] getEllipsoid ()
public int getSymmetryTranslation (int, int[], int)
public int getCellTranslation (int, int[], int)
java.lang.String getSymmetryOperatorList ()
public int getModelIndex ()
public int getMoleculeNumber ()
java.lang.String getClientAtomStringProperty (java.lang.String)
public byte getSpecialAtomID ()
public float getFractionalCoord (char)
public float getFractionalUnitCoord (char)
public javax.vecmath.Point3f getFractionalCoord ()
public javax.vecmath.Point3f getFractionalUnitCoord (boolean)
public float getFractionalUnitDistance (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f)
void setFractionalCoord (int, float)
void setFractionalCoord (javax.vecmath.Point3f)
boolean isCursorOnTopOf (int, int, int, org.jmol.modelset.Atom)
public java.lang.String getInfo ()
java.lang.String getInfoXYZ (boolean)
java.lang.String getIdentityXYZ ()
java.lang.String getIdentity (boolean)
public int getGroupIndex ()
public java.lang.String getGroup3 (boolean)
public java.lang.String getGroup1 (char)
boolean isGroup3 (java.lang.String)
boolean isProtein ()
boolean isCarbohydrate ()
boolean isNucleic ()
boolean isDna ()
boolean isRna ()
boolean isPurine ()
boolean isPyrimidine ()
int getSeqcode ()
public int getResno ()
public boolean isClickable ()
public int getClickabilityFlags ()
public void setClickable (int)
public boolean isVisible (int)
public float getGroupPhi ()
public float getGroupPsi ()
public char getChainID ()
public int getSurfaceDistance100 ()
public javax.vecmath.Vector3f getVibrationVector ()
public float getVibrationCoord (char)
public int getPolymerLength ()
public org.jmol.util.Quaternion getQuaternion (char)
int getPolymerIndex ()
public int getSelectedGroupCountWithinChain ()
public int getSelectedGroupIndexWithinChain ()
public int getSelectedMonomerCountWithinPolymer ()
public int getSelectedMonomerIndexWithinPolymer ()
org.jmol.modelset.Chain getChain ()
java.lang.String getModelNumberForLabel ()
public int getModelNumber ()
public int getModelFileIndex ()
public int getModelFileNumber ()
public byte getProteinStructureType ()
public int getStrucNo ()
public java.lang.String getStructureId ()
public java.lang.String getProteinStructureTag ()
public short getGroupID ()
java.lang.String getSeqcodeString ()
int getSeqNumber ()
public char getInsertionCode ()
public boolean equals (java.lang.Object)
public int hashCode ()
public org.jmol.modelset.Atom findAromaticNeighbor (java.util.BitSet)
public org.jmol.modelset.Atom findAromaticNeighbor (int)
public static int atomPropertyInt (org.jmol.modelset.Atom, int)
public static float atomPropertyFloat (org.jmol.modelset.Atom, int)
public static java.lang.String atomPropertyString (org.jmol.modelset.Atom, int)
public static javax.vecmath.Tuple3f atomPropertyTuple (org.jmol.modelset.Atom, int)
boolean isWithinStructure (byte)
}
org/jmol/modelset/AtomCollection.class
<Unknown>
package org.jmol.modelset
public abstract org.jmol.modelset.AtomCollection extends java.lang.Object {
public org.jmol.viewer.Viewer viewer
protected org.jmol.g3d.Graphics3D g3d
public org.jmol.modelset.Atom[] atoms
int atomCount
String[] atomNames
String[] atomTypes
int[] atomSerials
byte[] specialAtomIDs
Object[] clientAtomReferences
javax.vecmath.Vector3f[] vibrationVectors
byte[] occupancies
short[] bfactor100s
float[] partialCharges
protected Object[][] ellipsoids
protected int[] surfaceDistance100s
protected boolean haveStraightness
private java.util.BitSet bsHidden
protected float maxBondingRadius
private float maxVanderwaalsRadius
private boolean hasBfactorRange
private int bfactor100Lo
private int bfactor100Hi
private int surfaceDistanceMax
private java.util.BitSet bsSurface
private int nSurfaceAtoms
protected org.jmol.bspt.Bspf bspf
public static final byte TAINT_ATOMNAME
public static final byte TAINT_ATOMTYPE
public static final byte TAINT_COORD
private static final byte TAINT_ELEMENT
private static final byte TAINT_FORMALCHARGE
private static final byte TAINT_OCCUPANCY
private static final byte TAINT_PARTIALCHARGE
private static final byte TAINT_TEMPERATURE
private static final byte TAINT_VALENCE
private static final byte TAINT_VANDERWAALS
private static final byte TAINT_VIBRATION
public static final byte TAINT_MAX
private static final String[] userSettableValues
protected java.util.BitSet[] tainted
private static final int minimumPixelSelectionRadius
private final java.util.BitSet bsEmpty
private final java.util.BitSet bsFoundRectangle
public void <init> ()
protected void releaseModelSet ()
protected void merge (org.jmol.modelset.AtomCollection)
public void setHaveStraightness (boolean)
protected boolean getHaveStraightness ()
public org.jmol.modelset.Atom[] getAtoms ()
public org.jmol.modelset.Atom getAtomAt (int)
public int getAtomCount ()
public boolean modelSetHasVibrationVectors ()
public java.lang.String[] getAtomNames ()
public java.lang.String[] getAtomTypes ()
public float[] getPartialCharges ()
public short[] getBFactors ()
public void setBsHidden (java.util.BitSet)
public boolean isAtomHidden (int)
public java.lang.String getAtomInfo (int, java.lang.String)
public java.lang.String getAtomInfoXYZ (int, boolean)
public java.lang.String getElementSymbol (int)
public int getElementNumber (int)
java.lang.String getElementName (int)
public java.lang.String getAtomName (int)
public int getAtomNumber (int)
public float getAtomX (int)
public float getAtomY (int)
public float getAtomZ (int)
public javax.vecmath.Point3f getAtomPoint3f (int)
public float getAtomRadius (int)
public float getAtomVdwRadius (int)
public short getAtomColix (int)
public java.lang.String getAtomChain (int)
public java.lang.String getAtomSequenceCode (int)
public int getAtomModelIndex (int)
public java.lang.Object[] getEllipsoid (int)
public org.jmol.util.Quaternion getQuaternion (int, char)
public java.lang.Object getHelixData (java.util.BitSet, int)
public int getAtomIndexFromAtomNumber (int, java.util.BitSet)
public void setFormalCharges (java.util.BitSet, int)
public float[] getAtomicCharges ()
protected float getRadiusVdwJmol (org.jmol.modelset.Atom)
public float getMaxVanderwaalsRadius ()
protected void findMaxRadii ()
public void clearBfactorRange ()
private void calcBfactorRange (java.util.BitSet)
public int getBfactor100Lo ()
public int getBfactor100Hi ()
public int getSurfaceDistanceMax ()
int getSurfaceDistance100 (int)
private void calcSurfaceDistances ()
public javax.vecmath.Point3f[] calculateSurface (java.util.BitSet, float)
public void setAtomCoord (java.util.BitSet, int, java.lang.Object)
private void setAtomVibrationVector (int, float, float, float)
public void setAtomCoord (int, float, float, float)
public void setAtomCoordRelative (int, float, float, float)
protected void setAtomCoordRelative (java.util.BitSet, float, float, float)
public void setAtomProperty (java.util.BitSet, int, int, float, java.lang.String, float[], java.lang.String[])
public float getVibrationCoord (int, char)
public javax.vecmath.Vector3f getVibrationVector (int, boolean)
protected void setVibrationVector (int, float, float, float)
private void setVibrationVector (int, int, float)
protected void setAtomName (int, java.lang.String)
protected void setAtomType (int, java.lang.String)
protected boolean setOccupancy (int, int)
protected boolean setPartialCharge (int, float)
protected boolean setBFactor (int, float)
protected void setEllipsoid (int, java.lang.Object[])
public void setAtomData (int, java.lang.String, java.lang.String)
private void loadCoordinates (java.lang.String, boolean)
public static int getUserSettableType (java.lang.String)
public java.util.BitSet getTaintedAtoms (byte)
protected void taint (int, byte)
private void untaint (int, byte)
public void setTaintedAtoms (java.util.BitSet, byte)
public java.lang.String getAtomicPropertyState (int, java.util.BitSet)
public static void getAtomicPropertyState (java.lang.StringBuffer, org.jmol.modelset.Atom[], int, byte, java.util.BitSet, java.lang.String, float[])
protected void findNearestAtomIndex (int, int, org.jmol.modelset.Atom[])
boolean isCursorOnTopOf (org.jmol.modelset.Atom, int, int, int, org.jmol.modelset.Atom)
public java.util.BitSet findAtomsInRectangle (java.awt.Rectangle, java.util.BitSet)
protected void fillAtomData (org.jmol.atomdata.AtomData, int)
protected javax.vecmath.Point3f[][] getAdditionalHydrogens (java.util.BitSet, int[])
public java.lang.String getHybridizationAndAxes (int, javax.vecmath.Vector3f, javax.vecmath.Vector3f, java.lang.String, boolean)
protected java.lang.String getChimeInfo (int, java.util.BitSet)
protected java.util.BitSet getAtomBits (int, java.lang.Object)
protected boolean isInLatticeCell (int, javax.vecmath.Point3f)
private java.util.BitSet getIdentifierOrNull (java.lang.String)
private java.util.BitSet getSpecName (java.lang.String)
private java.util.BitSet getSpecNameOrNull (java.lang.String, boolean)
private boolean isAtomNameMatch (org.jmol.modelset.Atom, java.lang.String, boolean)
protected java.util.BitSet getSeqcodeBits (int, boolean)
protected java.util.BitSet getChainBits (char)
public int[] getAtomIndices (java.util.BitSet)
public java.util.BitSet getAtomsWithin (float, javax.vecmath.Point4f)
public java.util.BitSet getVisibleSet ()
public java.util.BitSet getClickableSet ()
protected void deleteModelAtoms (int, int, java.util.BitSet)
static void <clinit> ()
}
org/jmol/modelset/AtomIndexIterator.class
<Unknown>
package org.jmol.modelset
public abstract org.jmol.modelset.AtomIndexIterator extends java.lang.Object {
public abstract boolean hasNext ()
public abstract int next ()
public abstract void release ()
public abstract float foundDistance2 ()
}
org/jmol/modelset/AtomIteratorWithinModel.class
<Unknown>
package org.jmol.modelset
public org.jmol.modelset.AtomIteratorWithinModel extends java.lang.Object implements org.jmol.modelset.AtomIndexIterator {
org.jmol.bspt.CubeIterator bsptIter
public void <init> ()
void initialize (org.jmol.bspt.Bspf, int, javax.vecmath.Point3f, float)
public boolean hasNext ()
public int next ()
public float foundDistance2 ()
public void release ()
}
org/jmol/modelset/AtomIteratorWithinSet.class
<Unknown>
package org.jmol.modelset
org.jmol.modelset.AtomIteratorWithinSet extends java.lang.Object implements org.jmol.modelset.AtomIndexIterator {
org.jmol.bspt.CubeIterator bsptIter
java.util.BitSet bsSelected
boolean isGreaterOnly
int atomIndex
int zerobase
int iNext
void <init> ()
void initialize (org.jmol.bspt.Bspf, int, int, javax.vecmath.Point3f, float, java.util.BitSet, boolean, int)
public boolean hasNext ()
public int next ()
public float foundDistance2 ()
public void release ()
}
org/jmol/modelset/Bond$BondSet.class
<Unknown>
package org.jmol.modelset
public org.jmol.modelset.Bond$BondSet extends java.util.BitSet {
private int[] associatedAtoms
public int[] getAssociatedAtoms ()
public void <init> (java.util.BitSet)
public void <init> (java.util.BitSet, int[])
}
org/jmol/modelset/Bond.class
<Unknown>
package org.jmol.modelset
public org.jmol.modelset.Bond extends java.lang.Object {
org.jmol.modelset.Atom atom1
org.jmol.modelset.Atom atom2
short order
short mad
short colix
int index
int shapeVisibilityFlags
static final int myVisibilityFlag
public short getMad ()
public short getColix ()
public int getShapeVisibilityFlags ()
void <init> (org.jmol.modelset.Atom, org.jmol.modelset.Atom, short, short, short)
public java.lang.String getIdentity ()
public boolean isCovalent ()
boolean isHydrogen ()
boolean isStereo ()
boolean isPartial ()
boolean isAromatic ()
int getValence ()
void deleteAtomReferences ()
public void setMad (short)
final void setShapeVisibility (int, boolean)
public void setColix (short)
public void setTranslucent (boolean, float)
boolean isTranslucent ()
public void setOrder (short)
public org.jmol.modelset.Atom getAtom1 ()
public org.jmol.modelset.Atom getAtom2 ()
public int getAtomIndex1 ()
public int getAtomIndex2 ()
float getRadius ()
public short getOrder ()
java.lang.String getOrderName ()
java.lang.String getOrderNumberAsString ()
short getColix1 ()
int getArgb1 ()
short getColix2 ()
int getArgb2 ()
public org.jmol.modelset.Atom getOtherAtom (org.jmol.modelset.Atom)
public void setShapeVisibilityFlags (int)
public void setIndex (int)
public boolean is (int)
static void <clinit> ()
}
org/jmol/modelset/BondCollection.class
<Unknown>
package org.jmol.modelset
public abstract org.jmol.modelset.BondCollection extends org.jmol.modelset.AtomCollection {
protected org.jmol.modelset.Bond[] bonds
protected int bondCount
protected static final boolean showRebondTimes
private static final int bondGrowthIncrement
protected static final int MAX_BONDS_LENGTH_TO_CACHE
protected static final int MAX_NUM_TO_CACHE
protected int[] numCached
protected org.jmol.modelset.Bond[][][] freeBonds
protected java.util.BitSet bsPseudoHBonds
private boolean haveWarned
protected short defaultCovalentMad
private java.util.BitSet bsAromaticSingle
private java.util.BitSet bsAromaticDouble
protected java.util.BitSet bsAromatic
public void <init> ()
protected void releaseModelSet ()
protected void merge (org.jmol.modelset.ModelSet)
public org.jmol.modelset.Bond[] getBonds ()
public org.jmol.modelset.Bond getBondAt (int)
public int getBondCount ()
public org.jmol.modelset.BondIterator getBondIterator (short, java.util.BitSet)
public org.jmol.modelset.BondIterator getBondIterator (java.util.BitSet)
public org.jmol.modelset.Atom getBondAtom1 (int)
public org.jmol.modelset.Atom getBondAtom2 (int)
public float getBondRadius (int)
public short getBondOrder (int)
public short getBondColix1 (int)
public short getBondColix2 (int)
public int getBondModelIndex (int)
public java.util.BitSet getBondsForSelectedAtoms (java.util.BitSet, boolean)
public org.jmol.modelset.Bond bondAtoms (org.jmol.modelset.Atom, org.jmol.modelset.Atom, short, short, java.util.BitSet)
protected org.jmol.modelset.Bond getOrAddBond (org.jmol.modelset.Atom, org.jmol.modelset.Atom, short, short, java.util.BitSet)
private org.jmol.modelset.Bond getOrAddHBond (org.jmol.modelset.Atom, org.jmol.modelset.Atom, short, short, java.util.BitSet, float)
protected org.jmol.modelset.Bond setBond (int, org.jmol.modelset.Bond)
protected org.jmol.modelset.Bond hBondMutually (org.jmol.modelset.Atom, org.jmol.modelset.Atom, short, short, float)
protected org.jmol.modelset.Bond bondMutually (org.jmol.modelset.Atom, org.jmol.modelset.Atom, short, short)
private void addBondToAtom (org.jmol.modelset.Atom, org.jmol.modelset.Bond)
private org.jmol.modelset.Bond[] addToBonds (org.jmol.modelset.Bond, org.jmol.modelset.Bond[])
void addHydrogenBond (org.jmol.modelset.Atom, org.jmol.modelset.Atom, short, java.util.BitSet, java.util.BitSet, float)
protected short getBondOrder (org.jmol.modelset.Atom, float, org.jmol.modelset.Atom, float, float, float, float)
protected boolean checkValencesAndBond (org.jmol.modelset.Atom, org.jmol.modelset.Atom, short, short, java.util.BitSet)
protected void deleteAllBonds ()
protected short getDefaultMadFromOrder (short)
protected int[] deleteConnections (float, float, short, java.util.BitSet, java.util.BitSet, boolean, boolean, float, float)
protected void deleteBonds (java.util.BitSet)
public void resetAromatic ()
public void assignAromaticBonds ()
protected void assignAromaticBonds (boolean, java.util.BitSet)
private boolean assignAromaticDouble (org.jmol.modelset.Bond)
private boolean assignAromaticSingle (org.jmol.modelset.Bond)
private boolean assignAromaticSingle (org.jmol.modelset.Atom, int)
private boolean assignAromaticDouble (org.jmol.modelset.Atom)
private boolean assignAromaticSingleHetero (org.jmol.modelset.Atom)
private void assignAromaticNandO (java.util.BitSet)
protected java.util.BitSet getAtomBits (int, java.lang.Object)
}
org/jmol/modelset/BondIterator.class
<Unknown>
package org.jmol.modelset
public abstract org.jmol.modelset.BondIterator extends java.lang.Object {
public abstract boolean hasNext ()
public abstract int nextIndex ()
public abstract org.jmol.modelset.Bond next ()
}
org/jmol/modelset/BondIteratorSelected.class
<Unknown>
package org.jmol.modelset
org.jmol.modelset.BondIteratorSelected extends java.lang.Object implements org.jmol.modelset.BondIterator {
private org.jmol.modelset.Bond[] bonds
private int bondCount
private short bondType
private int iBond
private java.util.BitSet bsSelected
private boolean bondSelectionModeOr
private boolean isBondBitSet
void <init> (org.jmol.modelset.Bond[], int, short, java.util.BitSet, boolean)
void <init> (org.jmol.modelset.Bond[], int, java.util.BitSet)
public boolean hasNext ()
public int nextIndex ()
public org.jmol.modelset.Bond next ()
}
org/jmol/modelset/BoxInfo.class
<Unknown>
package org.jmol.modelset
public org.jmol.modelset.BoxInfo extends java.lang.Object {
private final javax.vecmath.Point3f bbCorner0
private final javax.vecmath.Point3f bbCorner1
private final javax.vecmath.Point3f bbCenter
private final javax.vecmath.Vector3f bbVector
private final javax.vecmath.Point3f[] bbVertices
private static final javax.vecmath.Point3f[] unitBboxPoints
public void <init> ()
public javax.vecmath.Point3f getBoundBoxCenter ()
public javax.vecmath.Vector3f getBoundBoxCornerVector ()
public javax.vecmath.Point3f[] getBoundBoxPoints ()
javax.vecmath.Point3f[] getBboxVertices ()
java.util.Hashtable getBoundBoxInfo ()
void setBoundBox (javax.vecmath.Point3f, javax.vecmath.Point3f, boolean)
void reset ()
void addBoundBoxPoint (javax.vecmath.Point3f)
void setBbcage ()
boolean isWithin (javax.vecmath.Point3f)
static void <clinit> ()
}
org/jmol/modelset/Chain.class
<Unknown>
package org.jmol.modelset
public final org.jmol.modelset.Chain extends java.lang.Object {
org.jmol.modelset.ModelSet modelSet
org.jmol.modelset.Model model
char chainID
int groupCount
int selectedGroupCount
private boolean isDna
private boolean isRna
java.util.BitSet bsSelectedGroups
org.jmol.modelset.Group[] groups
public void <init> (org.jmol.modelset.ModelSet, org.jmol.modelset.Model, char)
public void setModelSet (org.jmol.modelset.ModelSet)
public char getChainID ()
public org.jmol.modelset.ModelSet getModelSet ()
public boolean isDna ()
public boolean isRna ()
public void setIsDna (boolean)
public void setIsRna (boolean)
public org.jmol.modelset.Group getGroup (int)
public int getGroupCount ()
public int getAtomCount ()
public org.jmol.modelset.Atom getAtom (int)
public void calcSelectedGroupsCount (java.util.BitSet)
public int selectSeqcodeRange (int, int, int, java.util.BitSet)
int getSelectedGroupCount ()
public final void updateOffsetsForAlternativeLocations (java.util.BitSet, int, byte[], int, int)
public void fixIndices (int)
}
org/jmol/modelset/Group.class
<Unknown>
package org.jmol.modelset
public org.jmol.modelset.Group extends java.lang.Object {
private int groupIndex
protected org.jmol.modelset.Chain chain
int seqcode
protected short groupID
protected boolean isAmino
int selectedIndex
protected int firstAtomIndex
protected int lastAtomIndex
private static final int SEQUENCE_NUMBER_FLAG
private static final int INSERTION_CODE_MASK
private static final int SEQUENCE_NUMBER_SHIFT
public int shapeVisibilityFlags
protected float phi
protected float psi
protected float omega
protected float straightness
private static java.util.Hashtable htGroup
static String[] group3Names
static short group3NameCount
public int getGroupIndex ()
public void setGroupIndex (int)
public int getFirstAtomIndex ()
public int getLastAtomIndex ()
public float getStraightness ()
public void setStraightness (float)
public float getPhi ()
public void setPhi (float)
public float getPsi ()
public void setPsi (float)
public void setOmega (float)
public float getOmega ()
public void <init> (org.jmol.modelset.Chain, java.lang.String, int, int, int)
public void setModelSet (org.jmol.modelset.ModelSet)
public final void setShapeVisibility (int, boolean)
final boolean isGroup3 (java.lang.String)
final java.lang.String getGroup3 ()
public static java.lang.String getGroup3 (short)
public final char getGroup1 ()
public final short getGroupID ()
public final char getChainID ()
public int getBioPolymerLength ()
public int getBioPolymerIndex ()
public java.lang.Object getStructure ()
public int getStrucNo ()
public byte getProteinStructureType ()
public int setProteinStructureType (byte, int)
public java.util.Hashtable getMyInfo ()
public boolean isProtein ()
public boolean isNucleic ()
public boolean isDna ()
public boolean isRna ()
public boolean isPurine ()
public boolean isPyrimidine ()
public boolean isCarbohydrate ()
static synchronized short addGroup3Name (java.lang.String)
public static short getGroupID (java.lang.String)
public static short lookupGroupID (java.lang.String)
public final int getResno ()
public final int getSeqcode ()
public final int getSeqNumber ()
public static final int getSequenceNumber (int)
public static final int getInsertionCodeValue (int)
public static final boolean haveSequenceNumber (int)
public final java.lang.String getSeqcodeString ()
public static int getSeqcode (int, char)
public static java.lang.String getSeqcodeString (int)
public char getInsertionCode ()
public static char getInsertionCode (int)
public final void selectAtoms (java.util.BitSet)
public boolean isSelected (java.util.BitSet)
boolean isHetero ()
public java.lang.String toString ()
protected int scaleToScreen (int, int)
protected boolean isCursorOnTopOf (org.jmol.modelset.Atom, int, int, int, org.jmol.modelset.Atom)
protected boolean isAtomHidden (int)
public org.jmol.modelset.Model getModel ()
public int getModelIndex ()
public int getSelectedMonomerCount ()
public int getSelectedMonomerIndex ()
public int getSelectedGroupIndex ()
public org.jmol.modelset.Atom getLeadAtom (org.jmol.modelset.Atom)
public org.jmol.modelset.Atom getLeadAtom ()
public org.jmol.util.Quaternion getQuaternion (char)
public void setProteinStructureId (int)
public java.lang.Object getHelixData (int, char, int)
public boolean isWithinStructure (byte)
public java.lang.String getProteinStructureTag ()
public java.lang.String getStructureId ()
static void <clinit> ()
}
org/jmol/modelset/HBond.class
<Unknown>
package org.jmol.modelset
public org.jmol.modelset.HBond extends org.jmol.modelset.Bond {
private float energy
private byte paletteID
void <init> (org.jmol.modelset.Atom, org.jmol.modelset.Atom, short, short, short, float)
public float getEnergy ()
public byte getPaletteId ()
public void setPaletteID (byte)
}
org/jmol/modelset/LabelToken.class
<Unknown>
package org.jmol.modelset
public org.jmol.modelset.LabelToken extends java.lang.Object {
private String text
private String key
private float[] data
private int tok
private int pt
private char ch1
private int width
private int precision
private boolean alignLeft
private boolean zeroPad
private boolean intAsFloat
private static final String labelTokenParams
private static final int[] labelTokenIds
private static final String twoCharLabelTokenParams
private static final int[] twoCharLabelTokenIds
public static final String STANDARD_LABEL
private static boolean isLabelPropertyTok (int)
private void <init> (java.lang.String)
private void <init> (int)
public static org.jmol.modelset.LabelToken[] compile (org.jmol.viewer.Viewer, java.lang.String, char, java.util.Hashtable)
private static int setToken (org.jmol.viewer.Viewer, java.lang.String, org.jmol.modelset.LabelToken, int, int, java.util.Hashtable)
public static java.lang.String formatLabel (org.jmol.modelset.Atom, java.lang.String)
public static java.lang.String formatLabel (org.jmol.modelset.Atom, java.lang.String, org.jmol.modelset.LabelToken[], char, int[])
private static void appendAtomTokenValue (org.jmol.modelset.Atom, org.jmol.modelset.LabelToken, java.lang.StringBuffer, int[])
public static java.util.Hashtable getBondLabelValues ()
public static java.lang.String formatLabel (org.jmol.modelset.Bond, org.jmol.modelset.LabelToken[], java.util.Hashtable, int[])
public static java.lang.String labelFormat (org.jmol.modelset.Measurement, java.lang.String, float, java.lang.String)
public java.lang.String format (float, java.lang.String, javax.vecmath.Tuple3f)
public static void setValues (org.jmol.modelset.LabelToken[], java.util.Hashtable)
public static java.lang.String getLabel (org.jmol.modelset.LabelToken[])
static void <clinit> ()
}
org/jmol/modelset/Measurement.class
<Unknown>
package org.jmol.modelset
public org.jmol.modelset.Measurement extends java.lang.Object {
org.jmol.viewer.Viewer viewer
public org.jmol.modelset.ModelSet modelSet
protected int count
protected int[] countPlusIndices
protected org.jmol.util.Point3fi[] points
private String strMeasurement
private String strFormat
protected float value
private boolean isVisible
private boolean isHidden
private boolean isDynamic
private boolean isTrajectory
private short colix
private int index
private javax.vecmath.AxisAngle4f aa
private javax.vecmath.Point3f pointArc
public int getCount ()
public void setCount (int)
public int[] getCountPlusIndices ()
public org.jmol.util.Point3fi[] getPoints ()
public int getAtomIndex (int)
public org.jmol.util.Point3fi getAtom (int)
public int getLastIndex ()
public java.lang.String getString ()
public java.lang.String getStringDetail ()
public java.lang.String getStrFormat ()
public float getValue ()
public boolean isVisible ()
public boolean isHidden ()
public boolean isDynamic ()
public boolean isTrajectory ()
public void setVisible (boolean)
public void setHidden (boolean)
public void setDynamic (boolean)
public short getColix ()
public void setColix (short)
public void setIndex (int)
public int getIndex ()
public javax.vecmath.AxisAngle4f getAxisAngle ()
public javax.vecmath.Point3f getPointArc ()
public void <init> (org.jmol.modelset.ModelSet, int[], org.jmol.util.Point3fi[], float, short, java.lang.String, int)
public void <init> (org.jmol.modelset.ModelSet, int[], org.jmol.util.Point3fi[])
public void refresh ()
public java.lang.String getMeasurementScript (java.lang.String, boolean)
public void formatMeasurement (java.lang.String, boolean)
protected void formatMeasurement ()
public void reformatDistanceIfSelected ()
private java.lang.String formatDistance (float)
private java.lang.String formatAngle (float)
private java.lang.String formatString (float, java.lang.String)
public boolean sameAs (int[], org.jmol.util.Point3fi[])
private boolean sameAs (int[], org.jmol.util.Point3fi[], int, int)
public boolean sameAs (int, int)
public java.util.Vector toVector ()
public float getMeasurement ()
public java.lang.String getLabel (int, boolean, boolean)
public void setModelIndex (short)
}
org/jmol/modelset/MeasurementPending.class
<Unknown>
package org.jmol.modelset
public org.jmol.modelset.MeasurementPending extends org.jmol.modelset.Measurement {
private boolean haveTarget
private boolean haveModified
int numSet
int lastIndex
public boolean haveTarget ()
public boolean haveModified ()
public int getNumSet ()
public void <init> (org.jmol.modelset.ModelSet)
private boolean checkPoint (org.jmol.util.Point3fi)
public int getIndexOf (int)
public int addPoint (int, org.jmol.util.Point3fi, boolean)
}
org/jmol/modelset/Model.class
<Unknown>
package org.jmol.modelset
public final org.jmol.modelset.Model extends java.lang.Object {
org.jmol.modelset.ModelSet modelSet
int modelIndex
int fileIndex
boolean isPDB
boolean isTrajectory
int trajectoryBaseIndex
int selectedTrajectory
boolean hasCalculatedHBonds
java.util.Hashtable dataFrames
int dataSourceFrame
String jmolData
String jmolFrameType
int firstAtomIndex
int atomCount
final java.util.BitSet bsAtoms
private int bondCount
int firstMolecule
int moleculeCount
int nAltLocs
int nInsertions
int groupCount
int chainCount
org.jmol.modelset.Chain[] chains
int bioPolymerCount
org.jmol.modelset.Polymer[] bioPolymers
int biosymmetryCount
java.util.Hashtable auxiliaryInfo
java.util.Properties properties
float defaultRotationRadius
org.jmol.viewer.StateManager$Orientation orientation
boolean structureTainted
public org.jmol.modelset.ModelSet getModelSet ()
public void resetBoundCount ()
int getBondCount ()
void <init> (org.jmol.modelset.ModelSet, int, int, java.lang.String, java.util.Properties, java.util.Hashtable)
void setNAltLocs (int)
void setNInsertions (int)
void addSecondaryStructure (byte, java.lang.String, int, int, char, int, char, int)
void calculateStructures ()
public boolean isStructureTainted ()
void setConformation (java.util.BitSet)
public org.jmol.modelset.Chain[] getChains ()
public int getChainCount (boolean)
public int getGroupCount (boolean)
public int getBioPolymerCount ()
void calcSelectedGroupsCount (java.util.BitSet)
void calcSelectedMonomersCount (java.util.BitSet)
void selectSeqcodeRange (int, int, char, java.util.BitSet, boolean)
int getGroupCount ()
org.jmol.modelset.Chain getChain (char)
org.jmol.modelset.Chain getChain (int)
public org.jmol.modelset.Polymer getBioPolymer (int)
void calcHydrogenBonds (java.util.BitSet, java.util.BitSet)
public boolean isAtomHidden (int)
public void addHydrogenBond (org.jmol.modelset.Atom, org.jmol.modelset.Atom, short, java.util.BitSet, java.util.BitSet, float)
public int getModelIndex ()
void fixIndices (int, int, java.util.BitSet)
}
org/jmol/modelset/ModelCollection$StateScript.class
<Unknown>
package org.jmol.modelset
public org.jmol.modelset.ModelCollection$StateScript extends java.lang.Object {
private int modelIndex
private java.util.BitSet bsBonds
private java.util.BitSet bsAtoms1
private java.util.BitSet bsAtoms2
private String script1
private String script2
boolean postDefinitions
void <init> (int, java.lang.String, java.util.BitSet, java.util.BitSet, java.util.BitSet, java.lang.String, boolean)
public boolean isValid ()
public java.lang.String toString ()
public boolean isConnect ()
public boolean deleteAtoms (int, java.util.BitSet, java.util.BitSet)
public void setModelIndex (int)
}
org/jmol/modelset/ModelCollection$Structure.class
<Unknown>
package org.jmol.modelset
org.jmol.modelset.ModelCollection$Structure extends java.lang.Object {
String typeName
byte type
char startChainID
int startSeqcode
char endChainID
int endSeqcode
int modelIndex
String structureID
int serialID
int strandCount
void <init> (int, java.lang.String, java.lang.String, int, int, char, int, char, int)
}
org/jmol/modelset/ModelCollection.class
<Unknown>
package org.jmol.modelset
public abstract org.jmol.modelset.ModelCollection extends org.jmol.modelset.BondCollection {
protected java.util.BitSet bsSymmetry
protected String modelSetName
protected org.jmol.modelset.Model[] models
protected int modelCount
org.jmol.api.SymmetryInterface[] unitCells
protected int[] modelNumbers
protected int[] modelFileNumbers
protected String[] modelNumbersForAtomLabel
protected String[] modelNames
protected String[] frameTitles
protected java.util.BitSet[] elementsPresent
protected boolean isXYZ
protected boolean isPDB
private java.util.Properties modelSetProperties
private java.util.Hashtable modelSetAuxiliaryInfo
protected org.jmol.modelset.Group[] groups
protected int groupCount
protected int baseGroupIndex
private int structureCount
private org.jmol.modelset.ModelCollection$Structure[] structures
protected boolean haveBioClasses
protected org.jmol.api.JmolBioResolver jbr
protected java.util.BitSet structuresDefinedInFile
protected boolean someModelsHaveSymmetry
protected boolean someModelsHaveAromaticBonds
protected boolean someModelsHaveFractionalCoordinates
protected org.jmol.modelset.Molecule[] molecules
protected int moleculeCount
private final javax.vecmath.Matrix3f matTemp
private final javax.vecmath.Matrix3f matInv
private final javax.vecmath.Point3f ptTemp
private final javax.vecmath.Point3f averageAtomPoint
private boolean isBbcageDefault
private java.util.BitSet bboxModels
private java.util.BitSet bboxAtoms
private final org.jmol.modelset.BoxInfo boxInfo
protected java.util.Vector stateScripts
private int thisStateModel
protected java.util.Vector trajectorySteps
private static final String[] pdbRecords
private java.util.BitSet bsTemp
private java.util.BitSet selectedMolecules
private int selectedMoleculeCount
private org.jmol.modelset.AtomIteratorWithinModel withinModelIterator
private org.jmol.modelset.AtomIteratorWithinSet withinAtomSetIterator
protected java.util.BitSet bsAll
private static float defaultHbondMax
private static float hbondMin
boolean proteinStructureTainted
private org.jmol.api.SymmetryInterface symTemp
public void <init> ()
protected void merge (org.jmol.modelset.ModelSet)
protected void releaseModelSet ()
public java.lang.String getModelSetName ()
public org.jmol.modelset.Model[] getModels ()
public int getModelCount ()
public org.jmol.api.SymmetryInterface[] getCellInfos ()
public org.jmol.api.SymmetryInterface getUnitCell (int)
public java.lang.String getModelName (int)
public java.lang.String getModelTitle (int)
public java.lang.String getModelFileName (int)
public void setFrameTitle (int, java.lang.String)
public java.lang.String getFrameTitle (int)
public java.lang.String getModelNumberForAtomLabel (int)
protected void calculatePolymers (java.util.BitSet)
protected void addBioPolymerToModel (org.jmol.modelset.Polymer, org.jmol.modelset.Model)
public float[] getNotionalUnitcell ()
public boolean setCrystallographicDefaults ()
public javax.vecmath.Point3f getAverageAtomPoint ()
public javax.vecmath.Point3f getBoundBoxCenter (int)
public javax.vecmath.Vector3f getBoundBoxCornerVector ()
public javax.vecmath.Point3f[] getBboxVertices ()
public java.util.Hashtable getBoundBoxInfo ()
public java.util.BitSet getBoundBoxModels ()
public void setBoundBox (javax.vecmath.Point3f, javax.vecmath.Point3f, boolean)
public java.lang.String getBoundBoxCommand (boolean)
public boolean setRotationRadius (int, float)
public float calcRotationRadius (int, javax.vecmath.Point3f)
public void calcBoundBoxDimensions (java.util.BitSet)
public org.jmol.modelset.BoxInfo getBoxInfo (java.util.BitSet)
private int calcAtomsMinMax (java.util.BitSet, org.jmol.modelset.BoxInfo)
private void calcUnitCellMinMax ()
public float calcRotationRadius (java.util.BitSet)
public javax.vecmath.Point3f getAtomSetCenter (java.util.BitSet)
public void setAtomProperty (java.util.BitSet, int, int, float, java.lang.String, float[], java.lang.String[])
public org.jmol.modelset.ModelCollection$StateScript addStateScript (java.lang.String, java.util.BitSet, java.util.BitSet, java.util.BitSet, java.lang.String, boolean, boolean)
protected void defineStructure (int, java.lang.String, java.lang.String, int, int, char, int, char, char, int, char)
protected void calculateStructuresAllExcept (java.util.BitSet, boolean)
public void setProteinType (java.util.BitSet, byte)
private void freezeModels ()
public java.util.BitSet setConformation (int, java.util.BitSet)
public java.util.BitSet setConformation (int, int)
public java.util.Hashtable getHeteroList (int)
protected void setModelSetProperties (java.util.Properties)
protected void setModelSetAuxiliaryInfo (java.util.Hashtable)
public java.util.Properties getModelSetProperties ()
public java.util.Hashtable getModelSetAuxiliaryInfo ()
public java.lang.String getModelSetProperty (java.lang.String)
public java.lang.Object getModelSetAuxiliaryInfo (java.lang.String)
protected boolean getModelSetAuxiliaryInfoBoolean (java.lang.String)
protected int getTrajectoryCount ()
public int getTrajectoryIndex (int)
public boolean isTrajectory (int)
public boolean isTrajectory (int[])
public java.util.BitSet getModelBitSet (java.util.BitSet, boolean)
public java.util.BitSet getIterativeModels (boolean)
public void selectDisplayedTrajectories (java.util.BitSet)
public java.lang.String getModelNumberDotted (int)
public int getModelNumber (int)
public int getModelFileNumber (int)
public java.util.Properties getModelProperties (int)
public java.lang.String getModelProperty (int, java.lang.String)
public java.util.Hashtable getModelAuxiliaryInfo (int)
public void setModelAuxiliaryInfo (int, java.lang.Object, java.lang.Object)
public java.lang.Object getModelAuxiliaryInfo (int, java.lang.String)
protected boolean getModelAuxiliaryInfoBoolean (int, java.lang.String)
protected int getModelAuxiliaryInfoInt (int, java.lang.String)
protected org.jmol.modelset.Model getModel (int)
public int getInsertionCountInModel (int)
public java.lang.String getModelFileType (int)
public static int modelFileNumberFromFloat (float)
public int getAltLocCountInModel (int)
private void propagateSecondaryStructure ()
public int getChainCount (boolean)
public int getBioPolymerCount ()
public int getBioPolymerCountInModel (int)
public void getPolymerPointsAndVectors (java.util.BitSet, java.util.Vector)
public void recalculateLeadMidpointsAndWingVectors (int)
public javax.vecmath.Point3f[] getPolymerLeadMidPoints (int, int)
public int getChainCountInModel (int, boolean)
public int getGroupCount ()
public int getGroupCountInModel (int)
public void calcSelectedGroupsCount (java.util.BitSet)
public void calcSelectedMonomersCount (java.util.BitSet)
public void calcHydrogenBonds (java.util.BitSet, java.util.BitSet)
public void calculateStraightness ()
public java.lang.String getPdbAtomData (java.util.BitSet)
public java.lang.String getPdbData (int, java.lang.String, java.util.BitSet, boolean)
public boolean isJmolDataFrame (int)
private boolean isJmolDataFrame (org.jmol.modelset.Atom)
public void setJmolDataFrame (java.lang.String, int, int)
public int getJmolDataFrameIndex (int, java.lang.String)
protected void clearDataFrameReference (int)
public java.lang.String getJmolFrameType (int)
public int getJmolDataSourceFrame (int)
public void saveModelOrientation (int, org.jmol.viewer.StateManager$Orientation)
public org.jmol.viewer.StateManager$Orientation getModelOrientation (int)
private java.lang.String getFullPDBHeader (int)
public java.lang.String getPDBHeader (int)
public java.lang.String getFileHeader (int)
public java.util.Hashtable getModelInfo (java.util.BitSet)
public int getAltLocIndexInModel (int, char)
public int getInsertionCodeIndexInModel (int, char)
public java.lang.String getAltLocListInModel (int)
private java.lang.String getInsertionListInModel (int)
public int getModelSymmetryCount (int)
public int[] getModelCellRange (int)
public boolean modelHasVibrationVectors (int)
public java.util.BitSet getElementsPresentBitSet (int)
private java.lang.String getSymmetryInfoAsString (int)
public void toCartesian (int, javax.vecmath.Point3f)
public void toFractional (int, javax.vecmath.Point3f)
public void toUnitCell (int, javax.vecmath.Point3f, javax.vecmath.Point3f)
public boolean setUnitCellOffset (int, javax.vecmath.Point3f)
public boolean setUnitCellOffset (int, int)
public java.util.Vector getMoleculeInfo (java.util.BitSet)
public int getMoleculeIndex (int)
public void rotateAtoms (javax.vecmath.Matrix3f, javax.vecmath.Matrix3f, java.util.BitSet, boolean, javax.vecmath.Point3f, boolean)
public java.util.BitSet getMoleculeBitSet (java.util.BitSet)
public java.util.BitSet getMoleculeBitSet (int)
public void invertSelected (javax.vecmath.Point3f, javax.vecmath.Point4f, java.util.BitSet)
public javax.vecmath.Vector3f getModelDipole (int)
public javax.vecmath.Vector3f calculateMolecularDipole (int)
public int getMoleculeCountInModel (int)
public void calcSelectedMoleculesCount (java.util.BitSet)
private void getMolecules ()
public java.util.BitSet getBranchBitSet (int, int)
private void getCovalentlyConnectedBitSet (org.jmol.modelset.Atom, java.util.BitSet, java.util.BitSet)
public boolean hasCalculatedHBonds (java.util.BitSet)
public void clearCalculatedHydrogenBonds (int, java.util.BitSet)
protected void initializeBspf ()
protected void initializeBspt (int)
public org.jmol.modelset.AtomIndexIterator getWithinAtomSetIterator (int, float, java.util.BitSet, boolean, boolean)
public org.jmol.modelset.AtomIndexIterator getWithinModelIterator (org.jmol.modelset.Atom, float)
private org.jmol.modelset.AtomIndexIterator getWithinModelIterator (int, javax.vecmath.Point3f, float)
public int getBondCountInModel (int)
public void setAtomCoordRelative (javax.vecmath.Point3f, java.util.BitSet)
public void setAtomCoord (java.util.BitSet, int, java.lang.Object)
private void recalculatePositionDependentQuantities ()
public int getAtomCountInModel (int)
public java.util.BitSet getModelAtomBitSet (int, boolean)
public java.util.BitSet getAtomBits (int, java.lang.Object)
public java.util.BitSet getAtomsWithin (float, java.util.BitSet, boolean)
public java.util.BitSet getAtomsWithin (float, javax.vecmath.Point3f, java.util.BitSet, int)
public java.util.BitSet getSequenceBits (java.lang.String, java.util.BitSet)
protected int[] makeConnections (float, float, short, int, java.util.BitSet, java.util.BitSet, java.util.BitSet, boolean)
public int autoBond (java.util.BitSet, java.util.BitSet, java.util.BitSet, java.util.BitSet)
private int[] autoBond (short, java.util.BitSet, java.util.BitSet, java.util.BitSet, boolean, boolean)
private static boolean checkMinAttachedAngle (org.jmol.modelset.Atom, org.jmol.modelset.Atom, float, javax.vecmath.Vector3f, javax.vecmath.Vector3f)
private static boolean checkMinAttachedAngle (org.jmol.modelset.Atom, org.jmol.modelset.Bond[], org.jmol.modelset.Atom, float, javax.vecmath.Vector3f, javax.vecmath.Vector3f)
protected int autoHbond (java.util.BitSet, java.util.BitSet, java.util.BitSet, float, float)
void setStructureIds ()
public java.lang.String getProteinStructureState (java.util.BitSet, boolean, boolean, boolean)
public java.lang.String getModelInfoAsString ()
public java.lang.String getSymmetryInfoAsString ()
public java.util.BitSet getAtomsConnected (float, float, int, java.util.BitSet)
public java.lang.String getModelExtract (java.util.BitSet)
private void getAtomRecordMOL (java.lang.StringBuffer, int)
private void getBondRecordMOL (java.lang.StringBuffer, int, int[])
public java.lang.String getChimeInfo (int, java.util.BitSet)
public java.lang.String getModelFileInfo (java.util.BitSet)
public java.util.Hashtable getAuxiliaryInfo (java.util.BitSet)
public java.util.Vector getAllAtomInfo (java.util.BitSet)
public void getAtomIdentityInfo (int, java.util.Hashtable)
private java.util.Hashtable getAtomInfoLong (int)
public java.util.Vector getAllBondInfo (java.util.BitSet)
private java.util.Hashtable getBondInfo (int)
public java.util.Hashtable getAllChainInfo (java.util.BitSet)
private java.util.Vector getChainInfo (int, java.util.BitSet)
public java.util.Hashtable getAllPolymerInfo (java.util.BitSet)
public java.lang.String getUnitCellInfoText ()
public java.util.Hashtable getSpaceGroupInfo (java.lang.String)
private void getSymTemp ()
public java.lang.Object getSymmetryInfo (java.util.BitSet, java.lang.String, int, javax.vecmath.Point3f, java.lang.String, int)
protected void deleteModel (int, int, int, java.util.BitSet, java.util.BitSet)
public javax.vecmath.Point3f[] getFrameOffsets (java.util.BitSet)
public java.lang.String getMoInfo (int)
static void <clinit> ()
}
org/jmol/modelset/ModelLoader.class
<Unknown>
package org.jmol.modelset
public final org.jmol.modelset.ModelLoader extends org.jmol.modelset.ModelSet {
private org.jmol.modelset.ModelLoader mergeModelSet
private boolean merging
private String jmolData
private final int[] specialAtomIndexes
private String[] group3Lists
private int[][] group3Counts
private boolean someModelsHaveUnitcells
private boolean isTrajectory
private String fileHeader
private static final int ATOM_GROWTH_INCREMENT
private final java.util.Hashtable htAtomMap
private static final int defaultGroupCount
private org.jmol.modelset.Chain[] chainOf
private String[] group3Of
private int[] seqcodes
private int[] firstAtomIndexes
private int currentModelIndex
private org.jmol.modelset.Model currentModel
private char currentChainID
private org.jmol.modelset.Chain currentChain
private int currentGroupSequenceNumber
private char currentGroupInsertionCode
private String currentGroup3
org.jmol.modelset.Group nullGroup
private int baseModelIndex
private int baseModelCount
private int baseAtomIndex
private int baseTrajectoryCount
private boolean appendNew
private int adapterModelCount
private int adapterTrajectoryCount
private static java.util.Hashtable htAtom
public void <init> (org.jmol.viewer.Viewer, java.lang.String)
public void <init> (org.jmol.viewer.Viewer, java.lang.Object, org.jmol.modelset.ModelLoader, java.lang.String)
private void initializeInfo (java.lang.String, int, java.util.Properties, java.util.Hashtable)
private void initializeBuild (int)
private void initializeGroupBuild ()
private void createModelSet (org.jmol.api.JmolAdapter, java.lang.Object)
protected void releaseModelSet ()
private void mergeModelArrays ()
private void initializeAtomBondModelCounts ()
private void initializeMerge ()
private void iterateOverAllNewModels (org.jmol.api.JmolAdapter, java.lang.Object)
private boolean setModelNameNumberProperties (int, int, java.lang.String, int, java.util.Properties, java.util.Hashtable, boolean, java.lang.String)
private void finalizeModels (int)
private void iterateOverAllNewAtoms (org.jmol.api.JmolAdapter, java.lang.Object)
private void addAtom (int, java.util.BitSet, int, java.lang.Object, short, java.lang.String, int, int, float, java.lang.Object[], int, float, float, float, float, boolean, int, char, java.lang.String, int, char, float, float, float, char, java.lang.Object, float)
private static byte lookupSpecialAtomID (java.lang.String)
private void checkNewGroup (int, int, char, java.lang.String, int, char)
private org.jmol.modelset.Chain getOrAllocateChain (org.jmol.modelset.Model, char)
private void growAtomArrays (int)
private void iterateOverAllNewBonds (org.jmol.api.JmolAdapter, java.lang.Object)
private void bondAtoms (java.lang.Object, java.lang.Object, short)
private void iterateOverAllNewStructures (org.jmol.api.JmolAdapter, java.lang.Object)
protected void defineStructure (int, java.lang.String, java.lang.String, int, int, char, int, char, char, int, char)
private void initializeUnitCellAndSymmetry ()
private void initializeBonding ()
private void finalizeGroupBuild ()
private void distinguishAndPropagateGroup (int, org.jmol.modelset.Chain, java.lang.String, int, int, int)
private void addGroup (org.jmol.modelset.Chain, org.jmol.modelset.Group)
private void countGroup (int, java.lang.String, java.lang.String)
private void freeze ()
private void setAtomNamesAndNumbers ()
private void findElementsPresent ()
private void finalizeShapes ()
public void createAtomDataSet (int, java.lang.Object, java.util.BitSet)
static void <clinit> ()
}
org/jmol/modelset/ModelSet.class
<Unknown>
package org.jmol.modelset
public abstract org.jmol.modelset.ModelSet extends org.jmol.modelset.ModelCollection {
private boolean selectionHaloEnabled
private boolean echoShapeActive
protected String modelSetTypeName
protected org.jmol.shape.Shape[] shapes
protected final org.jmol.modelset.Atom[] closest
private org.jmol.api.SymmetryInterface pointGroup
private static final boolean useRasMolHbondsCalculation
public void <init> ()
protected void releaseModelSet ()
public void setSelectionHaloEnabled (boolean)
public boolean getSelectionHaloEnabled ()
public boolean getEchoStateActive ()
public void setEchoStateActive (boolean)
public java.lang.String getModelSetTypeName ()
private org.jmol.shape.Shape allocateShape (int)
public org.jmol.shape.Shape getShape (int)
public int getModelNumberIndex (int, boolean, boolean)
public java.lang.String getTrajectoryInfo ()
public java.util.BitSet getBitSetTrajectories ()
public void setTrajectory (java.util.BitSet)
public void setTrajectory (int)
public java.util.BitSet getAtomBits (int, java.lang.Object)
public java.lang.String getAtomLabel (int)
private java.util.BitSet getSpecModel (int)
public int findNearestAtomIndex (int, int)
public void setShapeSize (int, int, float, java.util.BitSet)
public org.jmol.shape.Shape loadShape (int)
public void setShapeProperty (int, java.lang.String, java.lang.Object, java.util.BitSet)
public void releaseShape (int)
public java.lang.Object getShapeProperty (int, java.lang.String, int)
public boolean getShapeProperty (int, java.lang.String, java.lang.Object[])
public int getShapeIdFromObjectName (java.lang.String)
public void setModelVisibility ()
public void fillAtomData (org.jmol.atomdata.AtomData, int)
public boolean frankClicked (int, int)
public boolean checkObjectHovered (int, int, java.util.BitSet)
public org.jmol.util.Point3fi checkObjectClicked (int, int, int, java.util.BitSet)
public void checkObjectDragged (int, int, int, int, int, java.util.BitSet, int)
public java.util.Hashtable getShapeInfo ()
public void calculateStructures (java.util.BitSet)
public java.lang.String calculatePointGroup (java.util.BitSet)
public java.util.Hashtable getPointGroupInfo (java.util.BitSet)
public java.lang.String getPointGroupAsString (java.util.BitSet, boolean, java.lang.String, int, float)
private java.lang.Object calculatePointGroupForFirstModel (java.util.BitSet, boolean, boolean, boolean, java.lang.String, int, float)
private java.util.BitSet modelsOf (java.util.BitSet, java.util.BitSet)
public int autoHbond (java.util.BitSet, java.util.BitSet, java.util.BitSet, float, float)
protected void assignAromaticBonds (boolean)
public int[] makeConnections (float, float, short, int, java.util.BitSet, java.util.BitSet, java.util.BitSet, boolean)
public void setPdbConectBonding (int, int, java.util.BitSet)
public void deleteAllBonds ()
public java.lang.String getDefinedState (java.lang.StringBuffer, boolean)
public java.lang.String getState (java.lang.StringBuffer, boolean)
public int getVanderwaalsMar (int)
private void includeAllRelatedFrames (java.util.BitSet)
public java.util.BitSet deleteModels (java.util.BitSet)
public void setLabel (java.lang.String, java.util.BitSet)
public void setAtomLabel (java.lang.String, int)
public java.lang.Object getFileData (int)
}
org/jmol/modelset/Molecule.class
<Unknown>
package org.jmol.modelset
org.jmol.modelset.Molecule extends java.lang.Object {
org.jmol.modelset.ModelSet modelSet
int moleculeIndex
int modelIndex
int indexInModel
int nAtoms
int nElements
int[] elementCounts
int[] altElementCounts
int elementNumberMax
int altElementMax
String mf
java.util.BitSet atomList
void <init> (org.jmol.modelset.ModelSet, int, java.util.BitSet, int, int)
void getElementAndAtomCount (java.util.BitSet)
java.lang.String getMolecularFormula ()
java.util.Hashtable getInfo ()
}
org/jmol/modelset/Polymer.class
<Unknown>
package org.jmol.modelset
public abstract org.jmol.modelset.Polymer extends java.lang.Object {
protected javax.vecmath.Point3f[] leadMidpoints
protected javax.vecmath.Point3f[] leadPoints
protected javax.vecmath.Point3f[] sheetPoints
protected javax.vecmath.Vector3f[] wingVectors
protected int[] leadAtomIndices
protected int type
protected static final int TYPE_OTHER
protected static final int TYPE_AMINO
protected static final int TYPE_NUCLEIC
protected static final int TYPE_CARBOHYDRATE
public int getType ()
protected void <init> ()
public int getPolymerPointsAndVectors (int, java.util.BitSet, java.util.Vector, boolean, float)
public void addSecondaryStructure (byte, java.lang.String, int, int, char, int, char, int)
public void freeze ()
public void calculateStructures ()
public void clearStructures ()
public java.lang.String getSequence ()
public java.util.Hashtable getPolymerInfo (java.util.BitSet)
public void setConformation (java.util.BitSet, int)
public void calcHydrogenBonds (org.jmol.modelset.Polymer, java.util.BitSet, java.util.BitSet)
public void calcSelectedMonomersCount (java.util.BitSet)
public void getPolymerSequenceAtoms (int, int, int, int, java.util.BitSet, java.util.BitSet)
public javax.vecmath.Point3f[] getLeadMidpoints ()
public void recalculateLeadMidpointsAndWingVectors ()
public void getPdbData (char, char, int, int, boolean, java.util.BitSet, java.lang.StringBuffer, java.lang.StringBuffer, java.util.BitSet, boolean, java.util.BitSet)
}
org/jmol/modelsetbio/AlphaMonomer.class
<Unknown>
package org.jmol.modelsetbio
public org.jmol.modelsetbio.AlphaMonomer extends org.jmol.modelsetbio.Monomer {
static final byte[] alphaOffsets
protected org.jmol.modelsetbio.ProteinStructure proteinStructure
protected javax.vecmath.Point3f nitrogenHydrogenPoint
static org.jmol.modelsetbio.Monomer validateAndAllocate (org.jmol.modelset.Chain, java.lang.String, int, int, int, int[], org.jmol.modelset.Atom[])
void <init> (org.jmol.modelset.Chain, java.lang.String, int, int, int, byte[])
boolean isAlphaMonomer ()
public org.jmol.modelsetbio.ProteinStructure getProteinStructure ()
public java.lang.Object getStructure ()
void setStructure (org.jmol.modelsetbio.ProteinStructure)
public void setProteinStructureId (int)
public byte getProteinStructureType ()
public int getStrucNo ()
public boolean isHelix ()
public boolean isSheet ()
public int setProteinStructureType (byte, int)
public final org.jmol.modelset.Atom getAtom (byte)
public final javax.vecmath.Point3f getAtomPoint (byte)
boolean isConnectedAfter (org.jmol.modelsetbio.Monomer)
org.jmol.modelset.Atom getQuaternionFrameCenter (char)
public java.lang.Object getHelixData (int, char, int)
public org.jmol.util.Quaternion getQuaternion (char)
static void <clinit> ()
}
org/jmol/modelsetbio/AlphaPolymer.class
<Unknown>
package org.jmol.modelsetbio
public org.jmol.modelsetbio.AlphaPolymer extends org.jmol.modelsetbio.BioPolymer {
static final byte CODE_NADA
static final byte CODE_RIGHT_HELIX
static final byte CODE_BETA_SHEET
static final byte CODE_LEFT_HELIX
static final byte CODE_LEFT_TURN
static final byte CODE_RIGHT_TURN
static final byte TAG_NADA
static final byte TAG_TURN
static final byte TAG_SHEET
static final byte TAG_HELIX
void <init> (org.jmol.modelsetbio.Monomer[])
public void addSecondaryStructure (byte, java.lang.String, int, int, char, int, char, int)
void addSecondaryStructure (byte, java.lang.String, int, int, int, int)
void calcHydrogenBonds ()
public void calculateStructures ()
float[] calculateAnglesInDegrees ()
byte[] calculateCodes (float[])
void checkBetaSheetAlphaHelixOverlap (byte[], float[])
byte[] calculateRunsFourOrMore (byte[])
void extendRuns (byte[])
void searchForTurns (byte[], float[], byte[])
void addStructuresFromTags (byte[])
public void getPdbData (char, char, int, int, boolean, java.util.BitSet, java.lang.StringBuffer, java.lang.StringBuffer, java.util.BitSet, boolean, java.util.BitSet)
}
org/jmol/modelsetbio/AminoMonomer.class
<Unknown>
package org.jmol.modelsetbio
public org.jmol.modelsetbio.AminoMonomer extends org.jmol.modelsetbio.AlphaMonomer {
private static final byte CA
private static final byte O
private static final byte N
private static final byte C
private static final byte OT
static final byte[] interestingAminoAtomIDs
boolean nhChecked
private final javax.vecmath.Point3f ptTemp
private static final float beta
static org.jmol.modelsetbio.Monomer validateAndAllocate (org.jmol.modelset.Chain, java.lang.String, int, int, int, int[], org.jmol.modelset.Atom[])
private static boolean isBondedCorrectly (int, int, int, byte[], org.jmol.modelset.Atom[])
private static boolean isBondedCorrectly (int, byte[], org.jmol.modelset.Atom[])
private void <init> (org.jmol.modelset.Chain, java.lang.String, int, int, int, byte[])
boolean isAminoMonomer ()
org.jmol.modelset.Atom getNitrogenAtom ()
javax.vecmath.Point3f getNitrogenAtomPoint ()
org.jmol.modelset.Atom getCarbonylCarbonAtom ()
javax.vecmath.Point3f getCarbonylCarbonAtomPoint ()
org.jmol.modelset.Atom getCarbonylOxygenAtom ()
javax.vecmath.Point3f getCarbonylOxygenAtomPoint ()
org.jmol.modelset.Atom getInitiatorAtom ()
org.jmol.modelset.Atom getTerminatorAtom ()
boolean hasOAtom ()
boolean isConnectedAfter (org.jmol.modelsetbio.Monomer)
void findNearestAtomIndex (int, int, org.jmol.modelset.Atom[], short, short)
public void resetHydrogenPoint ()
javax.vecmath.Point3f getNitrogenHydrogenPoint ()
public boolean getNHPoint (javax.vecmath.Point3f, javax.vecmath.Vector3f)
org.jmol.modelset.Atom getQuaternionFrameCenter (char)
public org.jmol.util.Quaternion getQuaternion (char)
public boolean isWithinStructure (byte)
public java.lang.String getStructureId ()
public java.lang.String getProteinStructureTag ()
static void <clinit> ()
}
org/jmol/modelsetbio/AminoPolymer.class
<Unknown>
package org.jmol.modelsetbio
public org.jmol.modelsetbio.AminoPolymer extends org.jmol.modelsetbio.AlphaPolymer {
private boolean hasOAtoms
private static final float maxHbondAlphaDistance
private static final float maxHbondAlphaDistance2
private static final float minimumHbondDistance2
private static final double QConst
void <init> (org.jmol.modelsetbio.Monomer[])
boolean hasWingPoints ()
public void calcHydrogenBonds (org.jmol.modelset.Polymer, java.util.BitSet, java.util.BitSet)
private void calcProteinMainchainHydrogenBonds (org.jmol.modelsetbio.AminoPolymer, java.util.BitSet, java.util.BitSet)
private void bondAminoHydrogen (org.jmol.modelsetbio.AminoMonomer, int, javax.vecmath.Point3f, java.util.BitSet, java.util.BitSet)
private int calcHbondEnergy (org.jmol.modelset.Atom, javax.vecmath.Point3f, javax.vecmath.Point3f, org.jmol.modelsetbio.AminoMonomer)
private void createResidueHydrogenBond (org.jmol.modelsetbio.AminoMonomer, int, int, java.util.BitSet, java.util.BitSet, float)
public void calculateStructures ()
private boolean checkWingAtoms ()
public void freeze ()
protected boolean calcPhiPsiAngles ()
private void calcPhiPsiAngles (org.jmol.modelsetbio.AminoMonomer, org.jmol.modelsetbio.AminoMonomer)
protected float calculateRamachandranHelixAngle (int, char)
private static boolean isHelix (float, float)
private static boolean isSheet (float, float)
private static boolean isTurn (float, float)
}
org/jmol/modelsetbio/BioPolymer.class
<Unknown>
package org.jmol.modelsetbio
public abstract org.jmol.modelsetbio.BioPolymer extends org.jmol.modelset.Polymer {
org.jmol.modelsetbio.Monomer[] monomers
int monomerCount
protected org.jmol.modelset.Model model
private float sheetSmoothing
private final javax.vecmath.Vector3f unitVectorX
private int selectedMonomerCount
java.util.BitSet bsSelectedMonomers
private static final String[] qColor
public org.jmol.modelsetbio.Monomer[] getMonomers ()
public int getMonomerCount ()
void <init> (org.jmol.modelsetbio.Monomer[])
static org.jmol.modelsetbio.BioPolymer allocateBioPolymer (org.jmol.modelset.Group[], int, boolean)
public void clearStructures ()
void removeProteinStructure (int, int)
public int[] getLeadAtomIndices ()
int getIndex (char, int)
final javax.vecmath.Point3f getLeadPoint (int)
final javax.vecmath.Point3f getInitiatorPoint ()
final javax.vecmath.Point3f getTerminatorPoint ()
void getLeadMidPoint (int, javax.vecmath.Point3f)
void getLeadPoint (int, javax.vecmath.Point3f)
boolean hasWingPoints ()
final javax.vecmath.Point3f getWingPoint (int)
final javax.vecmath.Point3f getPointPoint (int)
public void setConformation (java.util.BitSet, int)
public void recalculateLeadMidpointsAndWingVectors ()
public javax.vecmath.Point3f[] getLeadMidpoints ()
javax.vecmath.Point3f[] getLeadPoints ()
public javax.vecmath.Point3f[] getControlPoints (boolean, float, boolean)
private javax.vecmath.Point3f[] getSheetPoints (float)
public final javax.vecmath.Vector3f[] getWingVectors ()
private final void calcLeadMidpointsAndWingVectors (boolean)
public void findNearestAtomIndex (int, int, org.jmol.modelset.Atom[], short[], int)
int getSelectedMonomerCount ()
public void calcSelectedMonomersCount (java.util.BitSet)
boolean isMonomerSelected (int)
public int getPolymerPointsAndVectors (int, java.util.BitSet, java.util.Vector, boolean, float)
public java.lang.String getSequence ()
public java.util.Hashtable getPolymerInfo (java.util.BitSet)
public void getPolymerSequenceAtoms (int, int, int, int, java.util.BitSet, java.util.BitSet)
public org.jmol.modelsetbio.ProteinStructure getProteinStructure (int)
protected boolean calcPhiPsiAngles ()
public static final void getPdbData (org.jmol.modelsetbio.BioPolymer, char, char, int, int, boolean, java.util.BitSet, java.lang.StringBuffer, java.lang.StringBuffer, java.util.BitSet, boolean, java.util.BitSet)
private static void getData (int, int, org.jmol.modelsetbio.BioPolymer, char, char, int, java.util.BitSet, java.util.BitSet, java.util.BitSet, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, java.lang.StringBuffer, java.lang.StringBuffer)
protected float calculateRamachandranHelixAngle (int, char)
private static float get3DStraightness (java.lang.String, org.jmol.util.Quaternion, org.jmol.util.Quaternion)
private static float getQuaternionStraightness (java.lang.String, org.jmol.util.Quaternion, org.jmol.util.Quaternion)
private static float getStraightness (float)
static void <clinit> ()
}
org/jmol/modelsetbio/CarbohydrateMonomer.class
<Unknown>
package org.jmol.modelsetbio
public org.jmol.modelsetbio.CarbohydrateMonomer extends org.jmol.modelsetbio.Monomer {
static final byte[] alphaOffsets
static org.jmol.modelsetbio.Monomer validateAndAllocate (org.jmol.modelset.Chain, java.lang.String, int, int, int, int[], org.jmol.modelset.Atom[])
private void <init> (org.jmol.modelset.Chain, java.lang.String, int, int, int, byte[])
public boolean isCarbohydrate ()
boolean isConnectedAfter (org.jmol.modelsetbio.Monomer)
static void <clinit> ()
}
org/jmol/modelsetbio/CarbohydratePolymer.class
<Unknown>
package org.jmol.modelsetbio
public org.jmol.modelsetbio.CarbohydratePolymer extends org.jmol.modelsetbio.BioPolymer {
void <init> (org.jmol.modelsetbio.Monomer[])
}
org/jmol/modelsetbio/Helix.class
<Unknown>
package org.jmol.modelsetbio
public org.jmol.modelsetbio.Helix extends org.jmol.modelsetbio.ProteinStructure {
void <init> (org.jmol.modelsetbio.AlphaPolymer, int, int, int)
public void calcAxis ()
}
org/jmol/modelsetbio/Monomer.class
<Unknown>
package org.jmol.modelsetbio
public abstract org.jmol.modelsetbio.Monomer extends org.jmol.modelset.Group {
org.jmol.modelsetbio.BioPolymer bioPolymer
protected final byte[] offsets
protected int monomerIndex
protected void <init> (org.jmol.modelset.Chain, java.lang.String, int, int, int, byte[])
void setBioPolymer (org.jmol.modelsetbio.BioPolymer, int)
public int getSelectedMonomerCount ()
public int getSelectedMonomerIndex ()
public org.jmol.modelsetbio.BioPolymer getBioPolymer ()
public int getBioPolymerLength ()
public int getBioPolymerIndex ()
protected static byte[] scanForOffsets (int, int[], byte[])
public boolean isDna ()
public boolean isRna ()
public final boolean isProtein ()
public final boolean isNucleic ()
void setStructure (org.jmol.modelsetbio.ProteinStructure)
public org.jmol.modelsetbio.ProteinStructure getProteinStructure ()
public byte getProteinStructureType ()
public boolean isHelix ()
public boolean isSheet ()
public void setProteinStructureId (int)
protected final org.jmol.modelset.Atom getAtomFromOffsetIndex (int)
protected final org.jmol.modelset.Atom getSpecialAtom (byte[], byte)
protected final javax.vecmath.Point3f getSpecialAtomPoint (byte[], byte)
final int getLeadAtomIndex ()
public final org.jmol.modelset.Atom getLeadAtom ()
final javax.vecmath.Point3f getLeadAtomPoint ()
public final org.jmol.modelset.Atom getWingAtom ()
public final javax.vecmath.Point3f getWingAtomPoint ()
final javax.vecmath.Point3f getPointAtomPoint ()
org.jmol.modelset.Atom getInitiatorAtom ()
org.jmol.modelset.Atom getTerminatorAtom ()
abstract boolean isConnectedAfter (org.jmol.modelsetbio.Monomer)
void findNearestAtomIndex (int, int, org.jmol.modelset.Atom[], short, short)
public java.util.Hashtable getMyInfo ()
static java.lang.String getStructureTypeName (byte)
final void updateOffsetsForAlternativeLocations (java.util.BitSet, int)
final void getMonomerSequenceAtoms (java.util.BitSet, java.util.BitSet)
protected static final boolean checkOptional (byte[], byte, int, int)
org.jmol.modelset.Atom getQuaternionFrameCenter (char)
protected java.lang.Object getHelixData2 (int, char, int)
public void resetHydrogenPoint ()
public java.lang.String getUniqueID ()
}
org/jmol/modelsetbio/NucleicMonomer.class
<Unknown>
package org.jmol.modelsetbio
public org.jmol.modelsetbio.NucleicMonomer extends org.jmol.modelsetbio.PhosphorusMonomer {
static final byte C6
private static final byte O2Pr
private static final byte C5
private static final byte N1
private static final byte C2
private static final byte N3
private static final byte C4
private static final byte O2
private static final byte N7
private static final byte C8
private static final byte N9
private static final byte O4
private static final byte O6
private static final byte N4
private static final byte NP
private static final byte N6
private static final byte N2
private static final byte H5T
private static final byte O5Pr
private static final byte H3T
private static final byte O3Pr
private static final byte C3Pr
private static final byte O1P
private static final byte O2P
static final byte[] interestingNucleicAtomIDs
private boolean hasRnaO2Prime
private static final byte[] ring6OffsetIndexes
private static final byte[] ring5OffsetIndexes
public static org.jmol.modelsetbio.Monomer validateAndAllocate (org.jmol.modelset.Chain, java.lang.String, int, int, int, int[], org.jmol.modelset.Atom[])
void <init> (org.jmol.modelset.Chain, java.lang.String, int, int, int, byte[])
public boolean isNucleicMonomer ()
public boolean isDna ()
public boolean isRna ()
public boolean isPurine ()
public boolean isPyrimidine ()
public boolean isGuanine ()
public byte getProteinStructureType ()
org.jmol.modelset.Atom getN1 ()
org.jmol.modelset.Atom getN3 ()
org.jmol.modelset.Atom getN2 ()
org.jmol.modelset.Atom getO2 ()
org.jmol.modelset.Atom getO6 ()
org.jmol.modelset.Atom getN4 ()
org.jmol.modelset.Atom getN6 ()
org.jmol.modelset.Atom getO4 ()
org.jmol.modelset.Atom getTerminatorAtom ()
public void getBaseRing6Points (javax.vecmath.Point3f[])
public boolean maybeGetBaseRing5Points (javax.vecmath.Point3f[])
boolean isConnectedAfter (org.jmol.modelsetbio.Monomer)
public void findNearestAtomIndex (int, int, org.jmol.modelset.Atom[], short, short)
public void setModelClickability ()
org.jmol.modelset.Atom getQuaternionFrameCenter (char)
public java.lang.Object getHelixData (int, char, int)
public org.jmol.util.Quaternion getQuaternion (char)
static void <clinit> ()
}
org/jmol/modelsetbio/NucleicPolymer.class
<Unknown>
package org.jmol.modelsetbio
public org.jmol.modelsetbio.NucleicPolymer extends org.jmol.modelsetbio.BioPolymer {
private static final short HBOND_MASK
void <init> (org.jmol.modelsetbio.Monomer[])
org.jmol.modelset.Atom getNucleicPhosphorusAtom (int)
boolean hasWingPoints ()
public void calcHydrogenBonds (org.jmol.modelset.Polymer, java.util.BitSet, java.util.BitSet)
void lookForHbonds (org.jmol.modelsetbio.NucleicPolymer, java.util.BitSet, java.util.BitSet)
public void getPdbData (char, char, int, int, boolean, java.util.BitSet, java.lang.StringBuffer, java.lang.StringBuffer, java.util.BitSet, boolean, java.util.BitSet)
}
org/jmol/modelsetbio/PhosphorusMonomer.class
<Unknown>
package org.jmol.modelsetbio
public org.jmol.modelsetbio.PhosphorusMonomer extends org.jmol.modelsetbio.Monomer {
private static final byte[] phosphorusOffsets
private static float MAX_ADJACENT_PHOSPHORUS_DISTANCE
protected boolean isPurine
protected boolean isPyrimidine
static org.jmol.modelsetbio.Monomer validateAndAllocate (org.jmol.modelset.Chain, java.lang.String, int, int, int, int[], org.jmol.modelset.Atom[])
protected void <init> (org.jmol.modelset.Chain, java.lang.String, int, int, int, byte[])
boolean isPhosphorusMonomer ()
public boolean isDna ()
public boolean isRna ()
public boolean isPurine ()
public boolean isPyrimidine ()
public java.lang.Object getStructure ()
public byte getProteinStructureType ()
boolean isConnectedAfter (org.jmol.modelsetbio.Monomer)
static void <clinit> ()
}
org/jmol/modelsetbio/PhosphorusPolymer.class
<Unknown>
package org.jmol.modelsetbio
org.jmol.modelsetbio.PhosphorusPolymer extends org.jmol.modelsetbio.BioPolymer {
void <init> (org.jmol.modelsetbio.Monomer[])
}
org/jmol/modelsetbio/ProteinStructure.class
<Unknown>
package org.jmol.modelsetbio
public abstract org.jmol.modelsetbio.ProteinStructure extends java.lang.Object {
static int globalSerialID
org.jmol.modelsetbio.AlphaPolymer apolymer
byte type
int monomerIndexFirst
int monomerIndexLast
int monomerCount
javax.vecmath.Point3f axisA
javax.vecmath.Point3f axisB
javax.vecmath.Vector3f axisUnitVector
final javax.vecmath.Vector3f vectorProjection
javax.vecmath.Point3f[] segments
int uniqueID
public String structureID
public int serialID
public int strandCount
void <init> (org.jmol.modelsetbio.AlphaPolymer, byte, int, int, int)
void addMonomer (int)
int removeMonomer (int)
public void calcAxis ()
void calcSegments ()
boolean lowerNeighborIsHelixOrSheet ()
boolean upperNeighborIsHelixOrSheet ()
public int getMonomerCount ()
public boolean isWithin (int)
public int getMonomerIndex ()
public int getIndex (org.jmol.modelsetbio.Monomer)
public javax.vecmath.Point3f[] getSegments ()
public javax.vecmath.Point3f getAxisStartPoint ()
public javax.vecmath.Point3f getAxisEndPoint ()
javax.vecmath.Point3f getStructureMidPoint (int)
public void getInfo (java.util.Hashtable)
void resetAxes ()
static void <clinit> ()
}
org/jmol/modelsetbio/Resolver.class
<Unknown>
package org.jmol.modelsetbio
public final org.jmol.modelsetbio.Resolver extends java.lang.Object implements org.jmol.api.JmolBioResolver {
public void <init> ()
public org.jmol.modelset.Group distinguishAndPropagateGroup (org.jmol.modelset.Chain, java.lang.String, int, int, int, int, int[], byte[], org.jmol.modelset.Atom[])
public org.jmol.modelset.Polymer buildBioPolymer (org.jmol.modelset.Group, org.jmol.modelset.Group[], int, boolean)
public void clearBioPolymers (org.jmol.modelset.Group[], int, java.util.BitSet)
}
org/jmol/modelsetbio/Sheet.class
<Unknown>
package org.jmol.modelsetbio
public org.jmol.modelsetbio.Sheet extends org.jmol.modelsetbio.ProteinStructure {
org.jmol.modelsetbio.AlphaPolymer alphaPolymer
javax.vecmath.Vector3f widthUnitVector
javax.vecmath.Vector3f heightUnitVector
void <init> (org.jmol.modelsetbio.AlphaPolymer, int, int, int)
public void calcAxis ()
void calcSheetUnitVectors ()
public javax.vecmath.Vector3f getWidthUnitVector ()
public javax.vecmath.Vector3f getHeightUnitVector ()
}
org/jmol/modelsetbio/Turn.class
<Unknown>
package org.jmol.modelsetbio
org.jmol.modelsetbio.Turn extends org.jmol.modelsetbio.ProteinStructure {
void <init> (org.jmol.modelsetbio.AlphaPolymer, int, int, int)
}
org/jmol/popup/JmolPopup$CheckboxMenuItemListener.class
<Unknown>
package org.jmol.popup
org.jmol.popup.JmolPopup$CheckboxMenuItemListener extends java.lang.Object implements java.awt.event.ItemListener {
private final org.jmol.popup.JmolPopup this$0
void <init> (org.jmol.popup.JmolPopup)
public void itemStateChanged (java.awt.event.ItemEvent)
}
org/jmol/popup/JmolPopup$MenuItemListener.class
<Unknown>
package org.jmol.popup
org.jmol.popup.JmolPopup$MenuItemListener extends java.lang.Object implements java.awt.event.ActionListener {
private final org.jmol.popup.JmolPopup this$0
void <init> (org.jmol.popup.JmolPopup)
public void actionPerformed (java.awt.event.ActionEvent)
}
org/jmol/popup/JmolPopup.class
<Unknown>
package org.jmol.popup
public abstract org.jmol.popup.JmolPopup extends java.lang.Object {
private static final boolean forceAwt
private static final boolean dumpList
org.jmol.api.JmolViewer viewer
java.awt.Component display
org.jmol.popup.JmolPopup$MenuItemListener mil
org.jmol.popup.JmolPopup$CheckboxMenuItemListener cmil
boolean asPopup
java.util.Hashtable htMenus
java.util.Properties menuText
Object frankPopup
int aboutComputedMenuBaseCount
String nullModelSetName
String modelSetName
String modelSetFileName
String modelSetRoot
java.util.Hashtable modelSetInfo
java.util.Hashtable modelInfo
java.util.Vector PDBOnly
java.util.Vector UnitcellOnly
java.util.Vector FramesOnly
java.util.Vector VibrationOnly
java.util.Vector SymmetryOnly
java.util.Vector SignedOnly
java.util.Vector AppletOnly
java.util.Vector ChargesOnly
java.util.Vector TemperatureOnly
boolean isPDB
boolean isSymmetry
boolean isUnitCell
boolean isMultiFrame
boolean isMultiConfiguration
boolean isVibration
boolean isApplet
boolean isSigned
boolean isZapped
boolean haveCharges
boolean haveBFactors
String altlocs
int modelIndex
int modelCount
int atomCount
static final int MAX_ITEMS
static final int TITLE_MAX_WIDTH
static String menuStructure
static final int UPDATE_ALL
static final int UPDATE_CONFIG
static final int UPDATE_SHOW
int updateMode
String group3List
int[] group3Counts
String configurationSelected
java.util.Hashtable htCheckbox
String currentMenuItemId
int thisx
int thisy
Object[][] frankList
int nFrankList
String currentFrankId
void <init> (org.jmol.api.JmolViewer, boolean)
public static org.jmol.popup.JmolPopup newJmolPopup (org.jmol.api.JmolViewer, boolean, java.lang.String, boolean)
public abstract void installMainMenu (java.lang.Object)
void build (java.lang.Object)
public java.lang.String getMenu (java.lang.String)
abstract java.lang.String getMenuCurrent ()
protected static void addCurrentItem (java.lang.StringBuffer, char, int, java.lang.String, java.lang.String, java.lang.String, java.lang.String)
private java.lang.String getMenuText (java.lang.String)
public void updateComputedMenus ()
private void updateWriteMenu ()
private void getViewerData ()
private void updateForShow ()
boolean checkBoolean (java.util.Hashtable, java.lang.String)
void updateSelectMenu ()
void updateElementsComputedMenu (java.util.BitSet)
void updateHeteroComputedMenu (java.util.Hashtable)
void updateSurfMoComputedMenu (java.util.Hashtable)
void updatePDBComputedMenus ()
int updateGroup3List (java.lang.Object, java.lang.String)
int augmentGroup3List (java.lang.Object, java.lang.String, boolean)
void updateSYMMETRYComputedMenus ()
private void updateSYMMETRYShowComputedMenu ()
private void updateSYMMETRYSelectComputedMenu ()
void updateFRAMESbyModelComputedMenu ()
void updateConfigurationComputedMenu ()
void updateModelSetComputedMenu ()
void updateFileTypeDependentMenus ()
java.lang.String getModelLabel ()
private void updateAboutSubmenu ()
private void updateLanguageSubmenu ()
private long convertToMegabytes (long)
private void addMenuItems (java.lang.String, java.lang.String, java.lang.Object, org.jmol.popup.PopupResourceBundle, boolean, boolean)
void rememberCheckbox (java.lang.String, java.lang.Object)
void setCheckBoxValue (java.lang.String, boolean)
java.lang.String fixScript (java.lang.String, java.lang.String)
java.lang.Object addMenuItem (java.lang.Object, java.lang.String)
java.lang.Object addCheckboxMenuItem (java.lang.Object, java.lang.String, java.lang.String, java.lang.String)
public void show (int, int)
void setFrankMenu (java.lang.String)
void restorePopupMenu ()
abstract void resetFrankMenu ()
abstract java.lang.Object getParent (java.lang.Object)
abstract void insertMenuSubMenu (java.lang.Object, java.lang.Object, int)
abstract int getPosition (java.lang.Object)
abstract void showPopupMenu (int, int)
abstract void showFrankMenu (int, int)
abstract void setCheckBoxState (java.lang.Object, boolean)
abstract void addMenuSeparator (java.lang.Object)
abstract java.lang.Object addMenuItem (java.lang.Object, java.lang.String, java.lang.String, java.lang.String)
abstract void setLabel (java.lang.Object, java.lang.String)
abstract void updateMenuItem (java.lang.Object, java.lang.String, java.lang.String)
abstract java.lang.Object addCheckboxMenuItem (java.lang.Object, java.lang.String, java.lang.String, java.lang.String, boolean)
abstract void addMenuSubMenu (java.lang.Object, java.lang.Object)
abstract java.lang.Object newMenu (java.lang.String, java.lang.String)
abstract void enableMenu (java.lang.Object, boolean)
abstract void enableMenuItem (java.lang.Object, boolean)
abstract void renameMenu (java.lang.Object, java.lang.String)
abstract void removeAll (java.lang.Object)
abstract int getMenuItemCount (java.lang.Object)
abstract void removeMenuItem (java.lang.Object, int)
abstract java.lang.String getId (java.lang.Object)
abstract void setCheckBoxValue (java.lang.Object)
abstract void createFrankPopup ()
abstract int getMenuItemHeight ()
long maxMemoryForNewerJvm ()
int availableProcessorsForNewerJvm ()
}
org/jmol/popup/JmolPopupAwt.class
<Unknown>
package org.jmol.popup
public org.jmol.popup.JmolPopupAwt extends org.jmol.popup.JmolPopup {
java.awt.PopupMenu awtPopup
java.awt.Menu mainMenu
java.awt.Menu elementComputedMenu
static int MENUITEM_HEIGHT
public void <init> (org.jmol.api.JmolViewer, boolean)
void showPopupMenu (int, int)
public void installMainMenu (java.lang.Object)
java.lang.Object getParent (java.lang.Object)
int getMenuItemHeight ()
int getPosition (java.lang.Object)
void insertMenuSubMenu (java.lang.Object, java.lang.Object, int)
void createFrankPopup ()
void showFrankMenu (int, int)
void resetFrankMenu ()
void addToMenu (java.lang.Object, java.awt.MenuItem)
void addMenuSeparator (java.lang.Object)
java.lang.Object addMenuItem (java.lang.Object, java.lang.String, java.lang.String, java.lang.String)
void setLabel (java.lang.Object, java.lang.String)
java.lang.String getId (java.lang.Object)
void setCheckBoxValue (java.lang.Object)
void setCheckBoxState (java.lang.Object, boolean)
void updateMenuItem (java.lang.Object, java.lang.String, java.lang.String)
java.lang.Object addCheckboxMenuItem (java.lang.Object, java.lang.String, java.lang.String, java.lang.String, boolean)
java.lang.Object cloneMenu (java.lang.Object)
void addMenuSubMenu (java.lang.Object, java.lang.Object)
java.lang.Object newMenu (java.lang.String, java.lang.String)
void setAutoscrolls (java.lang.Object)
void renameMenu (java.lang.Object, java.lang.String)
java.lang.Object newComputedMenu (java.lang.String, java.lang.String)
int getMenuItemCount (java.lang.Object)
void removeMenuItem (java.lang.Object, int)
void removeAll (java.lang.Object)
void enableMenu (java.lang.Object, boolean)
void enableMenuItem (java.lang.Object, boolean)
java.lang.String getMenuCurrent ()
private void getMenuCurrent (java.lang.StringBuffer, int, java.awt.Menu, java.lang.String)
static void <clinit> ()
}
org/jmol/popup/JmolPopupSwing.class
<Unknown>
package org.jmol.popup
public org.jmol.popup.JmolPopupSwing extends org.jmol.popup.JmolPopup {
javax.swing.JPopupMenu swingPopup
javax.swing.JMenu elementComputedMenu
javax.swing.JMenu mainMenu
static int MENUITEM_HEIGHT
public void <init> (org.jmol.api.JmolViewer, boolean)
void showPopupMenu (int, int)
public void installMainMenu (java.lang.Object)
java.lang.Object getParent (java.lang.Object)
int getMenuItemHeight ()
int getPosition (java.lang.Object)
void insertMenuSubMenu (java.lang.Object, java.lang.Object, int)
void createFrankPopup ()
void showFrankMenu (int, int)
void resetFrankMenu ()
void addToMenu (java.lang.Object, javax.swing.JComponent)
void addMenuSeparator (java.lang.Object)
java.lang.Object addMenuItem (java.lang.Object, java.lang.String, java.lang.String, java.lang.String)
void setLabel (java.lang.Object, java.lang.String)
java.lang.String getId (java.lang.Object)
void setCheckBoxValue (java.lang.Object)
void setCheckBoxState (java.lang.Object, boolean)
void updateMenuItem (java.lang.Object, java.lang.String, java.lang.String)
java.lang.Object addCheckboxMenuItem (java.lang.Object, java.lang.String, java.lang.String, java.lang.String, boolean)
java.lang.Object cloneMenu (java.lang.Object)
void addMenuSubMenu (java.lang.Object, java.lang.Object)
java.lang.Object newMenu (java.lang.String, java.lang.String)
void setAutoscrolls (java.lang.Object)
void renameMenu (java.lang.Object, java.lang.String)
java.lang.Object newComputedMenu (java.lang.String, java.lang.String)
int getMenuItemCount (java.lang.Object)
void removeMenuItem (java.lang.Object, int)
void removeAll (java.lang.Object)
void enableMenu (java.lang.Object, boolean)
void enableMenuItem (java.lang.Object, boolean)
long maxMemoryForNewerJvm ()
int availableProcessorsForNewerJvm ()
java.lang.String getMenuCurrent ()
private void getMenuCurrent (java.lang.StringBuffer, int, java.lang.Object, java.lang.String)
static void <clinit> ()
}
org/jmol/popup/PopupResourceBundle.class
<Unknown>
package org.jmol.popup
org.jmol.popup.PopupResourceBundle extends java.lang.Object {
private java.util.Properties structure
private java.util.Properties words
private static String[][] menuContents
private static String[][] structureContents
void <init> (java.lang.String, java.util.Properties)
java.lang.String getMenu (java.lang.String)
java.lang.String getStructure (java.lang.String)
void addStructure (java.lang.String, java.lang.String)
java.lang.String getWord (java.lang.String)
private static java.lang.String Box (java.lang.String)
private java.lang.String[] getWordContents ()
private void buildStructure (java.lang.String)
private java.lang.String dumpWords ()
private java.lang.String dumpStructure (java.lang.String[][])
public void setStructure (java.lang.String)
private void addItems (java.lang.String[][])
private void localize (boolean, java.util.Properties)
static void <clinit> ()
}
org/jmol/quantum/MOCalculation.class
<Unknown>
package org.jmol.quantum
public org.jmol.quantum.MOCalculation extends org.jmol.quantum.QuantumCalculation implements org.jmol.api.MOCalculationInterface {
private static int MAX_GRID
final float[] CX
final float[] CY
final float[] CZ
final float[] DXY
final float[] DXZ
final float[] DYZ
final float[] EX
final float[] EY
final float[] EZ
private String calculationType
private java.util.Vector shells
private float[][] gaussians
private int[][] slaterInfo
private float[][] slaterData
private float[] moCoefficients
private int moCoeff
private int gaussianPtr
private int firstAtomOffset
private boolean isElectronDensity
private float occupancy
protected float[][][] voxelDataTemp
boolean as5D
private static final float ROOT3
public void <init> ()
public void calculate (org.jmol.api.VolumeDataInterface, java.util.BitSet, java.lang.String, javax.vecmath.Point3f[], int, java.util.Vector, float[][], java.util.Hashtable, int[][], float[][], float[], float[])
public void calculateElectronDensity (float[])
private void createSlaterCube ()
private void createGaussianCube ()
private void check5D ()
private boolean checkCalculationType ()
private void processShell (int)
private void addData (int, int)
private void setTemp ()
private void addDataS (int)
private void addDataP (int)
private void addDataSP (int)
private void setCE (float[], float[], float, float, float, float, float)
private void setE (float[], float)
private void calcSP (float, float, float, float, float)
private void addData6D (int)
private void addData5D (int)
private void addData10F (int)
private void addData7F (int)
private void processSlater (int)
private void dumpInfo (int, java.lang.String)
private void dumpInfo (int, int)
static void <clinit> ()
}
org/jmol/quantum/MepCalculation.class
<Unknown>
package org.jmol.quantum
public org.jmol.quantum.MepCalculation extends org.jmol.quantum.QuantumCalculation implements org.jmol.api.MepCalculationInterface {
public void <init> ()
public void calculate (org.jmol.api.VolumeDataInterface, java.util.BitSet, javax.vecmath.Point3f[], float[])
private void processMep (float[])
}
org/jmol/quantum/QuantumCalculation$QMAtom.class
<Unknown>
package org.jmol.quantum
org.jmol.quantum.QuantumCalculation$QMAtom extends javax.vecmath.Point3f {
private float[] myX
private float[] myY
private float[] myZ
private float[] myX2
private float[] myY2
private float[] myZ2
private final org.jmol.quantum.QuantumCalculation this$0
void <init> (org.jmol.quantum.QuantumCalculation, javax.vecmath.Point3f, float[], float[], float[], float[], float[], float[])
protected void setXYZ (boolean)
}
org/jmol/quantum/QuantumCalculation.class
<Unknown>
package org.jmol.quantum
abstract org.jmol.quantum.QuantumCalculation extends java.lang.Object {
protected boolean doDebug
protected static final float bohr_per_angstrom
protected float[][][] voxelData
protected int xMin
protected int xMax
protected int yMin
protected int yMax
protected int zMin
protected int zMax
protected org.jmol.quantum.QuantumCalculation$QMAtom[] qmAtoms
protected int atomIndex
protected org.jmol.quantum.QuantumCalculation$QMAtom thisAtom
protected float[] xBohr
protected float[] yBohr
protected float[] zBohr
protected float[] originBohr
protected float[] stepBohr
protected int nX
protected int nY
protected int nZ
protected float[] X
protected float[] Y
protected float[] Z
protected float[] X2
protected float[] Y2
protected float[] Z2
protected float rangeBohr
void <init> ()
protected void initialize (int, int, int)
protected void setupCoordinates (float[], float[], java.util.BitSet, javax.vecmath.Point3f[])
private void setXYZBohr (float[], int, int)
}
org/jmol/shape/AtomShape.class
<Unknown>
package org.jmol.shape
public abstract org.jmol.shape.AtomShape extends org.jmol.shape.Shape {
public short[] mads
public short[] colixes
public byte[] paletteIDs
protected java.util.BitSet bsSizeSet
protected java.util.BitSet bsColixSet
public int atomCount
public org.jmol.modelset.Atom[] atoms
public boolean isActive
public void <init> ()
protected void initModelSet ()
public void setSize (int, java.util.BitSet)
public void setSize (int, float, java.util.BitSet)
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
protected void setColixAndPalette (short, byte, int)
public void setModelClickability ()
public java.lang.String getShapeState ()
}
org/jmol/shape/Axes.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.Axes extends org.jmol.shape.FontLineShape {
javax.vecmath.Point3f axisXY
float scale
final javax.vecmath.Point3f originPoint
final javax.vecmath.Point3f[] axisPoints
static final javax.vecmath.Point3f pt0
final javax.vecmath.Point3f ptTemp
private static final float MIN_AXIS_LEN
javax.vecmath.Vector3f corner
public void <init> ()
javax.vecmath.Point3f getOriginPoint (boolean)
javax.vecmath.Point3f getAxisPoint (int, boolean)
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
public void initShape ()
public java.lang.Object getProperty (java.lang.String, int)
void setScale (float)
public java.lang.String getShapeState ()
static void <clinit> ()
}
org/jmol/shape/AxesRenderer.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.AxesRenderer extends org.jmol.shape.FontLineShapeRenderer {
private static final String[] axisLabels
private final javax.vecmath.Point3f[] axisScreens
private final javax.vecmath.Point3f originScreen
private short[] colixes
public void <init> ()
protected void render ()
private void renderLabel (java.lang.String, org.jmol.g3d.Font3D, float, float, float, float, float)
static void <clinit> ()
}
org/jmol/shape/Balls.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.Balls extends org.jmol.shape.AtomShape {
public void <init> ()
public void setSize (int, float, java.util.BitSet)
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
public void setModelClickability ()
public void setVisibilityFlags (java.util.BitSet)
public java.lang.String getShapeState ()
}
org/jmol/shape/BallsRenderer.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.BallsRenderer extends org.jmol.shape.ShapeRenderer {
private int minX
private int minY
private int minZ
private int maxX
private int maxY
private int maxZ
public void <init> ()
protected void render ()
protected void renderBall (org.jmol.modelset.Atom)
}
org/jmol/shape/Bbcage.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.Bbcage extends org.jmol.shape.FontLineShape {
static final byte[] edges
boolean isVisible
int mad
public void <init> ()
public void initShape ()
public void setVisibilityFlags (java.util.BitSet)
static void <clinit> ()
}
org/jmol/shape/BbcageRenderer.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.BbcageRenderer extends org.jmol.shape.FontLineShapeRenderer {
final javax.vecmath.Point3f[] screens
public void <init> ()
protected void render ()
}
org/jmol/shape/Dots.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.Dots extends org.jmol.shape.AtomShape {
public org.jmol.geodesic.EnvelopeCalculation ec
public boolean isSurface
static final float SURFACE_DISTANCE_FOR_CALCULATION
java.util.BitSet bsOn
private java.util.BitSet bsSelected
private java.util.BitSet bsIgnore
static int MAX_LEVEL
int thisAtom
float thisRadius
int thisArgb
int lastSize
float lastSolventRadius
public void <init> ()
public void initShape ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
void initialize ()
public void setSize (int, float, java.util.BitSet)
public void setModelClickability ()
public java.lang.String getShapeState ()
static void <clinit> ()
}
org/jmol/shape/DotsRenderer.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.DotsRenderer extends org.jmol.shape.ShapeRenderer {
public boolean iShowSolid
javax.vecmath.Vector3f[] verticesTransformed
public int screenLevel
public int screenDotCount
public int[] screenCoordinates
public int[] faceMap
public void <init> ()
protected void initRenderer ()
protected void render ()
protected void render1 (org.jmol.shape.Dots)
private int calcScreenPoints (int[], float, int, int, int)
protected void renderConvex (short, int[], int)
protected void renderDots (int)
}
org/jmol/shape/Echo.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.Echo extends org.jmol.shape.TextShape {
private static final String FONTFACE
private static final int FONTSIZE
private static final short COLOR
public void <init> ()
public void initShape ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
public java.lang.Object getProperty (java.lang.String, int)
public java.lang.String getShapeState ()
}
org/jmol/shape/EchoRenderer.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.EchoRenderer extends org.jmol.shape.ShapeRenderer {
float imageFontScaling
org.jmol.modelset.Atom ptAtom
javax.vecmath.Point3i pt
public void <init> ()
protected void render ()
private void renderFrameTitle (java.lang.String)
}
org/jmol/shape/FontLineShape.class
<Unknown>
package org.jmol.shape
public abstract org.jmol.shape.FontLineShape extends org.jmol.shape.Shape {
org.jmol.g3d.Font3D font3d
String myType
public void <init> ()
public void initShape ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
public java.lang.String getShapeState ()
}
org/jmol/shape/FontLineShapeRenderer.class
<Unknown>
package org.jmol.shape
abstract org.jmol.shape.FontLineShapeRenderer extends org.jmol.shape.ShapeRenderer {
float imageFontScaling
javax.vecmath.Point3i pt0
javax.vecmath.Point3i pt1
void <init> ()
protected void render (int, javax.vecmath.Point3f[], javax.vecmath.Point3f[], javax.vecmath.Point3f[], int)
}
org/jmol/shape/Frank.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.Frank extends org.jmol.shape.FontLineShape {
static final String defaultFontName
static final String defaultFontStyle
static final int defaultFontSize
static final int frankMargin
String frankString
org.jmol.g3d.Font3D currentMetricsFont3d
org.jmol.g3d.Font3D baseFont3d
int frankWidth
int frankAscent
int frankDescent
public void <init> ()
public void initShape ()
public boolean wasClicked (int, int)
void calcMetrics ()
void getFont (float)
}
org/jmol/shape/FrankRenderer.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.FrankRenderer extends org.jmol.shape.FontLineShapeRenderer {
public void <init> ()
protected void render ()
}
org/jmol/shape/Halos.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.Halos extends org.jmol.shape.AtomShape {
short colixSelection
public void <init> ()
void initState ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
public void setVisibilityFlags (java.util.BitSet)
public java.lang.String getShapeState ()
}
org/jmol/shape/HalosRenderer.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.HalosRenderer extends org.jmol.shape.ShapeRenderer {
boolean isAntialiased
public void <init> ()
protected void render ()
void render1 (org.jmol.modelset.Atom, short, short)
}
org/jmol/shape/Hover.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.Hover extends org.jmol.shape.TextShape {
private static final String FONTFACE
private static final String FONTSTYLE
private static final int FONTSIZE
org.jmol.shape.Text hoverText
int atomIndex
javax.vecmath.Point3i xy
String text
String labelFormat
String[] atomFormats
String specialLabel
public void <init> ()
public void initShape ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
public java.lang.String getShapeState ()
}
org/jmol/shape/HoverRenderer.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.HoverRenderer extends org.jmol.shape.ShapeRenderer {
public void <init> ()
protected void render ()
java.lang.String fixLabel (org.jmol.modelset.Atom, java.lang.String)
}
org/jmol/shape/Labels.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.Labels extends org.jmol.shape.AtomShape {
String[] strings
String[] formats
short[] bgcolixes
byte[] fids
int[] offsets
private java.util.Hashtable atomLabels
private org.jmol.shape.Text text
private java.util.BitSet bsFontSet
private java.util.BitSet bsBgColixSet
private int defaultOffset
private int defaultAlignment
private int defaultZPos
private byte defaultFontId
private short defaultColix
private short defaultBgcolix
private byte defaultPaletteID
private int defaultPointer
private static int zeroOffset
byte zeroFontId
private boolean defaultsOnlyForNone
private boolean setDefaults
static final int POINTER_FLAGS
static final int ALIGN_FLAGS
static final int ZPOS_FLAGS
static final int GROUP_FLAG
static final int FRONT_FLAG
static final int SCALE_FLAG
static final int EXACT_OFFSET_FLAG
static final int FLAGS
static final int FLAG_OFFSET
int pickedAtom
int pickedOffset
public void <init> ()
public void initShape ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
private void setLabel (java.lang.String, java.util.BitSet)
private void setLabel (java.lang.String, int)
private void setLabel (java.lang.String, int, boolean, float)
public java.lang.Object getProperty (java.lang.String, int)
void putLabel (int, org.jmol.shape.Text)
org.jmol.shape.Text getLabel (int)
private void setColix (int, short, byte)
private void setBgcolix (int, short)
private void setOffsets (int, int, boolean)
private void setAlignment (int, int)
static int getAlignment (int)
private void setPointer (int, int)
private void setFront (int, boolean)
private void setGroup (int, boolean)
private void setFont (int, byte)
public void setModelClickability ()
private java.lang.String getDefaultState ()
public java.lang.String getShapeState ()
public synchronized boolean checkObjectDragged (int, int, int, int, int, java.util.BitSet)
private void move2D (int, int, int)
static void <clinit> ()
}
org/jmol/shape/LabelsRenderer.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.LabelsRenderer extends org.jmol.shape.ShapeRenderer {
byte fidPrevious
protected org.jmol.g3d.Font3D font3d
protected int ascent
protected int descent
private final float[] boxXY
public void <init> ()
protected void render ()
private int getMinZ (org.jmol.modelset.Atom[], org.jmol.modelset.Group)
}
org/jmol/shape/Measures.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.Measures extends org.jmol.shape.Shape {
private static final int measurementGrowthIncrement
private java.util.BitSet bsColixSet
private java.util.BitSet bsSelected
private String strFormat
private boolean isAllConnected
private float[] rangeMinMax
private org.jmol.modelset.Atom[] atoms
private int atomCount
int measurementCount
org.jmol.modelset.Measurement[] measurements
org.jmol.modelset.MeasurementPending measurementPending
short mad
short colix
org.jmol.g3d.Font3D font3d
public void <init> ()
protected void initModelSet ()
public void initShape ()
public void setSize (int, java.util.BitSet)
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
private org.jmol.modelset.Measurement setSingleItem (java.util.Vector)
public java.lang.Object getProperty (java.lang.String, int)
private void clear ()
private int findMeasurement (int[], org.jmol.util.Point3fi[])
private int findMeasurement (org.jmol.modelset.Measurement)
private void showHide (org.jmol.modelset.Measurement, boolean)
private void showHide (boolean)
private void toggle (org.jmol.modelset.Measurement)
private void toggleOn (int[])
private void delete (java.lang.Object)
private void define (java.util.Vector, boolean, boolean, boolean)
private void setIndices ()
private void define (org.jmol.modelset.Measurement, boolean, boolean, boolean)
private void define (org.jmol.modelset.Measurement, boolean, boolean)
private void deleteMeasurement (int)
private void nextMeasure (int, int, java.util.Vector, org.jmol.modelset.Measurement, int, boolean, boolean, boolean)
private boolean isConnected (org.jmol.modelset.Measurement, int)
private void setRange (float[])
private void setConnected (boolean)
private void pending (org.jmol.modelset.MeasurementPending)
private void reformatDistances ()
private void setFormats (java.lang.String)
private java.util.Vector getAllInfo ()
private java.lang.String getAllInfoAsString ()
private java.util.Hashtable getInfo (int)
private java.lang.String getInfoAsString (int)
void setVisibilityInfo ()
public java.lang.String getShapeState ()
private java.lang.String getState (int)
}
org/jmol/shape/MeasuresRenderer.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.MeasuresRenderer extends org.jmol.shape.FontLineShapeRenderer {
private short measurementMad
private org.jmol.g3d.Font3D font3d
private org.jmol.modelset.Measurement measurement
private boolean doJustify
org.jmol.util.Point3fi atomA
org.jmol.util.Point3fi atomB
org.jmol.util.Point3fi atomC
org.jmol.util.Point3fi atomD
private javax.vecmath.Point3i ptA
private javax.vecmath.Point3i ptB
private javax.vecmath.AxisAngle4f aaT
private javax.vecmath.Matrix3f matrixT
private javax.vecmath.Point3f pointT
public void <init> ()
protected void render ()
private org.jmol.util.Point3fi getAtom (int)
private void renderMeasurement (int, org.jmol.modelset.Measurement, boolean)
private int drawSegment (int, int, int, int, int, int)
void renderDistance (boolean)
private void renderAngle (boolean)
private void renderTorsion (boolean)
private void paintMeasurementString (int, int, int, int, boolean, int)
private void renderPendingMeasurement (org.jmol.modelset.MeasurementPending)
private void renderPendingWithCursor (int, org.jmol.modelset.MeasurementPending)
}
org/jmol/shape/Mesh.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.Mesh extends java.lang.Object {
public static final String PREVIOUS_MESH_ID
private org.jmol.api.JmolRendererInterface g3d
public String[] title
public javax.vecmath.Point3f[] vertices
public short[] normixes
public int[][] polygonIndexes
public java.util.BitSet[] bitsets
public String thisID
public boolean isValid
public String scriptCommand
public String colorCommand
public boolean visible
public short colix
public int vertexCount
public int polygonCount
public float scale
public boolean haveXyPoints
public int diameter
public float width
public javax.vecmath.Point3f ptCenter
public String meshType
public org.jmol.shape.Mesh linkedMesh
public int index
public int atomIndex
public int modelIndex
public int visibilityFlags
public boolean insideOut
public boolean showContourLines
public boolean showPoints
public boolean drawTriangles
public boolean fillTriangles
public boolean showTriangles
public boolean frontOnly
public boolean isTwoSided
public boolean isColorSolid
public boolean havePlanarContours
public static final int SEED_COUNT
public int lighting
public final javax.vecmath.Vector3f vAB
public final javax.vecmath.Vector3f vAC
public final javax.vecmath.Vector3f vTemp
protected boolean haveCheckByte
public java.util.Vector data1
public java.util.Vector data2
public void setVisibilityFlags (int)
public void <init> (java.lang.String, org.jmol.api.JmolRendererInterface, short, int)
public void clear (java.lang.String)
public void initialize (int)
public javax.vecmath.Vector3f[] getVertexNormals ()
public void initializeNormixes (int, javax.vecmath.Vector3f[])
public void setLighting (int)
private void flipLighting (int)
private void invertNormixes ()
public void setTranslucent (boolean, float)
public void sumVertexNormals (javax.vecmath.Vector3f[])
public void setPolygonCount (int)
public int addVertexCopy (javax.vecmath.Point3f)
public void addTriangle (int, int, int)
public void addQuad (int, int, int, int)
public void setColix (short)
public java.lang.String getState (java.lang.String)
}
org/jmol/shape/MeshCollection.class
<Unknown>
package org.jmol.shape
public abstract org.jmol.shape.MeshCollection extends org.jmol.shape.Shape {
public int meshCount
public org.jmol.shape.Mesh[] meshes
public org.jmol.shape.Mesh currentMesh
public int modelCount
public boolean isFixed
public String script
public int nUnnamed
public short colix
public String myType
public boolean explicitID
protected String previousMeshID
protected org.jmol.shape.Mesh linkedMesh
protected boolean iHaveModelIndex
protected int modelIndex
protected boolean allowContourLines
protected boolean haveContours
public String[] title
protected boolean allowMesh
protected java.util.Hashtable htObjects
public void <init> ()
private org.jmol.shape.Mesh setMesh (java.lang.String)
public void allocMesh (java.lang.String)
public void initShape ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
protected void checkExplicit (java.lang.String)
private void setProperty (int, boolean)
public java.lang.Object getProperty (java.lang.String, int)
private java.lang.Object getVertices (org.jmol.shape.Mesh)
private void deleteMesh ()
protected void deleteMesh (java.lang.String)
public void deleteMesh (int)
public org.jmol.shape.Mesh getMesh (java.lang.String)
public int getIndexFromName (java.lang.String)
public void setModelIndex (int, int)
public java.lang.String getShapeState ()
private void getMeshCommand (java.lang.StringBuffer, int)
private java.lang.String encapsulateData (java.lang.String, java.util.Vector, java.lang.String)
protected void getColorState (java.lang.StringBuffer, org.jmol.shape.Mesh)
public void setVisibilityFlags (java.util.BitSet)
protected void getModelIndex (java.lang.String)
}
org/jmol/shape/MeshRenderer.class
<Unknown>
package org.jmol.shape
public abstract org.jmol.shape.MeshRenderer extends org.jmol.shape.ShapeRenderer {
protected float imageFontScaling
protected float scalePixelsPerMicron
protected javax.vecmath.Point3f[] vertices
protected short[] normixes
protected javax.vecmath.Point3i[] screens
protected javax.vecmath.Vector3f[] transformedVectors
protected int vertexCount
protected boolean frontOnly
protected boolean antialias
protected org.jmol.shape.Mesh mesh
protected int diameter
protected float width
protected boolean isTranslucent
protected final javax.vecmath.Point3f pt1f
protected final javax.vecmath.Point3f pt2f
protected final javax.vecmath.Point3i pt1i
protected final javax.vecmath.Point3i pt2i
protected final javax.vecmath.Point3i pt3i
protected java.util.BitSet bsFaces
public void <init> ()
protected void render ()
public boolean render1 (org.jmol.shape.Mesh)
private boolean setVariables ()
protected void transform ()
protected boolean isPolygonDisplayable (int)
protected void render2 (boolean)
protected void renderPoints ()
protected void renderTriangles (boolean, boolean, boolean)
protected void drawLine (int, int, boolean)
protected void renderExport ()
}
org/jmol/shape/Object2d.class
<Unknown>
package org.jmol.shape
public abstract org.jmol.shape.Object2d extends java.lang.Object {
public static final int POINTER_NONE
public static final int POINTER_ON
public static final int POINTER_BACKGROUND
protected static final String[] hAlignNames
protected static final int ALIGN_NONE
public static final int ALIGN_LEFT
protected static final int ALIGN_CENTER
protected static final int ALIGN_RIGHT
protected static final String[] vAlignNames
public static final int VALIGN_XY
protected static final int VALIGN_TOP
protected static final int VALIGN_BOTTOM
protected static final int VALIGN_MIDDLE
public static final int VALIGN_XYZ
protected boolean isLabelOrHover
protected org.jmol.viewer.Viewer viewer
protected org.jmol.api.JmolRendererInterface g3d
public javax.vecmath.Point3f xyz
String target
protected String script
protected short colix
protected short bgcolix
protected int pointer
protected int align
public int valign
protected int movableX
protected int movableY
protected int movableZ
protected int movableXPercent
protected int movableYPercent
protected int movableZPercent
protected int offsetX
protected int offsetY
protected int z
protected int zSlab
protected int windowWidth
protected int windowHeight
protected boolean adjustForWindow
protected float boxWidth
protected float boxHeight
protected float boxX
protected float boxY
int modelIndex
boolean visible
boolean hidden
protected final float[] boxXY
protected float scalePixelsPerMicron
float getScalePixelsPerMicron ()
public void setScalePixelsPerMicron (float)
protected abstract void recalc ()
protected void <init> ()
protected void <init> (org.jmol.viewer.Viewer, org.jmol.g3d.Graphics3D, java.lang.String, short, int, int, float)
void setModel (int)
public void setVisibility (boolean)
public void setXYZ (javax.vecmath.Point3f)
public void setAdjustForWindow (boolean)
void setColix (short)
void setColix (java.lang.Object)
void setTranslucent (float, boolean)
void setBgColix (short)
void setBgColix (java.lang.Object)
public void setMovableX (int)
public void setMovableY (int)
public void setMovableZ (int)
public void setMovableXPercent (int)
public void setMovableYPercent (int)
public void setMovableZPercent (int)
void setXY (int, int)
void setZs (int, int)
public void setXYZs (int, int, int, int)
public void setScript (java.lang.String)
public java.lang.String getScript ()
void setOffset (int)
static int getXOffset (int)
static int getYOffset (int)
boolean setAlignment (java.lang.String)
static java.lang.String getAlignment (int)
boolean setAlignment (int)
void setPointer (int)
static java.lang.String getPointer (int)
protected void drawPointer (org.jmol.api.JmolRendererInterface)
protected void setBoxOffsetsInWindow (float, float, float)
protected void setWindow (org.jmol.api.JmolRendererInterface, float)
public boolean checkObjectClicked (int, int, java.util.BitSet)
public static boolean setProperty (java.lang.String, java.lang.Object, org.jmol.shape.Object2d)
public static int getOffset (int, int)
static void <clinit> ()
}
org/jmol/shape/Object2dShape.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.Object2dShape extends org.jmol.shape.Shape {
java.util.Hashtable objects
org.jmol.shape.Object2d currentObject
org.jmol.g3d.Font3D currentFont
Object currentColor
Object currentBgColor
float currentTranslucentLevel
float currentBgTranslucentLevel
protected String thisID
boolean isHover
boolean isAll
public void <init> ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
protected void initModelSet ()
public void setVisibilityFlags (java.util.BitSet)
public org.jmol.util.Point3fi checkObjectClicked (int, int, int, java.util.BitSet)
public boolean checkObjectHovered (int, int, java.util.BitSet)
}
org/jmol/shape/Shape.class
<Unknown>
package org.jmol.shape
public abstract org.jmol.shape.Shape extends java.lang.Object {
public org.jmol.viewer.Viewer viewer
public org.jmol.modelset.ModelSet modelSet
public org.jmol.g3d.Graphics3D g3d
public int shapeID
public int myVisibilityFlag
protected float translucentLevel
protected boolean translucentAllowed
public boolean isBioShape
public void <init> ()
public org.jmol.viewer.Viewer getViewer ()
public final void initializeShape (org.jmol.viewer.Viewer, org.jmol.g3d.Graphics3D, org.jmol.modelset.ModelSet, int)
public void setModelSet (org.jmol.modelset.ModelSet)
protected void initModelSet ()
public void initShape ()
public void setSize (int, java.util.BitSet)
public void setSize (int, float, java.util.BitSet)
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
public boolean getProperty (java.lang.String, java.lang.Object[])
public java.lang.Object getProperty (java.lang.String, int)
public int getIndexFromName (java.lang.String)
public boolean wasClicked (int, int)
public void findNearestAtomIndex (int, int, org.jmol.modelset.Atom[])
public void checkBoundsMinMax (javax.vecmath.Point3f, javax.vecmath.Point3f)
public void setModelClickability ()
public org.jmol.util.Point3fi checkObjectClicked (int, int, int, java.util.BitSet)
public boolean checkObjectHovered (int, int, java.util.BitSet)
public boolean checkObjectDragged (int, int, int, int, int, java.util.BitSet)
protected int coordinateInRange (int, int, javax.vecmath.Point3f, int, javax.vecmath.Point3i)
public short setColix (short, byte, int)
protected short setColix (short, byte, org.jmol.modelset.Atom)
protected short setColix (short, byte, org.jmol.modelset.Bond)
protected void remapColors ()
public java.util.Vector getShapeDetail ()
public java.lang.String getShapeState ()
public void setVisibilityFlags (java.util.BitSet)
public static void setStateInfo (java.util.Hashtable, int, java.lang.String)
public static void setStateInfo (java.util.Hashtable, int, int, java.lang.String)
public static java.lang.String getShapeCommands (java.util.Hashtable, java.util.Hashtable, int)
public static java.lang.String getShapeCommands (java.util.Hashtable, java.util.Hashtable, int, java.lang.String)
public static void appendCmd (java.lang.StringBuffer, java.lang.String)
public static java.lang.String getFontCommand (java.lang.String, org.jmol.g3d.Font3D)
public java.lang.String getColorCommand (java.lang.String, short)
public java.lang.String getColorCommand (java.lang.String, byte, short)
private java.lang.String encodeTransColor (byte, short, boolean)
java.lang.String encodeColor (short)
private static java.lang.String getTranslucentLabel (short)
public static short getColix (short[], int, org.jmol.modelset.Atom)
}
org/jmol/shape/ShapeRenderer.class
<Unknown>
package org.jmol.shape
public abstract org.jmol.shape.ShapeRenderer extends java.lang.Object {
protected org.jmol.viewer.Viewer viewer
protected org.jmol.api.JmolRendererInterface g3d
protected org.jmol.modelset.ModelSet modelSet
protected org.jmol.shape.Shape shape
protected int myVisibilityFlag
protected int shapeID
protected short colix
protected short mad
protected short madBeg
protected short madMid
protected short madEnd
protected boolean isGenerator
protected boolean slabbing
public void <init> ()
public void setGenerator (boolean)
public short getMad (int)
public final void setViewerG3dShapeID (org.jmol.viewer.Viewer, org.jmol.api.JmolRendererInterface, int)
protected void initRenderer ()
public void render (org.jmol.api.JmolRendererInterface, org.jmol.modelset.ModelSet, org.jmol.shape.Shape)
protected abstract void render ()
protected void renderLine (javax.vecmath.Point3f, javax.vecmath.Point3f, int, byte, javax.vecmath.Point3i, javax.vecmath.Point3i)
}
org/jmol/shape/Stars.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.Stars extends org.jmol.shape.AtomShape {
public void <init> ()
}
org/jmol/shape/StarsRenderer.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.StarsRenderer extends org.jmol.shape.ShapeRenderer {
public void <init> ()
protected void render ()
void render1 (org.jmol.modelset.Atom, short)
}
org/jmol/shape/Sticks.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.Sticks extends org.jmol.shape.Shape {
short myMask
boolean reportAll
java.util.BitSet bsOrderSet
java.util.BitSet bsSizeSet
java.util.BitSet bsColixSet
java.util.BitSet selectedBonds
private static final int MAX_BOND_CLICK_DISTANCE_SQUARED
private final javax.vecmath.Point3i ptXY
public void <init> ()
public void initShape ()
public void setSize (int, java.util.BitSet)
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
public java.lang.Object getProperty (java.lang.String, int)
public void setModelClickability ()
public java.lang.String getShapeState ()
public org.jmol.util.Point3fi checkObjectClicked (int, int, int, java.util.BitSet)
private org.jmol.modelset.Bond findPickedBond (int, int, java.util.BitSet, org.jmol.util.Point3fi)
}
org/jmol/shape/SticksRenderer.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.SticksRenderer extends org.jmol.shape.ShapeRenderer {
protected boolean showMultipleBonds
protected byte modeMultipleBond
protected byte endcaps
protected boolean ssbondsBackbone
protected boolean hbondsBackbone
protected boolean bondsBackbone
protected boolean hbondsSolid
protected org.jmol.modelset.Atom atomA
protected org.jmol.modelset.Atom atomB
protected org.jmol.modelset.Bond bond
int xA
int yA
int zA
int xB
int yB
int zB
int dx
int dy
int mag2d
protected short colixA
protected short colixB
protected int width
protected int bondOrder
private boolean renderWireframe
private boolean isAntialiased
protected boolean lineBond
int xAxis1
int yAxis1
int xAxis2
int yAxis2
int dxStep
int dyStep
private static int wideWidthMilliAngstroms
public void <init> ()
protected void render ()
protected void renderBond ()
int getRenderBondOrder (int)
protected void renderBond (int)
void resetAxisCoordinates ()
void stepAxisCoordinates ()
private void renderTriangle (org.jmol.modelset.Bond)
private int getAromaticDottedBondMask ()
void drawDashed (int, int, int, int, int, int)
void renderHbondDashed ()
protected void fillCylinder (short, short, byte, int, int, int, int, int, int, int)
static void <clinit> ()
}
org/jmol/shape/Text.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.Text extends org.jmol.shape.Object2d {
private float fontScale
private String text
private String textUnformatted
private boolean doFormatText
private String[] lines
org.jmol.g3d.Font3D font
private java.awt.FontMetrics fm
private byte fid
private int ascent
private int descent
private int lineHeight
private int textWidth
private int textHeight
private int[] widths
java.awt.Image image
public void setScalePixelsPerMicron (float)
void <init> (org.jmol.api.JmolRendererInterface, org.jmol.g3d.Font3D, java.lang.String, short, short, int, int, int, int, int, float)
void <init> (org.jmol.viewer.Viewer, org.jmol.g3d.Graphics3D, org.jmol.g3d.Font3D, java.lang.String, short, int, int, float)
private void getFontMetrics ()
void setFid (byte)
void setText (java.lang.String)
public void setImage (java.awt.Image)
void setFont (org.jmol.g3d.Font3D)
void setFontScale (float)
java.lang.String fixText (java.lang.String)
protected void recalc ()
private void formatText ()
void render (org.jmol.api.JmolRendererInterface, float, float, boolean)
private void setPosition (float)
private static void setBoxXY (float, float, float, float, float[], boolean)
private static void showBox (org.jmol.api.JmolRendererInterface, short, short, int, int, int, int, int, int, float, boolean)
static final void renderSimpleLabel (org.jmol.api.JmolRendererInterface, org.jmol.g3d.Font3D, java.lang.String, short, short, float[], int, int, int, int, float, int, boolean, short, boolean)
public java.lang.String getState ()
private int stringWidth (java.lang.String)
}
org/jmol/shape/TextShape.class
<Unknown>
package org.jmol.shape
public abstract org.jmol.shape.TextShape extends org.jmol.shape.Object2dShape {
public void <init> ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
}
org/jmol/shape/Uccage.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.Uccage extends org.jmol.shape.FontLineShape {
public void <init> ()
public java.lang.String getShapeState ()
public void initShape ()
}
org/jmol/shape/UccageRenderer.class
<Unknown>
package org.jmol.shape
public org.jmol.shape.UccageRenderer extends org.jmol.shape.FontLineShapeRenderer {
java.text.NumberFormat nf
byte fid
boolean doLocalize
final javax.vecmath.Point3f[] screens
final javax.vecmath.Point3f[] verticesT
public void <init> ()
protected void render ()
void render1 (int)
private java.lang.String nfformat (float)
private void renderInfo (org.jmol.api.SymmetryInterface)
}
org/jmol/shapebio/Backbone.class
<Unknown>
package org.jmol.shapebio
public org.jmol.shapebio.Backbone extends org.jmol.shapebio.BioShapeCollection {
java.util.BitSet bsSelected
public void <init> ()
public void initShape ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
public void setSize (int, java.util.BitSet)
public void setModelClickability ()
}
org/jmol/shapebio/BackboneRenderer.class
<Unknown>
package org.jmol.shapebio
public org.jmol.shapebio.BackboneRenderer extends org.jmol.shapebio.BioShapeRenderer {
public void <init> ()
protected void renderBioShape (org.jmol.shapebio.BioShape)
}
org/jmol/shapebio/BioShape.class
<Unknown>
package org.jmol.shapebio
org.jmol.shapebio.BioShape extends java.lang.Object {
int modelIndex
int modelVisibilityFlags
org.jmol.shapebio.BioShapeCollection shape
org.jmol.modelsetbio.BioPolymer bioPolymer
org.jmol.shape.Mesh[] meshes
boolean[] meshReady
short[] mads
short[] colixes
byte[] paletteIDs
java.util.BitSet bsColixSet
java.util.BitSet bsSizeSet
java.util.BitSet bsSizeDefault
boolean isActive
int monomerCount
org.jmol.modelsetbio.Monomer[] monomers
javax.vecmath.Vector3f[] wingVectors
int[] leadAtomIndices
boolean hasBfactorRange
int bfactorMin
int bfactorMax
int range
float floatRange
private static final double eightPiSquared100
void <init> (org.jmol.shapebio.BioShapeCollection, int, org.jmol.modelsetbio.BioPolymer)
void calcBfactorRange ()
short calcMeanPositionalDisplacement (int)
void findNearestAtomIndex (int, int, org.jmol.modelset.Atom[])
void setMad (short, java.util.BitSet)
private short setMad (int, short)
void falsifyMesh (int, boolean)
void setColix (short, byte, java.util.BitSet)
void setTranslucent (boolean, java.util.BitSet, float)
void setShapeState (java.util.Hashtable, java.util.Hashtable)
void setModelClickability ()
}
org/jmol/shapebio/BioShapeCollection.class
<Unknown>
package org.jmol.shapebio
public abstract org.jmol.shapebio.BioShapeCollection extends org.jmol.shape.Shape {
org.jmol.modelset.Atom[] atoms
short madOn
short madHelixSheet
short madTurnRandom
short madDnaRna
boolean isActive
org.jmol.shapebio.BioShape[] bioShapes
public void <init> ()
public final void initModelSet ()
public void setSize (int, java.util.BitSet)
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
public java.lang.String getShapeState ()
void initialize ()
public void findNearestAtomIndex (int, int, org.jmol.modelset.Atom[])
public void setVisibilityFlags (java.util.BitSet)
public void setModelClickability ()
int getMpsShapeCount ()
org.jmol.shapebio.BioShape getBioShape (int)
}
org/jmol/shapebio/BioShapeRenderer.class
<Unknown>
package org.jmol.shapebio
abstract org.jmol.shapebio.BioShapeRenderer extends org.jmol.shape.MeshRenderer {
private boolean invalidateMesh
private boolean invalidateSheets
private boolean isHighRes
private boolean isTraceAlpha
private boolean ribbonBorder
private boolean haveControlPointScreens
private int aspectRatio
private int hermiteLevel
private float sheetSmoothing
private org.jmol.shape.Mesh[] meshes
private boolean[] meshReady
protected int monomerCount
protected org.jmol.modelsetbio.Monomer[] monomers
protected boolean isNucleic
protected boolean isCarbohydrate
protected java.util.BitSet bsVisible
protected javax.vecmath.Point3i[] ribbonTopScreens
protected javax.vecmath.Point3i[] ribbonBottomScreens
protected javax.vecmath.Point3f[] controlPoints
protected javax.vecmath.Point3i[] controlPointScreens
protected int[] leadAtomIndices
protected javax.vecmath.Vector3f[] wingVectors
protected short[] mads
protected short[] colixes
protected byte[] structureTypes
private final javax.vecmath.Point3f pointT
private int iPrev
private int iNext
private int iNext2
private int iNext3
private int diameterBeg
private int diameterMid
private int diameterEnd
private boolean doCap0
private boolean doCap1
private final javax.vecmath.Point3i screenArrowTop
private final javax.vecmath.Point3i screenArrowTopPrev
private final javax.vecmath.Point3i screenArrowBot
private final javax.vecmath.Point3i screenArrowBotPrev
private static final int ABSOLUTE_MIN_MESH_SIZE
private static final int MIN_MESH_RENDER_SIZE
private javax.vecmath.Point3f[] controlHermites
private javax.vecmath.Vector3f[] wingHermites
private javax.vecmath.Point3f[] radiusHermites
private javax.vecmath.Vector3f norm
private final javax.vecmath.Vector3f Z
private final javax.vecmath.Vector3f wing
private final javax.vecmath.Vector3f wing0
private final javax.vecmath.Vector3f wing1
private final javax.vecmath.Vector3f wingT
private final javax.vecmath.AxisAngle4f aa
private final javax.vecmath.Point3f pt
private final javax.vecmath.Point3f pt1
private final javax.vecmath.Point3f ptPrev
private final javax.vecmath.Point3f ptNext
private final javax.vecmath.Matrix3f mat
void <init> ()
protected abstract void renderBioShape (org.jmol.shapebio.BioShape)
protected void render ()
private void freeTempArrays ()
private boolean initializePolymer (org.jmol.shapebio.BioShape)
private void setStructureTypes ()
protected boolean isHelix (int)
protected void calcScreenControlPoints ()
protected void calcScreenControlPoints (javax.vecmath.Point3f[])
protected javax.vecmath.Point3i[] calcScreens (float)
private void calc1Screen (javax.vecmath.Point3f, javax.vecmath.Vector3f, short, float, javax.vecmath.Point3i)
protected short getLeadColix (int)
private void setNeighbors (int)
protected void renderHermiteCylinder (javax.vecmath.Point3i[], int)
private boolean setMads (int, boolean)
private boolean checkDiameter (int)
protected void renderHermiteConic (int, boolean)
protected void renderHermiteRibbon (boolean, int, boolean)
protected void renderHermiteArrowHead (int)
protected void renderCone (int, javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f)
private boolean createMeshCylinder (int, int, int, int, int)
}
org/jmol/shapebio/Cartoon.class
<Unknown>
package org.jmol.shapebio
public org.jmol.shapebio.Cartoon extends org.jmol.shapebio.Rockets {
public void <init> ()
public void initShape ()
}
org/jmol/shapebio/CartoonRenderer.class
<Unknown>
package org.jmol.shapebio
public org.jmol.shapebio.CartoonRenderer extends org.jmol.shapebio.RocketsRenderer {
private boolean newRockets
private boolean renderAsRockets
javax.vecmath.Point3i ptConnect
private final javax.vecmath.Point3f[] ring6Points
private final javax.vecmath.Point3i[] ring6Screens
private final javax.vecmath.Point3f[] ring5Points
private final javax.vecmath.Point3i[] ring5Screens
public void <init> ()
protected void renderBioShape (org.jmol.shapebio.BioShape)
void renderNucleic ()
protected void render1 ()
private void renderRockets ()
private void renderNucleicBaseStep (org.jmol.modelsetbio.NucleicMonomer, short, javax.vecmath.Point3i)
private void renderRing6 ()
private void renderRing5 ()
}
org/jmol/shapebio/MeshRibbon.class
<Unknown>
package org.jmol.shapebio
public org.jmol.shapebio.MeshRibbon extends org.jmol.shapebio.Strands {
public void <init> ()
public void initShape ()
}
org/jmol/shapebio/MeshRibbonRenderer.class
<Unknown>
package org.jmol.shapebio
public org.jmol.shapebio.MeshRibbonRenderer extends org.jmol.shapebio.StrandsRenderer {
public void <init> ()
protected void renderBioShape (org.jmol.shapebio.BioShape)
protected void render2Strand (boolean, float, float)
}
org/jmol/shapebio/Ribbons.class
<Unknown>
package org.jmol.shapebio
public org.jmol.shapebio.Ribbons extends org.jmol.shapebio.BioShapeCollection {
public void <init> ()
}
org/jmol/shapebio/RibbonsRenderer.class
<Unknown>
package org.jmol.shapebio
public org.jmol.shapebio.RibbonsRenderer extends org.jmol.shapebio.MeshRibbonRenderer {
public void <init> ()
protected void renderBioShape (org.jmol.shapebio.BioShape)
}
org/jmol/shapebio/Rockets.class
<Unknown>
package org.jmol.shapebio
public org.jmol.shapebio.Rockets extends org.jmol.shapebio.BioShapeCollection {
public void <init> ()
public void initShape ()
}
org/jmol/shapebio/RocketsRenderer.class
<Unknown>
package org.jmol.shapebio
public org.jmol.shapebio.RocketsRenderer extends org.jmol.shapebio.BioShapeRenderer {
private static final float MIN_CONE_HEIGHT
protected boolean renderAsBarrels
protected javax.vecmath.Point3f[] cordMidPoints
protected boolean tPending
private org.jmol.modelsetbio.ProteinStructure proteinstructurePending
private int startIndexPending
private int endIndexPending
private javax.vecmath.Point3f screenA
private javax.vecmath.Point3f screenB
private javax.vecmath.Point3f screenC
private static final byte[] boxFaces
private final javax.vecmath.Point3f[] corners
private final javax.vecmath.Point3f[] screenCorners
private final javax.vecmath.Point3f pointTipOffset
private final javax.vecmath.Vector3f scaledWidthVector
private final javax.vecmath.Vector3f scaledHeightVector
private static final byte[] arrowHeadFaces
private final javax.vecmath.Vector3f lengthVector
private final javax.vecmath.Point3f pointCorner
public void <init> ()
protected void renderBioShape (org.jmol.shapebio.BioShape)
protected boolean isSheet (int)
protected void calcRopeMidPoints (boolean)
protected void render1 ()
protected void renderSpecialSegment (org.jmol.modelsetbio.Monomer, short, short)
protected void renderPending ()
private void renderPendingRocketSegment (int, javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f, boolean)
private void renderPendingSheet (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f, boolean)
void buildBox (javax.vecmath.Point3f, javax.vecmath.Vector3f, javax.vecmath.Vector3f, javax.vecmath.Vector3f)
void buildArrowHeadBox (javax.vecmath.Point3f, javax.vecmath.Vector3f, javax.vecmath.Vector3f, javax.vecmath.Point3f)
void drawBox (javax.vecmath.Point3f, javax.vecmath.Point3f)
void drawArrowHeadBox (javax.vecmath.Point3f, javax.vecmath.Point3f)
static void <clinit> ()
}
org/jmol/shapebio/Strands.class
<Unknown>
package org.jmol.shapebio
public org.jmol.shapebio.Strands extends org.jmol.shapebio.BioShapeCollection {
boolean isMesh
public void <init> ()
}
org/jmol/shapebio/StrandsRenderer.class
<Unknown>
package org.jmol.shapebio
public org.jmol.shapebio.StrandsRenderer extends org.jmol.shapebio.BioShapeRenderer {
protected int strandCount
protected float strandSeparation
protected float baseOffset
public void <init> ()
protected void renderBioShape (org.jmol.shapebio.BioShape)
protected boolean setStrandCount ()
protected void render1 ()
private void render1Strand (javax.vecmath.Point3i[])
}
org/jmol/shapebio/Trace.class
<Unknown>
package org.jmol.shapebio
public org.jmol.shapebio.Trace extends org.jmol.shapebio.BioShapeCollection {
public void <init> ()
public void initShape ()
}
org/jmol/shapebio/TraceRenderer.class
<Unknown>
package org.jmol.shapebio
public org.jmol.shapebio.TraceRenderer extends org.jmol.shapebio.BioShapeRenderer {
public void <init> ()
protected void renderBioShape (org.jmol.shapebio.BioShape)
}
org/jmol/shapespecial/Dipole.class
<Unknown>
package org.jmol.shapespecial
org.jmol.shapespecial.Dipole extends java.lang.Object {
String thisID
short mad
short colix
short type
javax.vecmath.Point3f origin
javax.vecmath.Point3f center
javax.vecmath.Vector3f vector
String dipoleInfo
float dipoleValue
boolean isUserValue
float offsetSide
float offsetAngstroms
int offsetPercent
int visibilityFlags
int modelIndex
boolean visible
boolean noCross
boolean haveAtoms
boolean isValid
org.jmol.modelset.Atom[] atoms
javax.vecmath.Point3f[] coords
org.jmol.modelset.Bond bond
static final short DIPOLE_TYPE_UNKNOWN
static final short DIPOLE_TYPE_POINTS
static final short DIPOLE_TYPE_ATOMS
static final short DIPOLE_TYPE_BOND
static final short DIPOLE_TYPE_MOLECULAR
static final short DIPOLE_TYPE_POINTVECTOR
void <init> ()
void <init> (int, java.lang.String, java.lang.String, short, short, boolean)
void setTranslucent (boolean, float)
void set (java.lang.String, java.lang.String, org.jmol.modelset.Atom[], float, short, float, int, float, javax.vecmath.Point3f, javax.vecmath.Vector3f)
private void set (javax.vecmath.Point3f, javax.vecmath.Point3f)
void set (float)
void set (javax.vecmath.Point3f, javax.vecmath.Point3f, float)
void set (javax.vecmath.Point3f, javax.vecmath.Vector3f)
void set (org.jmol.modelset.Atom, org.jmol.modelset.Atom, float)
void centerDipole ()
boolean isBondType ()
public java.lang.String getShapeState ()
}
org/jmol/shapespecial/Dipoles.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.Dipoles extends org.jmol.shape.Shape {
static final short DEFAULT_MAD
static final float DEFAULT_OFFSETSIDE
int dipoleCount
org.jmol.shapespecial.Dipole[] dipoles
private org.jmol.shapespecial.Dipole currentDipole
private org.jmol.shapespecial.Dipole tempDipole
private javax.vecmath.Point3f startCoord
private javax.vecmath.Point3f endCoord
private float dipoleValue
private boolean isUserValue
private boolean isBond
private boolean iHaveTwoEnds
private int atomIndex1
private int atomIndex2
private short colix
private javax.vecmath.Vector3f calculatedDipole
private String wildID
private static final float E_ANG_PER_DEBYE
public void <init> ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
private void setProperty (int, boolean, int, float)
private void setProperty (int, org.jmol.shapespecial.Dipole, int, float)
public java.lang.Object getProperty (java.lang.String, int)
private void getBondDipoles ()
private boolean isBondDipole (int)
private void setColixDipole (short, short, java.util.BitSet)
private void setDipole ()
private void setDipole (org.jmol.modelset.Atom, org.jmol.modelset.Atom, float, float)
private int getDipoleIndex (java.lang.String, java.lang.String)
private boolean isSameAtoms (org.jmol.shapespecial.Dipole, java.lang.String)
private int getDipoleIndex (int, int)
private void deleteDipole (org.jmol.shapespecial.Dipole)
private org.jmol.shapespecial.Dipole findDipole (java.lang.String)
private org.jmol.shapespecial.Dipole findDipole (org.jmol.modelset.Atom, org.jmol.modelset.Atom, boolean)
private org.jmol.shapespecial.Dipole findBondDipole (org.jmol.modelset.Bond)
private org.jmol.shapespecial.Dipole findDipole (java.lang.String, java.lang.String)
private org.jmol.shapespecial.Dipole allocDipole (java.lang.String, java.lang.String)
private void dumpDipoles (java.lang.String)
private void clear (boolean)
public int getIndexFromName (java.lang.String)
public java.util.Vector getShapeDetail ()
private void setModelIndex ()
public void setVisibilityFlags (java.util.BitSet)
public java.lang.String getShapeState ()
}
org/jmol/shapespecial/DipolesRenderer.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.DipolesRenderer extends org.jmol.shape.ShapeRenderer {
private float dipoleVectorScale
private final javax.vecmath.Vector3f offset
private final javax.vecmath.Point3i[] screens
private final javax.vecmath.Point3f[] points
private javax.vecmath.Point3f cross0
private javax.vecmath.Point3f cross1
private static final int cylinderBase
private static final int cross
private static final int crossEnd
private static final int center
private static final int arrowHeadBase
private static final int arrowHeadTip
private int diameter
private int headWidthPixels
private int crossWidthPixels
private static final float arrowHeadOffset
private static final float arrowHeadWidthFactor
private static final float crossOffset
private static final float crossWidth
public void <init> ()
protected void render ()
private boolean transform (org.jmol.shapespecial.Dipole)
private void renderDipoleVector (org.jmol.shapespecial.Dipole)
}
org/jmol/shapespecial/Draw.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.Draw extends org.jmol.shape.MeshCollection {
org.jmol.shapespecial.DrawMesh[] dmeshes
org.jmol.shapespecial.DrawMesh thisMesh
private javax.vecmath.Point3f[] ptList
private javax.vecmath.Vector3f offset
private int nPoints
private int diameter
private float width
private float newScale
private float length
private boolean isCurve
private boolean isArc
private boolean isArrow
private boolean isLine
private boolean isVector
private boolean isCircle
private boolean isPerpendicular
private boolean isCylinder
private boolean isVertices
private boolean isPlane
private boolean isReversed
private boolean isRotated45
private boolean isCrossed
private boolean isValid
private boolean noHead
private int indicatedModelIndex
private int[] modelInfo
private boolean makePoints
private int nidentifiers
private int nbitsets
private javax.vecmath.Point4f plane
private java.util.BitSet bsAllModels
private java.util.Vector vData
private static final int PT_COORD
private static final int PT_IDENTIFIER
private static final int PT_BITSET
private static final int PT_MODEL_INDEX
private static final int PT_MODEL_BASED_POINTS
private final javax.vecmath.Vector3f vAB
private final javax.vecmath.Vector3f vAC
private static final int MAX_OBJECT_CLICK_DISTANCE_SQUARED
private org.jmol.shapespecial.DrawMesh pickedMesh
private int pickedModel
private int pickedVertex
private final javax.vecmath.Point3i ptXY
public void <init> ()
public void allocMesh (java.lang.String)
void setPropertySuper (java.lang.String, java.lang.Object, java.util.BitSet)
public void initShape ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
private void resetObjects ()
public java.lang.Object getProperty (java.lang.String, int)
private javax.vecmath.Point3f getSpinCenter (java.lang.String, int, int)
private javax.vecmath.Vector3f getSpinAxis (java.lang.String, int)
private boolean setDrawing ()
private void addPoint (javax.vecmath.Point3f, int)
private boolean setPoints (int, int)
private void setPolygon (int)
private static void scaleDrawing (org.jmol.shapespecial.DrawMesh, float)
private static final void setAxes (org.jmol.shapespecial.DrawMesh)
public void setVisibilityFlags (java.util.BitSet)
public org.jmol.util.Point3fi checkObjectClicked (int, int, int, java.util.BitSet)
private org.jmol.util.Point3fi getPickedPoint (javax.vecmath.Point3f)
public boolean checkObjectHovered (int, int, java.util.BitSet)
public synchronized boolean checkObjectDragged (int, int, int, int, int, java.util.BitSet)
private void move2D (org.jmol.shapespecial.DrawMesh, int[], int, int, int, boolean)
private boolean findPickedObject (int, int, boolean, java.util.BitSet)
private java.lang.String getDrawCommand (org.jmol.shapespecial.DrawMesh)
private java.lang.String getDrawCommand (org.jmol.shapespecial.DrawMesh, int)
static boolean isPolygonDisplayable (org.jmol.shape.Mesh, int)
private static java.lang.String getVertexList (org.jmol.shapespecial.DrawMesh, int, int)
public java.util.Vector getShapeDetail ()
public java.lang.String getShapeState ()
static javax.vecmath.Point3f randomPoint ()
}
org/jmol/shapespecial/DrawMesh.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.DrawMesh extends org.jmol.shape.Mesh {
java.util.BitSet modelFlags
int drawType
int[] drawTypes
javax.vecmath.Point3f[] ptCenters
javax.vecmath.Vector3f axis
javax.vecmath.Vector3f[] axes
int drawVertexCount
int[] drawVertexCounts
boolean isFixed
boolean isVector
float drawArrowScale
boolean nohead
java.util.BitSet bsMeshesVisible
void <init> (java.lang.String, org.jmol.g3d.Graphics3D, short, int)
final void setCenter (int)
void offset (javax.vecmath.Vector3f)
public void deleteAtoms (int)
}
org/jmol/shapespecial/DrawRenderer.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.DrawRenderer extends org.jmol.shape.MeshRenderer {
private int drawType
private org.jmol.shapespecial.DrawMesh dmesh
private javax.vecmath.Point3f[] controlHermites
private final javax.vecmath.Point3f vpt0
private final javax.vecmath.Point3f vpt1
private final javax.vecmath.Point3f vpt2
private final javax.vecmath.Vector3f vTemp
private final javax.vecmath.Vector3f vTemp2
private final javax.vecmath.Point3f pt0f
private final javax.vecmath.Point3i pt0i
public void <init> ()
protected void render ()
protected boolean isPolygonDisplayable (int)
protected void render2 (boolean)
private void renderXyArrow (int)
private void renderArrowHead (javax.vecmath.Point3f, javax.vecmath.Point3f, float, boolean, boolean)
private void renderHandles ()
private void renderInfo ()
}
org/jmol/shapespecial/Ellipsoids$Ellipsoid.class
<Unknown>
package org.jmol.shapespecial
org.jmol.shapespecial.Ellipsoids$Ellipsoid extends java.lang.Object {
String id
javax.vecmath.Vector3f[] axes
float[] lengths
javax.vecmath.Point3f center
double[] coef
short colix
int modelIndex
float scale
boolean visible
boolean isValid
boolean isOn
void <init> (java.lang.String, int)
}
org/jmol/shapespecial/Ellipsoids.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.Ellipsoids extends org.jmol.shape.AtomShape {
java.util.Hashtable htEllipsoids
boolean haveEllipsoids
org.jmol.shapespecial.Ellipsoids$Ellipsoid ellipsoid
private static float[] crtval
public void <init> ()
public int getIndexFromName (java.lang.String)
public void setSize (int, java.util.BitSet)
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
private void updateEquation (org.jmol.shapespecial.Ellipsoids$Ellipsoid)
public java.lang.String getShapeState ()
public void setVisibilityFlags (java.util.BitSet)
static final float getRadius (int)
static void <clinit> ()
}
org/jmol/shapespecial/EllipsoidsRenderer.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.EllipsoidsRenderer extends org.jmol.shape.ShapeRenderer {
private org.jmol.shapespecial.Ellipsoids ellipsoids
private boolean drawDots
private boolean drawArcs
private boolean drawAxes
private boolean drawFill
private boolean drawBall
private boolean wireframeOnly
private int dotCount
private int[] coords
private javax.vecmath.Vector3f[] axes
private final float[] factoredLengths
private int diameter
private int diameter0
private int selectedOctant
private javax.vecmath.Point3i[] selectedPoints
private int iCutout
private javax.vecmath.Matrix3f mat
private javax.vecmath.Matrix3f mTemp
private javax.vecmath.Matrix4f mDeriv
private javax.vecmath.Matrix3f matScreenToCartesian
private javax.vecmath.Matrix3f matScreenToEllipsoid
private javax.vecmath.Matrix3f matEllipsoidToScreen
private double[] coef
private final javax.vecmath.Vector3f v1
private final javax.vecmath.Vector3f v2
private final javax.vecmath.Vector3f v3
private final javax.vecmath.Point3f pt1
private final javax.vecmath.Point3f pt2
private final javax.vecmath.Point3i s0
private final javax.vecmath.Point3i s1
private final javax.vecmath.Point3i s2
private static final float toRadians
private static final float[] cossin
private final javax.vecmath.Point3i[] screens
private final javax.vecmath.Point3f[] points
private static int[] axisPoints
private static int[] octants
private int dx
private float perspectiveFactor
private javax.vecmath.Point3f center
private static final javax.vecmath.Vector3f[] unitVectors
private static final javax.vecmath.Vector3f[] unitAxisVectors
public void <init> ()
protected void render ()
private void render1 (org.jmol.modelset.Atom, java.lang.Object[])
private void setMatrices ()
private void setAxes (float)
private void renderAxes ()
private void renderDots (javax.vecmath.Point3f)
private void renderArcs (javax.vecmath.Point3f)
private void renderArc (javax.vecmath.Point3f, int, int)
protected void renderEllipsoid (org.jmol.shapespecial.Ellipsoids$Ellipsoid)
protected void renderBall ()
private void setSelectedOctant ()
static void <clinit> ()
}
org/jmol/shapespecial/GeoSurface.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.GeoSurface extends org.jmol.shape.Dots {
public void <init> ()
public void initShape ()
}
org/jmol/shapespecial/GeoSurfaceRenderer.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.GeoSurfaceRenderer extends org.jmol.shape.DotsRenderer {
private javax.vecmath.Point3i facePt1
private javax.vecmath.Point3i facePt2
private javax.vecmath.Point3i facePt3
public void <init> ()
protected void render ()
protected void renderConvex (short, int[], int)
private void renderSurface (int[])
}
org/jmol/shapespecial/Polyhedra$Polyhedron.class
<Unknown>
package org.jmol.shapespecial
org.jmol.shapespecial.Polyhedra$Polyhedron extends java.lang.Object {
int modelIndex
final org.jmol.modelset.Atom centralAtom
final org.jmol.modelset.Atom[] vertices
int ptCenter
boolean visible
final short[] normixes
byte[] planes
int visibilityFlags
boolean collapsed
float myFaceCenterOffset
float myDistanceFactor
private final org.jmol.shapespecial.Polyhedra this$0
void <init> (org.jmol.shapespecial.Polyhedra, org.jmol.modelset.Atom, int, int, int, org.jmol.modelset.Atom[], short[], byte[])
java.lang.String getState (java.util.Hashtable)
}
org/jmol/shapespecial/Polyhedra.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.Polyhedra extends org.jmol.shape.AtomShape {
private static final float DEFAULT_DISTANCE_FACTOR
private static final float DEFAULT_FACECENTEROFFSET
private static final int EDGES_NONE
static final int EDGES_ALL
static final int EDGES_FRONT
private static final int MAX_VERTICES
private static final int FACE_COUNT_MAX
private org.jmol.modelset.Atom[] otherAtoms
int polyhedronCount
org.jmol.shapespecial.Polyhedra$Polyhedron[] polyhedrons
int drawEdges
private float radius
private int nVertices
float faceCenterOffset
float distanceFactor
boolean isCollapsed
private boolean iHaveCenterBitSet
private boolean bondedOnly
private boolean haveBitSetVertices
private java.util.BitSet centers
private java.util.BitSet bsVertices
private java.util.BitSet bsVertexCount
private short[] normixesT
private byte[] planesT
private static final javax.vecmath.Point3f randomPoint
private javax.vecmath.Vector3f align1
private javax.vecmath.Vector3f align2
private final javax.vecmath.Vector3f vAB
private final javax.vecmath.Vector3f vAC
private static float minDistanceForPlanarity
public void <init> ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
private void deletePolyhedra ()
private void setVisible (boolean)
private void buildPolyhedra ()
private org.jmol.shapespecial.Polyhedra$Polyhedron constructBondsPolyhedron (int)
private org.jmol.shapespecial.Polyhedra$Polyhedron constructBitSetPolyhedron (int)
private org.jmol.shapespecial.Polyhedra$Polyhedron constructRadiusPolyhedron (int)
private org.jmol.shapespecial.Polyhedra$Polyhedron validatePolyhedronNew (org.jmol.modelset.Atom, int, org.jmol.modelset.Atom[])
private java.lang.String faceId (int, int, int)
private boolean isAligned (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f)
private boolean isPlanar (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f)
public void setVisibilityFlags (java.util.BitSet)
public java.lang.String getShapeState ()
static void <clinit> ()
}
org/jmol/shapespecial/PolyhedraRenderer.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.PolyhedraRenderer extends org.jmol.shape.ShapeRenderer {
private int drawEdges
public void <init> ()
protected void render ()
private void render1 (org.jmol.shapespecial.Polyhedra$Polyhedron, short)
private void drawFace (short, org.jmol.modelset.Atom, org.jmol.modelset.Atom, org.jmol.modelset.Atom, boolean, boolean)
private void fillFace (short, org.jmol.modelset.Atom, org.jmol.modelset.Atom, org.jmol.modelset.Atom)
}
org/jmol/shapespecial/Vectors.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.Vectors extends org.jmol.shape.AtomShape {
public void <init> ()
protected void initModelSet ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
public java.lang.Object getProperty (java.lang.String, int)
public java.lang.String getShapeState ()
}
org/jmol/shapespecial/VectorsRenderer.class
<Unknown>
package org.jmol.shapespecial
public org.jmol.shapespecial.VectorsRenderer extends org.jmol.shape.ShapeRenderer {
final javax.vecmath.Point3f pointVectorEnd
final javax.vecmath.Point3f pointArrowHead
final javax.vecmath.Point3i screenVectorEnd
final javax.vecmath.Point3i screenArrowHead
final javax.vecmath.Vector3f headOffsetVector
int diameter
int headWidthPixels
float vectorScale
float headScale
boolean doShaft
static final float arrowHeadOffset
public void <init> ()
protected void render ()
boolean transform (short, org.jmol.modelset.Atom, javax.vecmath.Vector3f)
void renderVector (org.jmol.modelset.Atom)
}
org/jmol/shapesurface/Isosurface.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.Isosurface extends org.jmol.shape.MeshCollection implements org.jmol.jvxl.api.MeshDataServer {
private org.jmol.shapesurface.IsosurfaceMesh[] isomeshes
private org.jmol.shapesurface.IsosurfaceMesh thisMesh
private int lighting
private boolean iHaveBitSets
private boolean explicitContours
private int atomIndex
private int moNumber
private short defaultColix
private javax.vecmath.Point3f center
private boolean isPhaseColored
private boolean isColorExplicit
protected org.jmol.jvxl.readers.SurfaceGenerator sg
private org.jmol.jvxl.data.JvxlData jvxlData
private org.jmol.util.ColorEncoder colorEncoder
private int indexColorPositive
private int indexColorNegative
private int nLCAO
private javax.vecmath.Point4f lcaoDir
private boolean associateNormals
private static final int MAX_OBJECT_CLICK_DISTANCE_SQUARED
private final javax.vecmath.Point3i ptXY
public void <init> ()
public void allocMesh (java.lang.String)
public void initShape ()
private void newSg ()
protected void clearSg ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
private void setPropertySuper (java.lang.String, java.lang.Object, java.util.BitSet)
public java.lang.Object getProperty (java.lang.String, int)
protected void getColorState (java.lang.StringBuffer, org.jmol.shape.Mesh)
private boolean getScriptBitSets (java.lang.String, java.util.BitSet[])
private void initializeIsosurface ()
private void initState ()
private void discardTempData (boolean)
private short getDefaultColix ()
private void drawLcaoCartoon (javax.vecmath.Vector3f, javax.vecmath.Vector3f, javax.vecmath.Vector3f, int)
private void createLcaoLobe (javax.vecmath.Vector3f, float, int)
public void invalidateTriangles ()
public void fillMeshData (org.jmol.jvxl.data.MeshData, int)
public void notifySurfaceGenerationCompleted ()
public void notifySurfaceMappingCompleted ()
public javax.vecmath.Point3f[] calculateGeodesicSurface (java.util.BitSet, float)
public int getSurfacePointIndexAndFraction (float, boolean, int, int, int, javax.vecmath.Point3i, int, int, float, float, javax.vecmath.Point3f, javax.vecmath.Vector3f, boolean, float[])
public int addVertexCopy (javax.vecmath.Point3f, float, int)
public void addTriangleCheck (int, int, int, int, boolean, int)
private void setModelIndex ()
protected void setScriptInfo ()
private void setJvxlInfo ()
public java.util.Vector getShapeDetail ()
protected void remapColors ()
private java.lang.String getUserColorScheme (java.lang.String)
public float getValue (int, int, int)
public boolean checkObjectHovered (int, int, java.util.BitSet)
public org.jmol.util.Point3fi checkObjectClicked (int, int, int, java.util.BitSet)
private void navigate (int)
private void setHeading (javax.vecmath.Point3f, javax.vecmath.Vector3f, int)
private boolean getClosestNormal (org.jmol.shapesurface.IsosurfaceMesh, javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Vector3f)
private void getClosestPoint (org.jmol.shapesurface.IsosurfaceMesh, int, javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Vector3f)
private java.lang.String findValue (int, int, boolean, java.util.BitSet)
public int getColixArgb (short)
}
org/jmol/shapesurface/IsosurfaceMesh.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.IsosurfaceMesh extends org.jmol.shape.Mesh {
org.jmol.jvxl.data.JvxlData jvxlData
int vertexIncrement
int firstRealVertex
int dataType
boolean hasGridPoints
Object calculatedArea
Object calculatedVolume
public boolean isSolvent
public float[] vertexValues
public short[] vertexColixes
java.util.Hashtable assocGridPointMap
java.util.Hashtable assocGridPointNormals
public short[] polygonColixes
private int lastColor
private short lastColix
private int iA
private int iB
private int iC
java.util.BitSet[] surfaceSet
int[] vertexSets
int nSets
int thisSet
javax.vecmath.Point3f[] centers
public static final int CONTOUR_NPOLYGONS
public static final int CONTOUR_BITSET
public static final int CONTOUR_VALUE
public static final int CONTOUR_COLOR
public static final int CONTOUR_FDATA
public static final int CONTOUR_POINTS
void <init> (java.lang.String, org.jmol.g3d.Graphics3D, short, int)
void clear (java.lang.String, boolean)
void allocVertexColixes ()
int addVertexCopy (javax.vecmath.Point3f, float, int, boolean)
int addVertexCopy (javax.vecmath.Point3f, float)
public void setTranslucent (boolean, float)
void addTriangleCheck (int, int, int, int, int)
void invalidateTriangles ()
private boolean setABC (int)
java.lang.Object calculateArea ()
java.lang.Object calculateVolume ()
public void sumVertexNormals (javax.vecmath.Vector3f[])
javax.vecmath.Point3f[] getCenters ()
javax.vecmath.Point4f getFacePlane (int, javax.vecmath.Vector3f)
java.util.Vector[] getContours ()
public static void setContourVector (java.util.Vector, int, java.util.BitSet, float, int, java.lang.StringBuffer)
private void get3dContour (java.util.Vector, float, int)
private float checkPt (int, int, float)
public static javax.vecmath.Point3f getContourPoint (javax.vecmath.Point3f[], int, int, float)
private void dumpData ()
}
org/jmol/shapesurface/IsosurfaceRenderer.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.IsosurfaceRenderer extends org.jmol.shape.MeshRenderer {
private boolean iShowNormals
protected boolean iHideBackground
protected boolean isBicolorMap
protected short backgroundColix
protected int nError
protected float[] vertexValues
protected org.jmol.shapesurface.IsosurfaceMesh imesh
private final javax.vecmath.Point3f ptTemp
private final javax.vecmath.Point3i ptTempi
public void <init> ()
protected void render ()
protected void transform ()
protected void render2 (boolean)
private void renderLonePair (boolean)
private void renderContourLines ()
protected void renderPoints ()
protected void renderTriangles (boolean, boolean, boolean)
private void renderNormals ()
}
org/jmol/shapesurface/LcaoCartoon.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.LcaoCartoon extends org.jmol.shapesurface.Isosurface {
private String thisType
private int myColorPt
private String lcaoID
private java.util.BitSet thisSet
private boolean isMolecular
private javax.vecmath.Vector3f rotationAxis
private Float lcaoScale
private boolean isTranslucent
private float translucentLevel
private Integer lcaoColorPos
private Integer lcaoColorNeg
boolean isLonePair
boolean isRadical
public void <init> ()
public void initShape ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
private void setLcaoOn (boolean)
private void setLcaoOn (int, boolean)
private void deleteLcaoCartoon ()
private void deleteLcaoCartoon (int)
private void createLcaoCartoon ()
private void createLcaoCartoon (int)
private java.lang.String getID (java.lang.String, int)
public java.lang.String getShapeState ()
}
org/jmol/shapesurface/LcaoCartoonRenderer.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.LcaoCartoonRenderer extends org.jmol.shapesurface.IsosurfaceRenderer {
public void <init> ()
}
org/jmol/shapesurface/MolecularOrbital.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.MolecularOrbital extends org.jmol.shapesurface.Isosurface {
private String moTranslucency
private Float moTranslucentLevel
private javax.vecmath.Point4f moPlane
private Float moCutoff
private Float moResolution
private Float moScale
private Integer moColorPos
private Integer moColorNeg
private boolean moIsPositiveOnly
private int moFill
private int moMesh
private int moDots
private int moFrontOnly
private String moTitleFormat
private boolean moDebug
private int myColorPt
private String strID
private int moNumber
private java.util.Hashtable htModels
private java.util.Hashtable thisModel
public void <init> ()
public void initShape ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
private java.lang.String getId (int)
public java.lang.Object getProperty (java.lang.String, int)
protected void clearSg ()
private boolean getSettings (java.lang.String)
private void setOrbital (int)
public java.lang.String getShapeState ()
private java.lang.String getMoState (int)
}
org/jmol/shapesurface/MolecularOrbitalRenderer.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.MolecularOrbitalRenderer extends org.jmol.shapesurface.IsosurfaceRenderer {
private java.text.NumberFormat nf
public void <init> ()
protected void render ()
private void renderInfo ()
}
org/jmol/shapesurface/Pmesh.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.Pmesh extends org.jmol.shapesurface.Isosurface {
public void <init> ()
public void initShape ()
}
org/jmol/shapesurface/PmeshRenderer.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.PmeshRenderer extends org.jmol.shapesurface.IsosurfaceRenderer {
public void <init> ()
}
org/jmol/smiles/InvalidSmilesException.class
<Unknown>
package org.jmol.smiles
public org.jmol.smiles.InvalidSmilesException extends java.lang.Exception {
public void <init> ()
public void <init> (java.lang.String)
public void <init> (java.lang.Throwable)
public void <init> (java.lang.String, java.lang.Throwable)
}
org/jmol/smiles/PatternMatcher.class
<Unknown>
package org.jmol.smiles
public org.jmol.smiles.PatternMatcher extends java.lang.Object implements org.jmol.api.SmilesMatcherInterface {
private int atomCount
private org.jmol.modelset.ModelSet modelSet
public void <init> ()
public void setModelSet (org.jmol.modelset.ModelSet)
public java.util.BitSet getSubstructureSet (java.lang.String) throws java.lang.Exception
public java.util.BitSet getSubstructureSet (org.jmol.smiles.SmilesMolecule)
private void searchMatch (java.util.BitSet, org.jmol.smiles.SmilesMolecule, int)
private void searchMatch (java.util.BitSet, org.jmol.smiles.SmilesMolecule, org.jmol.smiles.SmilesAtom, int, int)
}
org/jmol/smiles/SmilesAtom.class
<Unknown>
package org.jmol.smiles
public org.jmol.smiles.SmilesAtom extends java.lang.Object {
private int number
private String symbol
private int atomicMass
private int charge
private int hydrogenCount
private int matchingAtom
private String chiralClass
private int chiralOrder
private org.jmol.smiles.SmilesBond[] bonds
private int bondsCount
private static final int INITIAL_BONDS
public static final String DEFAULT_CHIRALITY
public static final String CHIRALITY_ALLENE
public static final String CHIRALITY_OCTAHEDRAL
public static final String CHIRALITY_SQUARE_PLANAR
public static final String CHIRALITY_TETRAHEDRAL
public static final String CHIRALITY_TRIGONAL_BIPYRAMIDAL
public void <init> (int)
public void createMissingHydrogen (org.jmol.smiles.SmilesMolecule)
public int getNumber ()
public java.lang.String getSymbol ()
public void setSymbol (java.lang.String)
public int getAtomicMass ()
public void setAtomicMass (int)
public int getCharge ()
public void setCharge (int)
public int getMatchingAtom ()
public void setMatchingAtom (int)
public java.lang.String getChiralClass ()
public void setChiralClass (java.lang.String)
public int getChiralOrder ()
public void setChiralOrder (int)
public int getHydrogenCount ()
public void setHydrogenCount (int)
public int getBondsCount ()
public org.jmol.smiles.SmilesBond getBond (int)
public void addBond (org.jmol.smiles.SmilesBond)
}
org/jmol/smiles/SmilesBond.class
<Unknown>
package org.jmol.smiles
public org.jmol.smiles.SmilesBond extends java.lang.Object {
public static final int TYPE_UNKOWN
public static final int TYPE_NONE
public static final int TYPE_SINGLE
public static final int TYPE_DOUBLE
public static final int TYPE_TRIPLE
public static final int TYPE_AROMATIC
public static final int TYPE_DIRECTIONAL_1
public static final int TYPE_DIRECTIONAL_2
public static final char CODE_NONE
public static final char CODE_SINGLE
public static final char CODE_DOUBLE
public static final char CODE_TRIPLE
public static final char CODE_AROMATIC
public static final char CODE_DIRECTIONAL_1
public static final char CODE_DIRECTIONAL_2
private org.jmol.smiles.SmilesAtom atom1
private org.jmol.smiles.SmilesAtom atom2
private int bondType
public void <init> (org.jmol.smiles.SmilesAtom, org.jmol.smiles.SmilesAtom, int)
public static int getBondTypeFromCode (char)
public org.jmol.smiles.SmilesAtom getAtom1 ()
public void setAtom1 (org.jmol.smiles.SmilesAtom)
public org.jmol.smiles.SmilesAtom getAtom2 ()
public void setAtom2 (org.jmol.smiles.SmilesAtom)
public int getBondType ()
public void setBondType (int)
}
org/jmol/smiles/SmilesMolecule.class
<Unknown>
package org.jmol.smiles
public org.jmol.smiles.SmilesMolecule extends java.lang.Object {
private org.jmol.smiles.SmilesAtom[] atoms
private int atomsCount
private org.jmol.smiles.SmilesBond[] bonds
private int bondsCount
private static final int INITIAL_ATOMS
private static final int INITIAL_BONDS
public void <init> ()
public org.jmol.smiles.SmilesAtom createAtom ()
public int getAtomsCount ()
public org.jmol.smiles.SmilesAtom getAtom (int)
public org.jmol.smiles.SmilesBond createBond (org.jmol.smiles.SmilesAtom, org.jmol.smiles.SmilesAtom, int)
public int getBondsCount ()
public org.jmol.smiles.SmilesBond getBond (int)
}
org/jmol/smiles/SmilesParser.class
<Unknown>
package org.jmol.smiles
public org.jmol.smiles.SmilesParser extends java.lang.Object {
private org.jmol.smiles.SmilesBond[] ringBonds
public void <init> ()
public org.jmol.smiles.SmilesMolecule parseSmiles (java.lang.String) throws org.jmol.smiles.InvalidSmilesException
private void parseSmiles (org.jmol.smiles.SmilesMolecule, java.lang.String, org.jmol.smiles.SmilesAtom) throws org.jmol.smiles.InvalidSmilesException
private org.jmol.smiles.SmilesAtom parseAtom (org.jmol.smiles.SmilesMolecule, java.lang.String, org.jmol.smiles.SmilesAtom, int, boolean) throws org.jmol.smiles.InvalidSmilesException
private void parseRing (org.jmol.smiles.SmilesMolecule, java.lang.String, org.jmol.smiles.SmilesAtom, int) throws org.jmol.smiles.InvalidSmilesException
}
org/jmol/symmetry/HallInfo$RotationTerm.class
<Unknown>
package org.jmol.symmetry
org.jmol.symmetry.HallInfo$RotationTerm extends java.lang.Object {
String inputCode
String primitiveCode
String lookupCode
String translationString
org.jmol.symmetry.Rotation rotation
org.jmol.symmetry.Translation translation
javax.vecmath.Matrix4f seitzMatrix12ths
boolean isImproper
int order
char axisType
char diagonalReferenceAxis
boolean allPositive
private final org.jmol.symmetry.HallInfo this$0
void <init> (org.jmol.symmetry.HallInfo)
void <init> (org.jmol.symmetry.HallInfo, java.lang.String, int, char)
java.lang.String dumpInfo ()
java.lang.String getXYZ (boolean)
private void getRotationInfo (java.lang.String, int, char)
}
org/jmol/symmetry/HallInfo.class
<Unknown>
package org.jmol.symmetry
org.jmol.symmetry.HallInfo extends java.lang.Object {
String hallSymbol
String primitiveHallSymbol
char latticeCode
String latticeExtension
boolean isCentrosymmetric
int nRotations
org.jmol.symmetry.HallInfo$RotationTerm[] rotationTerms
javax.vecmath.Point3i vector12ths
String vectorCode
void <init> (java.lang.String)
java.lang.String dumpInfo ()
private java.lang.String getLatticeDesignation ()
private java.lang.String extractLatticeInfo (java.lang.String)
private java.lang.String extractVectorInfo (java.lang.String)
private java.lang.String extractRotationInfo (java.lang.String, int, char)
}
org/jmol/symmetry/PointGroup$Operation.class
<Unknown>
package org.jmol.symmetry
org.jmol.symmetry.PointGroup$Operation extends java.lang.Object {
int type
int order
int index
int typeIndex
javax.vecmath.Vector3f normalOrAxis
private final org.jmol.symmetry.PointGroup this$0
void <init> (org.jmol.symmetry.PointGroup)
void <init> (org.jmol.symmetry.PointGroup, javax.vecmath.Vector3f, int)
void <init> (org.jmol.symmetry.PointGroup, javax.vecmath.Vector3f)
java.lang.String getLabel ()
}
org/jmol/symmetry/PointGroup.class
<Unknown>
package org.jmol.symmetry
org.jmol.symmetry.PointGroup extends java.lang.Object {
private static final int[] axesMaxN
private static final int[] nUnique
private static final int s3
private static final int s4
private static final int s5
private static final int s6
private static final int s8
private static final int s10
private static final int s12
private static final int firstProper
private static final int c2
private static final int c3
private static final int c4
private static final int c5
private static final int c6
private static final int c8
private static final int maxAxis
private int[] nAxes
private org.jmol.symmetry.PointGroup$Operation[][] axes
private int nAtoms
private float radius
private float distanceTolerance
private float linearTolerance
private float cosTolerance
private String name
private org.jmol.symmetry.PointGroup$Operation principalAxis
private org.jmol.symmetry.PointGroup$Operation principalPlane
private final javax.vecmath.Vector3f vTemp
private int centerAtomIndex
private boolean haveInversionCenter
private final javax.vecmath.Point3f center
private javax.vecmath.Point3f[] atoms
private int[] elements
private static final int ATOM_COUNT_MAX
int maxElement
int[] eCounts
static final int OPERATION_PLANE
static final int OPERATION_PROPER_AXIS
static final int OPERATION_IMPROPER_AXIS
static final int OPERATION_INVERSION_CENTER
static final String[] typeNames
int nOps
String drawInfo
String drawType
int drawIndex
java.util.Hashtable info
String textInfo
java.lang.String getName ()
static org.jmol.symmetry.PointGroup getPointGroup (org.jmol.symmetry.PointGroup, org.jmol.modelset.Atom[], java.util.BitSet, boolean, float, float)
private void <init> ()
private boolean isEqual (org.jmol.symmetry.PointGroup)
private boolean set (org.jmol.symmetry.PointGroup, org.jmol.modelset.Atom[], java.util.BitSet, boolean, float, float)
private org.jmol.symmetry.PointGroup$Operation setPrincipalAxis (int, int)
private org.jmol.symmetry.PointGroup$Operation setPrincipalPlane (int, int)
private boolean getAtomsAndElements (org.jmol.modelset.Atom[], java.util.BitSet)
private void findInversionCenter ()
private boolean checkOperation (org.jmol.util.Quaternion, javax.vecmath.Point3f, int)
private boolean isLinear (javax.vecmath.Point3f[])
private boolean isParallel (javax.vecmath.Vector3f, javax.vecmath.Vector3f)
private boolean isPerpendicular (javax.vecmath.Vector3f, javax.vecmath.Vector3f)
private void getElementCounts ()
private int findCAxes ()
private void getAllAxes (javax.vecmath.Vector3f)
private int getHighestOrder ()
private boolean checkAxisOrder (int, javax.vecmath.Vector3f, javax.vecmath.Point3f)
private void addAxis (int, javax.vecmath.Vector3f)
private boolean haveAxis (int, javax.vecmath.Vector3f)
private int findPlanes ()
private int getPlane (int, javax.vecmath.Vector3f, javax.vecmath.Point3f)
private void findAdditionalAxes (int)
java.lang.Object getInfo (int, boolean, boolean, java.lang.String, int, float)
boolean isDrawType (java.lang.String, int)
static void <clinit> ()
}
org/jmol/symmetry/Rotation.class
<Unknown>
package org.jmol.symmetry
org.jmol.symmetry.Rotation extends java.lang.Object {
String rotCode
javax.vecmath.Matrix4f seitzMatrix
javax.vecmath.Matrix4f seitzMatrixInv
static final org.jmol.symmetry.Rotation[] hallRotationTerms
void <init> ()
private void <init> (java.lang.String, java.lang.String)
static final org.jmol.symmetry.Rotation lookup (java.lang.String)
static void <clinit> ()
}
org/jmol/symmetry/SpaceGroup.class
<Unknown>
package org.jmol.symmetry
org.jmol.symmetry.SpaceGroup extends java.lang.Object {
int index
String hallSymbol
String hmSymbol
String hmSymbolFull
String hmSymbolExt
String hmSymbolAbbr
String hmSymbolAlternative
String hmSymbolAbbrShort
char ambiguityType
char uniqueAxis
char axisChoice
String intlTableNumber
String intlTableNumberFull
String intlTableNumberExt
org.jmol.symmetry.HallInfo hallInfo
int latticeParameter
char latticeCode
org.jmol.symmetry.SymmetryOperation[] operations
int operationCount
boolean doNormalize
org.jmol.symmetry.SymmetryOperation[] finalOperations
private static String[] canonicalSeitzList
java.util.Hashtable xyzList
String line
String term
private static int sgIndex
private static final org.jmol.symmetry.SpaceGroup[] spaceGroupDefinitions
void <init> (boolean)
private void <init> (java.lang.String)
static org.jmol.symmetry.SpaceGroup createSpaceGroup (int, java.lang.String, float[], boolean)
static int determineSpaceGroupIndex (java.lang.String)
static org.jmol.symmetry.SpaceGroup determineSpaceGroup (java.lang.String, float, float, float, float, float, float, int)
int addSymmetry (java.lang.String)
void setFinalOperations (javax.vecmath.Point3f[], int, int, boolean)
int getOperationCount ()
javax.vecmath.Matrix4f getOperation (int)
java.lang.String getXyz (int, boolean)
void newPoint (int, javax.vecmath.Point3f, javax.vecmath.Point3f, int, int, int)
java.lang.Object rotateEllipsoid (int, javax.vecmath.Point3f, javax.vecmath.Vector3f[], org.jmol.symmetry.UnitCell, javax.vecmath.Point3f, javax.vecmath.Point3f)
static java.lang.String getInfo (java.lang.String, org.jmol.api.SymmetryInterface)
java.lang.String dumpInfo (org.jmol.api.SymmetryInterface)
java.lang.String getName ()
java.lang.String getLatticeDesignation ()
void setLattice (int)
private void buildSpaceGroup (java.lang.String)
private java.lang.Object dumpCanonicalSeitzList ()
private static final java.lang.String dumpAll ()
private static final java.lang.String dumpAllSeitz ()
private void setLattice (char, boolean)
private static final org.jmol.symmetry.SpaceGroup createSpaceGroup (java.lang.String, boolean)
private static final org.jmol.symmetry.SpaceGroup determineSpaceGroup (java.lang.String)
private static final org.jmol.symmetry.SpaceGroup determineSpaceGroup (java.lang.String, org.jmol.symmetry.SpaceGroup)
private static final org.jmol.symmetry.SpaceGroup determineSpaceGroup (java.lang.String, float[])
private static final int determineSpaceGroupIndex (java.lang.String, float, float, float, float, float, float, int)
private static final char determineUniqueAxis (float, float, float, float, float, float)
private int addOperation (java.lang.String)
private void generateOperatorsFromXyzInfo (java.lang.String)
private void generateAllOperators (org.jmol.symmetry.HallInfo)
private void addSymmetry (java.lang.String, javax.vecmath.Matrix4f)
private java.lang.String extractLine ()
private java.lang.String extractTerm (char)
static void <clinit> ()
}
org/jmol/symmetry/Symmetry.class
<Unknown>
package org.jmol.symmetry
public org.jmol.symmetry.Symmetry extends java.lang.Object implements org.jmol.api.SymmetryInterface {
private org.jmol.symmetry.PointGroup pointGroup
private org.jmol.symmetry.SpaceGroup spaceGroup
private org.jmol.symmetry.SymmetryInfo symmetryInfo
private org.jmol.symmetry.UnitCell unitCell
public void <init> ()
public org.jmol.api.SymmetryInterface setPointGroup (org.jmol.api.SymmetryInterface, org.jmol.modelset.Atom[], java.util.BitSet, boolean, float, float)
public java.lang.String getPointGroupName ()
public java.lang.Object getPointGroupInfo (int, boolean, boolean, java.lang.String, int, float)
public void setSpaceGroup (boolean)
public int addSpaceGroupOperation (java.lang.String)
public void setLattice (int)
public java.lang.String getSpaceGroupName ()
public java.lang.Object getSpaceGroup ()
public void setSpaceGroup (org.jmol.api.SymmetryInterface)
public boolean createSpaceGroup (int, java.lang.String, float[], boolean)
public boolean haveSpaceGroup ()
public int determineSpaceGroupIndex (java.lang.String)
public java.lang.String getSpaceGroupInfo (java.lang.String, org.jmol.api.SymmetryInterface)
public java.lang.Object getLatticeDesignation ()
public void setFinalOperations (javax.vecmath.Point3f[], int, int, boolean)
public int getSpaceGroupOperationCount ()
public javax.vecmath.Matrix4f getSpaceGroupOperation (int)
public java.lang.String getSpaceGroupXyz (int, boolean)
public void newSpaceGroupPoint (int, javax.vecmath.Point3f, javax.vecmath.Point3f, int, int, int)
public java.lang.Object rotateEllipsoid (int, javax.vecmath.Point3f, javax.vecmath.Vector3f[], javax.vecmath.Point3f, javax.vecmath.Point3f)
public boolean haveUnitCell ()
public java.lang.String getUnitsymmetryInfo ()
public void setUnitCell (float[])
public void toCartesian (javax.vecmath.Point3f)
public java.lang.Object[] getEllipsoid (float[])
public javax.vecmath.Point3f ijkToPoint3f (int)
public void toFractional (javax.vecmath.Point3f)
public javax.vecmath.Point3f[] getUnitCellVertices ()
public javax.vecmath.Point3f getCartesianOffset ()
public float[] getNotionalUnitCell ()
public void toUnitCell (javax.vecmath.Point3f, javax.vecmath.Point3f)
public void setUnitCellOffset (javax.vecmath.Point3f)
public void setOffset (int)
public javax.vecmath.Point3f getFractionalOffset ()
public float getUnitsymmetryInfo (int)
public int getModelIndex ()
public void setModelIndex (int)
public boolean getCoordinatesAreFractional ()
public int[] getCellRange ()
public java.lang.String getSymmetryInfoString ()
public java.lang.String[] getSymmetryOperations ()
public boolean isPeriodic ()
public void setSymmetryInfo (int, java.util.Hashtable)
public float getUnitCellInfo (int)
public java.lang.String getUnitCellInfo ()
public java.lang.Object[] getSymmetryOperationDescription (int, org.jmol.api.SymmetryInterface, javax.vecmath.Point3f, java.lang.String)
}
org/jmol/symmetry/SymmetryInfo.class
<Unknown>
package org.jmol.symmetry
org.jmol.symmetry.SymmetryInfo extends java.lang.Object {
boolean coordinatesAreFractional
boolean isMultiCell
String spaceGroup
String[] symmetryOperations
String symmetryInfoString
int modelIndex
int[] cellRange
private javax.vecmath.Point3f periodicOriginXyz
boolean isPeriodic ()
void <init> ()
float[] setSymmetryInfo (int, java.util.Hashtable)
}
org/jmol/symmetry/SymmetryOperation.class
<Unknown>
package org.jmol.symmetry
org.jmol.symmetry.SymmetryOperation extends javax.vecmath.Matrix4f {
String xyzOriginal
String xyz
boolean doNormalize
boolean isFinalized
private javax.vecmath.Point4f temp
private static final String[] twelfths
javax.vecmath.Point3f atomTest
void <init> ()
void <init> (boolean)
void <init> (org.jmol.symmetry.SymmetryOperation, javax.vecmath.Point3f[], int, int, boolean)
void doFinalize ()
java.lang.String getXyz (boolean)
void newPoint (javax.vecmath.Point3f, javax.vecmath.Point3f, int, int, int)
java.lang.String dumpInfo ()
static final java.lang.String dumpSeitz (javax.vecmath.Matrix4f)
static final java.lang.String dumpCanonicalSeitz (javax.vecmath.Matrix4f)
boolean setMatrixFromXYZ (java.lang.String)
private float normalizeTwelfths (float)
static final java.lang.String getXYZFromMatrix (javax.vecmath.Matrix4f, boolean, boolean, boolean)
private static final java.lang.String twelfthsOf (float)
private static final java.lang.String xyzFraction (float, boolean, boolean)
private void setOffset (javax.vecmath.Point3f[], int, int)
private void transformCartesian (org.jmol.symmetry.UnitCell, javax.vecmath.Point3f)
javax.vecmath.Vector3f[] rotateEllipsoid (javax.vecmath.Point3f, javax.vecmath.Vector3f[], org.jmol.symmetry.UnitCell, javax.vecmath.Point3f, javax.vecmath.Point3f)
public java.lang.Object[] getProduct (org.jmol.symmetry.SymmetryOperation, org.jmol.api.SymmetryInterface, javax.vecmath.Point3f, java.lang.String)
public java.lang.Object[] getDescription (org.jmol.api.SymmetryInterface, javax.vecmath.Point3f, java.lang.String)
private static java.lang.Object[] getDescription (javax.vecmath.Matrix4f, java.lang.String, org.jmol.api.SymmetryInterface, javax.vecmath.Point3f, java.lang.String)
private static void drawLine (java.lang.StringBuffer, java.lang.String, float, javax.vecmath.Point3f, javax.vecmath.Point3f, java.lang.String)
private static java.lang.String fcoord (javax.vecmath.Tuple3f)
private static java.lang.String fc (float)
private static javax.vecmath.Tuple3f approx (javax.vecmath.Tuple3f)
private static float approx (float)
private static float approx (float, float)
public static void normalizeTranslation (javax.vecmath.Matrix4f)
static void <clinit> ()
}
org/jmol/symmetry/Translation.class
<Unknown>
package org.jmol.symmetry
org.jmol.symmetry.Translation extends java.lang.Object {
char translationCode
int rotationOrder
int rotationShift12ths
javax.vecmath.Point3i vectorShift12ths
static final String[] latticeTranslationData
static final int nLatticeTypes
static final org.jmol.symmetry.Translation[] hallTranslationTerms
void <init> ()
void <init> (char, int)
private void <init> (char, int, javax.vecmath.Point3i)
private void <init> (char, int, int)
static final java.lang.String getHallLatticeEquivalent (int)
static final int getLatticeIndex (char)
static final char getLatticeCode (int)
static final java.lang.String getLatticeDesignation (int)
static final java.lang.String getLatticeDesignation (char, boolean)
static final java.lang.String getLatticeExtension (char, boolean)
static void <clinit> ()
}
org/jmol/symmetry/UnitCell$Data.class
<Unknown>
package org.jmol.symmetry
org.jmol.symmetry.UnitCell$Data extends java.lang.Object {
double cosAlpha
double sinAlpha
double cosBeta
double sinBeta
double cosGamma
double sinGamma
double volume
double cA_
double cB_
double a_
double b_
double c_
static final double twoP2
private final org.jmol.symmetry.UnitCell this$0
void <init> (org.jmol.symmetry.UnitCell)
java.lang.Object[] getEllipsoid (float[])
}
org/jmol/symmetry/UnitCell.class
<Unknown>
package org.jmol.symmetry
org.jmol.symmetry.UnitCell extends java.lang.Object {
static final float toRadians
static final javax.vecmath.Point3f[] unitCubePoints
float a
float b
float c
float alpha
float beta
float gamma
boolean isPrimitive
float[] notionalUnitcell
private javax.vecmath.Matrix4f matrixCartesianToFractional
private javax.vecmath.Matrix4f matrixFractionalToCartesian
private javax.vecmath.Point3f[] vertices
private javax.vecmath.Point3f cartesianOffset
private javax.vecmath.Point3f fractionalOffset
private org.jmol.symmetry.UnitCell$Data data
void <init> (float[])
final void toCartesian (javax.vecmath.Point3f)
final void toFractional (javax.vecmath.Point3f)
private final void toFractionalUnitCell (javax.vecmath.Point3f)
private static float toFractional (float)
final void toUnitCell (javax.vecmath.Point3f, javax.vecmath.Point3f)
void setOffset (javax.vecmath.Point3f)
void setOffset (int)
static javax.vecmath.Point3f ijkToPoint3f (int)
final java.lang.String dumpInfo (boolean)
javax.vecmath.Point3f[] getVertices ()
javax.vecmath.Point3f getCartesianOffset ()
javax.vecmath.Point3f getFractionalOffset ()
float[] getNotionalUnitCell ()
float getInfo (int)
private void setUnitCell (float[])
java.lang.Object[] getEllipsoid (float[])
private void constructFractionalMatrices ()
private void calcUnitcellVertices ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/ar/Messages_ar$1.class
Messages_ar.java
package org.jmol.translation.JmolApplet.ar
org.jmol.translation.JmolApplet.ar.Messages_ar$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.ar.Messages_ar this$0
void <init> (org.jmol.translation.JmolApplet.ar.Messages_ar)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/ar/Messages_ar.class
Messages_ar.java
package org.jmol.translation.JmolApplet.ar
public org.jmol.translation.JmolApplet.ar.Messages_ar extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/ca/Messages_ca$1.class
Messages_ca.java
package org.jmol.translation.JmolApplet.ca
org.jmol.translation.JmolApplet.ca.Messages_ca$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.ca.Messages_ca this$0
void <init> (org.jmol.translation.JmolApplet.ca.Messages_ca)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/ca/Messages_ca.class
Messages_ca.java
package org.jmol.translation.JmolApplet.ca
public org.jmol.translation.JmolApplet.ca.Messages_ca extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/cs/Messages_cs$1.class
Messages_cs.java
package org.jmol.translation.JmolApplet.cs
org.jmol.translation.JmolApplet.cs.Messages_cs$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.cs.Messages_cs this$0
void <init> (org.jmol.translation.JmolApplet.cs.Messages_cs)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/cs/Messages_cs.class
Messages_cs.java
package org.jmol.translation.JmolApplet.cs
public org.jmol.translation.JmolApplet.cs.Messages_cs extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/da/Messages_da$1.class
Messages_da.java
package org.jmol.translation.JmolApplet.da
org.jmol.translation.JmolApplet.da.Messages_da$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.da.Messages_da this$0
void <init> (org.jmol.translation.JmolApplet.da.Messages_da)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/da/Messages_da.class
Messages_da.java
package org.jmol.translation.JmolApplet.da
public org.jmol.translation.JmolApplet.da.Messages_da extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/de/Messages_de$1.class
Messages_de.java
package org.jmol.translation.JmolApplet.de
org.jmol.translation.JmolApplet.de.Messages_de$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.de.Messages_de this$0
void <init> (org.jmol.translation.JmolApplet.de.Messages_de)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/de/Messages_de.class
Messages_de.java
package org.jmol.translation.JmolApplet.de
public org.jmol.translation.JmolApplet.de.Messages_de extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/el/Messages_el$1.class
Messages_el.java
package org.jmol.translation.JmolApplet.el
org.jmol.translation.JmolApplet.el.Messages_el$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.el.Messages_el this$0
void <init> (org.jmol.translation.JmolApplet.el.Messages_el)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/el/Messages_el.class
Messages_el.java
package org.jmol.translation.JmolApplet.el
public org.jmol.translation.JmolApplet.el.Messages_el extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/en_GB/Messages_en_GB$1.class
Messages_en_GB.java
package org.jmol.translation.JmolApplet.en_GB
org.jmol.translation.JmolApplet.en_GB.Messages_en_GB$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.en_GB.Messages_en_GB this$0
void <init> (org.jmol.translation.JmolApplet.en_GB.Messages_en_GB)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/en_GB/Messages_en_GB.class
Messages_en_GB.java
package org.jmol.translation.JmolApplet.en_GB
public org.jmol.translation.JmolApplet.en_GB.Messages_en_GB extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/es/Messages_es$1.class
Messages_es.java
package org.jmol.translation.JmolApplet.es
org.jmol.translation.JmolApplet.es.Messages_es$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.es.Messages_es this$0
void <init> (org.jmol.translation.JmolApplet.es.Messages_es)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/es/Messages_es.class
Messages_es.java
package org.jmol.translation.JmolApplet.es
public org.jmol.translation.JmolApplet.es.Messages_es extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/et/Messages_et$1.class
Messages_et.java
package org.jmol.translation.JmolApplet.et
org.jmol.translation.JmolApplet.et.Messages_et$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.et.Messages_et this$0
void <init> (org.jmol.translation.JmolApplet.et.Messages_et)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/et/Messages_et.class
Messages_et.java
package org.jmol.translation.JmolApplet.et
public org.jmol.translation.JmolApplet.et.Messages_et extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/fr/Messages_fr$1.class
Messages_fr.java
package org.jmol.translation.JmolApplet.fr
org.jmol.translation.JmolApplet.fr.Messages_fr$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.fr.Messages_fr this$0
void <init> (org.jmol.translation.JmolApplet.fr.Messages_fr)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/fr/Messages_fr.class
Messages_fr.java
package org.jmol.translation.JmolApplet.fr
public org.jmol.translation.JmolApplet.fr.Messages_fr extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/hu/Messages_hu$1.class
Messages_hu.java
package org.jmol.translation.JmolApplet.hu
org.jmol.translation.JmolApplet.hu.Messages_hu$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.hu.Messages_hu this$0
void <init> (org.jmol.translation.JmolApplet.hu.Messages_hu)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/hu/Messages_hu.class
Messages_hu.java
package org.jmol.translation.JmolApplet.hu
public org.jmol.translation.JmolApplet.hu.Messages_hu extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/it/Messages_it$1.class
Messages_it.java
package org.jmol.translation.JmolApplet.it
org.jmol.translation.JmolApplet.it.Messages_it$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.it.Messages_it this$0
void <init> (org.jmol.translation.JmolApplet.it.Messages_it)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/it/Messages_it.class
Messages_it.java
package org.jmol.translation.JmolApplet.it
public org.jmol.translation.JmolApplet.it.Messages_it extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/ko/Messages_ko$1.class
Messages_ko.java
package org.jmol.translation.JmolApplet.ko
org.jmol.translation.JmolApplet.ko.Messages_ko$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.ko.Messages_ko this$0
void <init> (org.jmol.translation.JmolApplet.ko.Messages_ko)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/ko/Messages_ko.class
Messages_ko.java
package org.jmol.translation.JmolApplet.ko
public org.jmol.translation.JmolApplet.ko.Messages_ko extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/nb/Messages_nb$1.class
Messages_nb.java
package org.jmol.translation.JmolApplet.nb
org.jmol.translation.JmolApplet.nb.Messages_nb$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.nb.Messages_nb this$0
void <init> (org.jmol.translation.JmolApplet.nb.Messages_nb)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/nb/Messages_nb.class
Messages_nb.java
package org.jmol.translation.JmolApplet.nb
public org.jmol.translation.JmolApplet.nb.Messages_nb extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/nl/Messages_nl$1.class
Messages_nl.java
package org.jmol.translation.JmolApplet.nl
org.jmol.translation.JmolApplet.nl.Messages_nl$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.nl.Messages_nl this$0
void <init> (org.jmol.translation.JmolApplet.nl.Messages_nl)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/nl/Messages_nl.class
Messages_nl.java
package org.jmol.translation.JmolApplet.nl
public org.jmol.translation.JmolApplet.nl.Messages_nl extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/pl/Messages_pl$1.class
Messages_pl.java
package org.jmol.translation.JmolApplet.pl
org.jmol.translation.JmolApplet.pl.Messages_pl$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.pl.Messages_pl this$0
void <init> (org.jmol.translation.JmolApplet.pl.Messages_pl)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/pl/Messages_pl.class
Messages_pl.java
package org.jmol.translation.JmolApplet.pl
public org.jmol.translation.JmolApplet.pl.Messages_pl extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/pt/Messages_pt$1.class
Messages_pt.java
package org.jmol.translation.JmolApplet.pt
org.jmol.translation.JmolApplet.pt.Messages_pt$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.pt.Messages_pt this$0
void <init> (org.jmol.translation.JmolApplet.pt.Messages_pt)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/pt/Messages_pt.class
Messages_pt.java
package org.jmol.translation.JmolApplet.pt
public org.jmol.translation.JmolApplet.pt.Messages_pt extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/pt_BR/Messages_pt_BR$1.class
Messages_pt_BR.java
package org.jmol.translation.JmolApplet.pt_BR
org.jmol.translation.JmolApplet.pt_BR.Messages_pt_BR$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.pt_BR.Messages_pt_BR this$0
void <init> (org.jmol.translation.JmolApplet.pt_BR.Messages_pt_BR)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/pt_BR/Messages_pt_BR.class
Messages_pt_BR.java
package org.jmol.translation.JmolApplet.pt_BR
public org.jmol.translation.JmolApplet.pt_BR.Messages_pt_BR extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/sl/Messages_sl$1.class
Messages_sl.java
package org.jmol.translation.JmolApplet.sl
org.jmol.translation.JmolApplet.sl.Messages_sl$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.sl.Messages_sl this$0
void <init> (org.jmol.translation.JmolApplet.sl.Messages_sl)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/sl/Messages_sl.class
Messages_sl.java
package org.jmol.translation.JmolApplet.sl
public org.jmol.translation.JmolApplet.sl.Messages_sl extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/sv/Messages_sv$1.class
Messages_sv.java
package org.jmol.translation.JmolApplet.sv
org.jmol.translation.JmolApplet.sv.Messages_sv$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.sv.Messages_sv this$0
void <init> (org.jmol.translation.JmolApplet.sv.Messages_sv)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/sv/Messages_sv.class
Messages_sv.java
package org.jmol.translation.JmolApplet.sv
public org.jmol.translation.JmolApplet.sv.Messages_sv extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/tr/Messages_tr$1.class
Messages_tr.java
package org.jmol.translation.JmolApplet.tr
org.jmol.translation.JmolApplet.tr.Messages_tr$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.tr.Messages_tr this$0
void <init> (org.jmol.translation.JmolApplet.tr.Messages_tr)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/tr/Messages_tr.class
Messages_tr.java
package org.jmol.translation.JmolApplet.tr
public org.jmol.translation.JmolApplet.tr.Messages_tr extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/uk/Messages_uk$1.class
Messages_uk.java
package org.jmol.translation.JmolApplet.uk
org.jmol.translation.JmolApplet.uk.Messages_uk$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.uk.Messages_uk this$0
void <init> (org.jmol.translation.JmolApplet.uk.Messages_uk)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/uk/Messages_uk.class
Messages_uk.java
package org.jmol.translation.JmolApplet.uk
public org.jmol.translation.JmolApplet.uk.Messages_uk extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/zh_CN/Messages_zh_CN$1.class
Messages_zh_CN.java
package org.jmol.translation.JmolApplet.zh_CN
org.jmol.translation.JmolApplet.zh_CN.Messages_zh_CN$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.zh_CN.Messages_zh_CN this$0
void <init> (org.jmol.translation.JmolApplet.zh_CN.Messages_zh_CN)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/zh_CN/Messages_zh_CN.class
Messages_zh_CN.java
package org.jmol.translation.JmolApplet.zh_CN
public org.jmol.translation.JmolApplet.zh_CN.Messages_zh_CN extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/translation/JmolApplet/zh_TW/Messages_zh_TW$1.class
Messages_zh_TW.java
package org.jmol.translation.JmolApplet.zh_TW
org.jmol.translation.JmolApplet.zh_TW.Messages_zh_TW$1 extends java.lang.Object implements java.util.Enumeration {
private int idx
private final org.jmol.translation.JmolApplet.zh_TW.Messages_zh_TW this$0
void <init> (org.jmol.translation.JmolApplet.zh_TW.Messages_zh_TW)
public boolean hasMoreElements ()
public java.lang.Object nextElement ()
}
org/jmol/translation/JmolApplet/zh_TW/Messages_zh_TW.class
Messages_zh_TW.java
package org.jmol.translation.JmolApplet.zh_TW
public org.jmol.translation.JmolApplet.zh_TW.Messages_zh_TW extends java.util.ResourceBundle {
private static final String[] table
public void <init> ()
public java.lang.Object handleGetObject (java.lang.String) throws java.util.MissingResourceException
public java.util.Enumeration getKeys ()
public java.util.ResourceBundle getParent ()
static java.lang.String[] access$000 ()
static void <clinit> ()
}
org/jmol/util/ArrayUtil.class
<Unknown>
package org.jmol.util
public final org.jmol.util.ArrayUtil extends java.lang.Object {
public void <init> ()
public static java.lang.Object ensureLength (java.lang.Object, int)
public static java.lang.String[] ensureLength (java.lang.String[], int)
public static float[] ensureLength (float[], int)
public static int[] ensureLength (int[], int)
public static short[] ensureLength (short[], int)
public static byte[] ensureLength (byte[], int)
public static java.lang.Object doubleLength (java.lang.Object)
public static java.lang.String[] doubleLength (java.lang.String[])
public static float[] doubleLength (float[])
public static int[] doubleLength (int[])
public static short[] doubleLength (short[])
public static byte[] doubleLength (byte[])
public static boolean[] doubleLength (boolean[])
public static java.lang.Object setLength (java.lang.Object, int)
public static java.lang.Object deleteElements (java.lang.Object, int, int)
public static java.lang.String[] setLength (java.lang.String[], int)
public static float[] setLength (float[], int)
public static int[] setLength (int[], int)
public static int[] arrayCopy (int[], int, int, boolean)
public static short[] setLength (short[], int)
public static byte[] setLength (byte[], int)
public static boolean[] setLength (boolean[], int)
public static void swap (short[], int, int)
public static void swap (int[], int, int)
public static void swap (float[], int, int)
public static java.lang.String dumpArray (java.lang.String, float[][], int, int, int, int)
public static java.lang.String dumpIntArray (int[], int)
public static java.lang.Object getMinMax (java.lang.Object, int)
public static java.lang.Object sortOrReverse (java.lang.Object, int, boolean)
}
org/jmol/util/Base64.class
<Unknown>
package org.jmol.util
public org.jmol.util.Base64 extends java.lang.Object {
private static String base64
private static int[] decode64
public void <init> ()
public static void write (byte[], java.io.OutputStream) throws java.io.IOException
public static byte[] getBytes64 (byte[])
public static java.lang.StringBuffer getBase64 (java.lang.StringBuffer)
public static java.lang.StringBuffer getBase64 (byte[])
public static byte[] decodeBase64 (java.lang.String)
private static byte[] toBytes (java.lang.StringBuffer)
static void <clinit> ()
}
org/jmol/util/BinaryDocument.class
<Unknown>
package org.jmol.util
public org.jmol.util.BinaryDocument extends java.lang.Object {
protected java.io.DataInputStream stream
protected boolean isRandom
protected boolean isBigEndian
long nBytes
public void <init> ()
public void close ()
public void setStream (java.io.BufferedInputStream, boolean)
public void setStream (java.io.DataInputStream)
public void setRandom (boolean)
public byte readByte () throws java.lang.Exception
public int readByteArray (byte[]) throws java.io.IOException
public void readByteArray (byte[], int, int) throws java.lang.Exception
public java.lang.String readString (int) throws java.lang.Exception
public short readShort () throws java.lang.Exception
public int readInt () throws java.lang.Exception
public int readUnsignedShort () throws java.lang.Exception
public long readLong () throws java.lang.Exception
public float readFloat () throws java.lang.Exception
public double readDouble () throws java.lang.Exception
private int readLEInt () throws java.lang.Exception
private long readLELong () throws java.lang.Exception
public void seek (long)
public long getPosition ()
}
org/jmol/util/BitSetUtil.class
<Unknown>
package org.jmol.util
public final org.jmol.util.BitSetUtil extends java.lang.Object {
private static final java.util.BitSet bsNull
public void <init> ()
public static int length (java.util.BitSet)
public static int firstSetBit (java.util.BitSet)
public static int cardinalityOf (java.util.BitSet)
public static java.util.BitSet setAll (int)
public static void andNot (java.util.BitSet, java.util.BitSet)
public static java.util.BitSet copy (java.util.BitSet)
public static void copy (java.util.BitSet, java.util.BitSet)
public static void clear (java.util.BitSet)
public static java.util.BitSet copyInvert (java.util.BitSet, int)
public static java.util.BitSet invertInPlace (java.util.BitSet, int)
public static java.util.BitSet toggleInPlace (java.util.BitSet, java.util.BitSet, int)
public static boolean compareBits (java.util.BitSet, java.util.BitSet)
public static boolean haveCommon (java.util.BitSet, java.util.BitSet)
public static java.util.BitSet deleteBits (java.util.BitSet, java.util.BitSet)
static void <clinit> ()
}
org/jmol/util/CifDataReader.class
<Unknown>
package org.jmol.util
public org.jmol.util.CifDataReader extends java.lang.Object {
private org.jmol.api.JmolLineReader reader
private java.io.BufferedReader br
private String line
public String str
public int ich
public int cch
public boolean wasUnQuoted
public String strPeeked
public int ichPeeked
public int fieldCount
public String[] loopData
java.util.Hashtable data
java.util.Hashtable allData
public void <init> (org.jmol.api.JmolLineReader)
public void <init> (java.io.BufferedReader)
public static java.util.Hashtable readCifData (java.io.BufferedReader)
private java.util.Hashtable getAllCifData ()
public java.lang.String readLine ()
public boolean getData () throws java.lang.Exception
public java.lang.String getNextToken () throws java.lang.Exception
private void setString (java.lang.String)
private java.lang.String setStringNextLine () throws java.lang.Exception
private boolean hasMoreTokens ()
private java.lang.String nextToken ()
public java.lang.String getNextDataToken () throws java.lang.Exception
public java.lang.String peekToken () throws java.lang.Exception
public java.lang.String getTokenPeeked ()
public java.lang.String fullTrim (java.lang.String)
private void getCifLoopData () throws java.lang.Exception
}
org/jmol/util/ColorEncoder.class
<Unknown>
package org.jmol.util
public org.jmol.util.ColorEncoder extends java.lang.Object {
public static final String BYELEMENT_PREFIX
public static final String BYRESIDUE_PREFIX
private static final String BYELEMENT_JMOL
private static final String BYELEMENT_RASMOL
private static final String BYRESIDUE_SHAPELY
private static final String BYRESIDUE_AMINO
private static final String[] colorSchemes
public static final int ROYGB
public static final int BGYOR
public static final int RWB
public static final int BWR
public static final int LOW
public static final int HIGH
public static final int JMOL
public static final int RASMOL
public static final int SHAPELY
public static final int AMINO
public static final int COLOR_RGB
public static final int USER
public static final int RESU
private int palette
private static int[] userScale
private static int[] thisScale
private static String thisName
private static boolean isColorIndex
private static java.util.Hashtable schemes
private static int[] rasmolScale
private static int[] argbsCpk
private static int[] argbsRoygb
private static int[] argbsRwb
private static int[] argbsShapely
private static int[] argbsAmino
private static int ihalf
private static final int GRAY
public void <init> ()
private static final int schemeIndex (java.lang.String)
public static synchronized int[] getRasmolScale (boolean)
public static synchronized int makeColorScheme (java.lang.String, int[], boolean)
private static void checkColorIndex ()
private static java.lang.String fixName (java.lang.String)
public int setColorScheme (java.lang.String)
public java.lang.String getColorSchemeName ()
public static final java.lang.String getColorSchemeName (int)
public static final int getColorScheme (java.lang.String, boolean)
private static final int getColorScheme (java.lang.String, boolean, boolean)
public static final void setUserScale (int[])
public static final java.lang.String getState (java.lang.StringBuffer)
public static java.lang.String getColorSchemeList (int[])
public static final int[] getColorSchemeArray (int)
public final int getArgbFromPalette (float, float, float)
public static final int getArgbFromPalette (float, float, float, int)
public static final short getColorIndexFromPalette (float, float, float, int)
public static final short getColorIndex (int)
public static final int quantize (float, float, float, int)
public static final int colorIndex (int, int)
public short getColorIndexFromPalette (float, float, float)
static void <clinit> ()
}
org/jmol/util/CommandHistory.class
<Unknown>
package org.jmol.util
public final org.jmol.util.CommandHistory extends java.lang.Object {
public static final String ERROR_FLAG
public static final String NOHISTORYLINE_FLAG
public static final String NOHISTORYATALL_FLAG
static final int DEFAULT_MAX_SIZE
private java.util.Vector commandList
private int maxSize
private int nextCommand
private int cursorPos
boolean isOn
public void <init> ()
public void <init> (int)
public void clear ()
public void reset (int)
public void setMaxSize (int)
public java.lang.String getCommandUp ()
public java.lang.String getCommandDown ()
private java.lang.String getCommand ()
public void addCommand (java.lang.String)
public java.lang.String getSetHistory (int)
public java.lang.String removeCommand ()
public java.lang.String removeCommand (int)
private void addCommandLine (java.lang.String)
}
org/jmol/util/CompoundDocument$CmpDocDirectoryEntry.class
<Unknown>
package org.jmol.util
org.jmol.util.CompoundDocument$CmpDocDirectoryEntry extends java.lang.Object {
byte[] unicodeName
short nBytesUnicodeName
byte entryType
byte[] uniqueID
byte[] userflags
int SIDfirstSector
int lenStream
byte[] unused
String entryName
boolean isStandard
boolean isEmpty
private final org.jmol.util.CompoundDocument this$0
void <init> (org.jmol.util.CompoundDocument)
final boolean readData ()
}
org/jmol/util/CompoundDocument$CmpDocHeader.class
<Unknown>
package org.jmol.util
org.jmol.util.CompoundDocument$CmpDocHeader extends java.lang.Object {
byte[] magicNumbers
byte[] uniqueID
byte revNumber
byte verNumber
short sectorPower
short shortSectorPower
byte[] unused
int nSATsectors
int SID_DIR_start
byte[] unused2
int minBytesStandardStream
int SID_SSAT_start
int SID_MSAT_next
int nAdditionalMATsectors
int[] MSAT0
private final org.jmol.util.CompoundDocument this$0
void <init> (org.jmol.util.CompoundDocument)
final boolean readData ()
}
org/jmol/util/CompoundDocument.class
<Unknown>
package org.jmol.util
public org.jmol.util.CompoundDocument extends org.jmol.util.BinaryDocument {
org.jmol.util.CompoundDocument$CmpDocHeader header
java.util.Vector directory
org.jmol.util.CompoundDocument$CmpDocDirectoryEntry rootEntry
int[] SAT
int[] SSAT
int sectorSize
int shortSectorSize
int nShortSectorsPerStandardSector
int nIntPerSector
int nDirEntriesperSector
StringBuffer data
public void <init> (java.io.BufferedInputStream)
public static boolean isCompoundDocument (java.io.InputStream) throws java.lang.Exception
public static boolean isCompoundDocument (byte[])
public java.util.Vector getDirectory ()
public java.lang.String getDirectoryListing (java.lang.String)
public java.lang.StringBuffer getAllData ()
public void getAllData (java.lang.String, java.lang.String, java.util.Hashtable)
public java.lang.StringBuffer getAllData (java.lang.String)
public java.lang.StringBuffer getFileAsString (java.lang.String)
private long getOffset (int)
private void gotoSector (int)
private boolean readHeader ()
private void getSectorAllocationTable ()
private void getShortSectorAllocationTable ()
private void getDirectoryTable ()
private java.lang.StringBuffer getFileAsString (org.jmol.util.CompoundDocument$CmpDocDirectoryEntry, boolean)
private java.lang.StringBuffer getStandardStringData (int, int, boolean)
private int getSectorData (java.lang.StringBuffer, byte[], int, int, boolean) throws java.lang.Exception
private java.lang.StringBuffer getShortStringData (int, int, boolean)
}
org/jmol/util/DCT.class
<Unknown>
package org.jmol.util
org.jmol.util.DCT extends java.lang.Object {
private static final int N
private static final int NN
int[][] quantum
double[][] divisors
private int[] quantum_luminance
private double[] DivisorsLuminance
private int[] quantum_chrominance
private double[] DivisorsChrominance
private static final double[] AANscaleFactor
void <init> (int)
private void initMatrix (int)
private static void AANscale (double[], int[], int)
static double[][] forwardDCT (float[][])
static int[] quantizeBlock (double[][], double[])
static void <clinit> ()
}
org/jmol/util/DefaultLogger.class
<Unknown>
package org.jmol.util
public org.jmol.util.DefaultLogger extends java.lang.Object implements org.jmol.util.LoggerInterface {
public void <init> ()
protected void log (java.io.PrintStream, int, java.lang.String, java.lang.Throwable)
public void debug (java.lang.String)
public void info (java.lang.String)
public void warn (java.lang.String)
public void warn (java.lang.String, java.lang.Throwable)
public void error (java.lang.String)
public void error (java.lang.String, java.lang.Throwable)
public void fatal (java.lang.String)
public void fatal (java.lang.String, java.lang.Throwable)
}
org/jmol/util/Eigen.class
<Unknown>
package org.jmol.util
public org.jmol.util.Eigen extends java.lang.Object {
private double[] d
private double[] e
private double[][] Vx
private double[][] Vo
public void <init> (double[][])
public double[][] getEigenvectors ()
public double[] getEigenvalues ()
private void tred2 ()
private void tql2 ()
private static double hypot (double, double)
public void dump ()
private void dump (int)
public static float[][] toFloat3x3 (double[][])
public static float[] toFloat (double[])
}
org/jmol/util/Escape.class
<Unknown>
package org.jmol.util
public org.jmol.util.Escape extends java.lang.Object {
private static final String escapable
static String ESCAPE_SET
static int nEscape
public void <init> ()
public static java.lang.String escape (java.lang.Object)
public static java.lang.String escapeColor (int)
public static java.lang.String escape (javax.vecmath.Point4f)
public static java.lang.String escape (javax.vecmath.Tuple3f)
public static java.lang.String escape (float[], boolean)
public static java.lang.String escape (float[][], boolean)
public static java.lang.String escape (float[][][], boolean)
public static java.lang.String escape (int[])
public static java.lang.String escapeChopped (java.lang.String)
public static java.lang.String escape (java.lang.String)
private static java.lang.String chop (java.lang.String)
public static java.lang.String escape (java.lang.String[])
public static java.lang.String escapeDoubleArray (java.lang.Object)
private static java.lang.String escapeNice (java.lang.String)
private static java.lang.String unicode (char)
public static java.lang.Object unescapePoint (java.lang.String)
public static java.util.BitSet unescapeBitset (java.lang.String)
public static int unescapeColor (java.lang.String)
public static java.lang.String escape (java.util.BitSet, boolean)
public static java.lang.String escape (java.util.BitSet)
private static java.lang.String packageJSON (java.lang.String, java.lang.StringBuffer)
private static java.lang.String packageJSON (java.lang.String, java.lang.String)
private static java.lang.String packageReadable (java.lang.String, java.lang.String, java.lang.StringBuffer)
private static java.lang.String packageReadable (java.lang.String, java.lang.String, java.lang.String)
private static java.lang.String fixString (java.lang.String)
public static java.lang.String toJSON (java.lang.String, java.lang.Object)
public static java.lang.String toReadable (java.lang.Object)
public static java.lang.String toReadable (java.lang.String, java.lang.Object)
public static java.lang.String escapeModelFileNumber (int)
public static java.lang.Object encapsulateData (java.lang.String, java.lang.Object)
public static java.lang.Object unescapePointOrBitset (java.lang.String)
static void <clinit> ()
}
org/jmol/util/Huffman.class
<Unknown>
package org.jmol.util
org.jmol.util.Huffman extends java.lang.Object {
private int bufferPutBits
private int bufferPutBuffer
int ImageHeight
int ImageWidth
private int[][] DC_matrix0
private int[][] AC_matrix0
private int[][] DC_matrix1
private int[][] AC_matrix1
private int[][][] DC_matrix
private int[][][] AC_matrix
int NumOfDCTables
int NumOfACTables
static final int[] bitsDCluminance
static final int[] valDCluminance
static final int[] bitsDCchrominance
static final int[] valDCchrominance
static final int[] bitsACluminance
static final int[] valACluminance
static final int[] bitsACchrominance
static final int[] valACchrominance
static final int[] jpegNaturalOrder
void <init> (int, int)
void HuffmanBlockEncoder (java.io.BufferedOutputStream, int[], int, int, int)
void bufferIt (java.io.BufferedOutputStream, int, int)
void flushBuffer (java.io.BufferedOutputStream)
private void initHuf ()
static void <clinit> ()
}
org/jmol/util/Int2IntHash$Entry.class
<Unknown>
package org.jmol.util
org.jmol.util.Int2IntHash$Entry extends java.lang.Object {
int key
int value
org.jmol.util.Int2IntHash$Entry next
void <init> (int, int, org.jmol.util.Int2IntHash$Entry)
}
org/jmol/util/Int2IntHash.class
<Unknown>
package org.jmol.util
public org.jmol.util.Int2IntHash extends java.lang.Object {
int entryCount
org.jmol.util.Int2IntHash$Entry[] entries
public void <init> (int)
public void <init> ()
public synchronized int get (int)
public synchronized void put (int, int)
private void rehash ()
}
org/jmol/util/JpegEncoder.class
<Unknown>
package org.jmol.util
public org.jmol.util.JpegEncoder extends java.awt.Frame {
private java.io.BufferedOutputStream outStream
private org.jmol.util.JpegInfo JpegObj
private org.jmol.util.Huffman Huf
private org.jmol.util.DCT dct
private int Quality
public void <init> (java.awt.Image, int, java.io.OutputStream, java.lang.String)
public static byte[] getBytes (java.awt.Image, int, java.lang.String)
public static void write (java.awt.Image, int, java.io.OutputStream, java.lang.String)
public void setQuality (int)
public void Compress ()
private static void WriteCompressedData (java.io.BufferedOutputStream, org.jmol.util.JpegInfo, org.jmol.util.DCT, org.jmol.util.Huffman)
private static void WriteEOI (java.io.BufferedOutputStream)
private static void WriteHeaders (java.io.BufferedOutputStream, org.jmol.util.JpegInfo, org.jmol.util.DCT)
static void WriteDHTHeader (int[], int[], java.io.BufferedOutputStream)
static void WriteMarker (byte[], java.io.BufferedOutputStream)
static void WriteArray (byte[], java.io.BufferedOutputStream)
}
org/jmol/util/JpegInfo.class
<Unknown>
package org.jmol.util
org.jmol.util.JpegInfo extends java.lang.Object {
String Comment
private java.awt.Image imageobj
int imageHeight
int imageWidth
int[] BlockWidth
int[] BlockHeight
int Precision
int NumberOfComponents
float[][][] Components
int[] CompID
int[] HsampFactor
int[] VsampFactor
int[] QtableNumber
int[] DCtableNumber
int[] ACtableNumber
private boolean[] lastColumnIsDummy
private boolean[] lastRowIsDummy
int Ss
int Se
int Ah
int Al
private int[] compWidth
private int[] compHeight
private int MaxHsampFactor
private int MaxVsampFactor
public void <init> (java.awt.Image, java.lang.String)
java.lang.String getComment ()
private void getYCCArray ()
}
org/jmol/util/Logger.class
<Unknown>
package org.jmol.util
public final org.jmol.util.Logger extends java.lang.Object {
private static org.jmol.util.LoggerInterface _logger
public static final int LEVEL_FATAL
public static final int LEVEL_ERROR
public static final int LEVEL_WARN
public static final int LEVEL_INFO
public static final int LEVEL_DEBUG
public static final int LEVEL_DEBUGHIGH
public static final int LEVEL_MAX
private static final boolean[] _activeLevels
private static boolean _logLevel
public static boolean debugging
static long startTime
public void <init> ()
private static boolean getProperty (java.lang.String, boolean)
public static void setLogger (org.jmol.util.LoggerInterface)
public static boolean isActiveLevel (int)
public static void setActiveLevel (int, boolean)
public static void setLogLevel (int)
public static java.lang.String getLevel (int)
public static boolean logLevel ()
public static void logLevel (boolean)
public static void debug (java.lang.String)
public static void info (java.lang.String)
public static void warn (java.lang.String)
public static void warn (java.lang.String, java.lang.Throwable)
public static void error (java.lang.String)
public static void error (java.lang.String, java.lang.Throwable)
public static void fatal (java.lang.String)
public static void fatal (java.lang.String, java.lang.Throwable)
public static void startTimer ()
public static long checkTimer (java.lang.String)
public static void checkMemory ()
static void <clinit> ()
}
org/jmol/util/LoggerInterface.class
<Unknown>
package org.jmol.util
public abstract org.jmol.util.LoggerInterface extends java.lang.Object {
public abstract void debug (java.lang.String)
public abstract void info (java.lang.String)
public abstract void warn (java.lang.String)
public abstract void warn (java.lang.String, java.lang.Throwable)
public abstract void error (java.lang.String)
public abstract void error (java.lang.String, java.lang.Throwable)
public abstract void fatal (java.lang.String)
public abstract void fatal (java.lang.String, java.lang.Throwable)
}
org/jmol/util/Measure.class
<Unknown>
package org.jmol.util
public final org.jmol.util.Measure extends java.lang.Object {
public static final float radiansPerDegree
public void <init> ()
public static float computeTorsion (javax.vecmath.Tuple3f, javax.vecmath.Tuple3f, javax.vecmath.Tuple3f, javax.vecmath.Tuple3f, boolean)
public static float computeAngle (javax.vecmath.Tuple3f, javax.vecmath.Tuple3f, javax.vecmath.Tuple3f, javax.vecmath.Vector3f, javax.vecmath.Vector3f, boolean)
public static float computeAngle (javax.vecmath.Tuple3f, javax.vecmath.Tuple3f, javax.vecmath.Tuple3f, boolean)
public static java.lang.Object computeHelicalAxis (java.lang.String, int, javax.vecmath.Point3f, javax.vecmath.Point3f, org.jmol.util.Quaternion)
public static javax.vecmath.Point4f getPlaneThroughPoints (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Vector3f, javax.vecmath.Vector3f, javax.vecmath.Vector3f)
public static float distanceToPlane (javax.vecmath.Point4f, javax.vecmath.Point3f)
public static float distanceToPlane (javax.vecmath.Point4f, float, javax.vecmath.Point3f)
public static float distanceToPlane (javax.vecmath.Vector3f, float, javax.vecmath.Point3f)
public static void calcNormalizedNormal (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Vector3f, javax.vecmath.Vector3f, javax.vecmath.Vector3f)
public static float getDirectedNormalThroughPoints (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Vector3f, javax.vecmath.Vector3f, javax.vecmath.Vector3f)
public static float getNormalThroughPoints (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Vector3f, javax.vecmath.Vector3f, javax.vecmath.Vector3f)
public static void getNormalFromCenter (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f, boolean, javax.vecmath.Vector3f)
public static void calcXYNormalToLine (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Vector3f)
public static void projectOntoAxis (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Vector3f, javax.vecmath.Vector3f)
public static void calcBestAxisThroughPoints (javax.vecmath.Point3f[], javax.vecmath.Point3f, javax.vecmath.Vector3f, javax.vecmath.Vector3f, int)
public static float findAxis (javax.vecmath.Point3f[], int, javax.vecmath.Point3f, javax.vecmath.Vector3f, javax.vecmath.Vector3f)
public static void calcAveragePoint (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f)
public static void calcAveragePointN (javax.vecmath.Point3f[], int, javax.vecmath.Point3f)
}
org/jmol/util/Parser.class
<Unknown>
package org.jmol.util
public org.jmol.util.Parser extends java.lang.Object {
private static final float[] decimalScale
private static final float[] tensScale
public void <init> ()
public static float[] parseFloatArray (java.lang.String)
public static float[] parseFloatArray (java.lang.String, int[])
public static void parseFloatArray (java.lang.String, java.util.BitSet, float[])
public static int parseFloatArray (java.lang.String[], java.util.BitSet, float[])
public static float[][] parseFloatArray2d (java.lang.String)
public static float[][][] parseFloatArray3d (java.lang.String)
public static void setSelectedFloats (float, java.util.BitSet, float[])
public static float[] extractData (java.lang.String, int, int, int)
public static float[] parseFloatArrayFromMatchAndField (java.lang.String, java.util.BitSet, int, int, int[], int, int, float[], int)
public static void parseFloatArray (java.lang.String[], float[])
public static void parseFloatArray (java.lang.String[], float[], int)
public static float parseFloat (java.lang.String)
public static float parseFloatStrict (java.lang.String)
public static int parseInt (java.lang.String)
public static java.lang.String[] getTokens (java.lang.String)
public static java.lang.String parseToken (java.lang.String)
public static java.lang.String parseTrimmed (java.lang.String)
public static java.lang.String parseTrimmed (java.lang.String, int)
public static java.lang.String parseTrimmed (java.lang.String, int, int)
public static int[] markLines (java.lang.String, char)
public static float parseFloat (java.lang.String, int[])
public static float parseFloat (java.lang.String, int, int[])
private static float parseFloatChecked (java.lang.String, int, int[], boolean)
private static boolean checkTrailingText (java.lang.String, int, int)
public static int parseInt (java.lang.String, int[])
public static int parseInt (java.lang.String, int, int[])
private static int parseIntChecked (java.lang.String, int, int[])
public static java.lang.String[] getTokens (java.lang.String, int)
public static int countTokens (java.lang.String, int)
public static java.lang.String parseToken (java.lang.String, int[])
public static java.lang.String parseToken (java.lang.String, int, int[])
private static java.lang.String parseTokenChecked (java.lang.String, int, int[])
private static java.lang.String parseTrimmedChecked (java.lang.String, int, int)
public static java.lang.String concatTokens (java.lang.String[], int, int)
public static java.lang.String getNextQuotedString (java.lang.String, int)
private static boolean isWhiteSpace (java.lang.String, int)
public static boolean isOneOf (java.lang.String, java.lang.String)
static void <clinit> ()
}
org/jmol/util/Point3fi.class
<Unknown>
package org.jmol.util
public org.jmol.util.Point3fi extends javax.vecmath.Point3f {
public int screenX
public int screenY
public int screenZ
public short screenDiameter
public short modelIndex
public void <init> ()
public boolean equals (java.lang.Object)
public int hashCode ()
}
org/jmol/util/Quadric.class
<Unknown>
package org.jmol.util
public org.jmol.util.Quadric extends java.lang.Object {
public void <init> ()
public static void getAxesForEllipsoid (double[], javax.vecmath.Vector3f[], float[])
public static javax.vecmath.Matrix3f setEllipsoidMatrix (javax.vecmath.Vector3f[], float[], javax.vecmath.Vector3f, javax.vecmath.Matrix3f)
public static void getEquationForQuadricWithCenter (float, float, float, javax.vecmath.Matrix3f, javax.vecmath.Vector3f, javax.vecmath.Matrix3f, double[], javax.vecmath.Matrix4f)
public static boolean getQuardricZ (double, double, double[], double[])
public static int getOctant (javax.vecmath.Point3f)
}
org/jmol/util/Quaternion.class
<Unknown>
package org.jmol.util
public org.jmol.util.Quaternion extends java.lang.Object {
public float q0
public float q1
public float q2
public float q3
public javax.vecmath.Matrix3f mat
private static final javax.vecmath.Point4f qZero
private static final org.jmol.util.Quaternion qTemp
public void <init> ()
public void <init> (org.jmol.util.Quaternion)
public void <init> (javax.vecmath.Tuple3f, float)
public void <init> (javax.vecmath.Matrix3f)
public void <init> (javax.vecmath.AxisAngle4f)
public void <init> (javax.vecmath.Point4f)
public void <init> (float, float, float, float)
public void set (org.jmol.util.Quaternion)
private void set (javax.vecmath.Point4f)
public void set (javax.vecmath.Tuple3f, float)
public void set (javax.vecmath.AxisAngle4f)
public void set (javax.vecmath.Matrix3f)
public void setRef (org.jmol.util.Quaternion)
public static final org.jmol.util.Quaternion getQuaternionFrame (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f)
public static final org.jmol.util.Quaternion getQuaternionFrame (javax.vecmath.Vector3f, javax.vecmath.Vector3f, javax.vecmath.Vector3f)
public javax.vecmath.Matrix3f getMatrix ()
private void setMatrix ()
public org.jmol.util.Quaternion add (float)
public org.jmol.util.Quaternion mul (float)
public org.jmol.util.Quaternion mul (org.jmol.util.Quaternion)
public org.jmol.util.Quaternion div (org.jmol.util.Quaternion)
public org.jmol.util.Quaternion divLeft (org.jmol.util.Quaternion)
public float dot (org.jmol.util.Quaternion)
public org.jmol.util.Quaternion inv ()
public org.jmol.util.Quaternion negate ()
private void fixQ (org.jmol.util.Quaternion)
public javax.vecmath.Vector3f getVector (int)
private javax.vecmath.Vector3f getVector (int, float)
public javax.vecmath.Vector3f getNormal ()
public float getTheta ()
public float getThetaRadians ()
public javax.vecmath.Vector3f getNormalDirected (javax.vecmath.Vector3f)
public javax.vecmath.Point4f getThetaDirected (javax.vecmath.Point4f)
public javax.vecmath.Point4f toPoint4f ()
public javax.vecmath.AxisAngle4f toAxisAngle4f ()
public javax.vecmath.Point3f transform (javax.vecmath.Point3f)
public void transform (javax.vecmath.Point3f, javax.vecmath.Point3f)
public javax.vecmath.Vector3f transform (javax.vecmath.Vector3f)
public org.jmol.util.Quaternion leftDifference (org.jmol.util.Quaternion)
public org.jmol.util.Quaternion rightDifference (org.jmol.util.Quaternion)
public java.lang.String getInfo ()
public java.lang.String draw (java.lang.String, java.lang.String, javax.vecmath.Point3f, float)
public java.lang.String toString ()
public java.lang.String toString0123 ()
static void <clinit> ()
}
org/jmol/util/TempArray.class
<Unknown>
package org.jmol.util
public org.jmol.util.TempArray extends java.lang.Object {
private static final int freePointsSize
private final int[] lengthsFreePoints
private final javax.vecmath.Point3f[][] freePoints
private static final int freeScreensSize
private final int[] lengthsFreeScreens
private final javax.vecmath.Point3i[][] freeScreens
private static final int freeBytesSize
private final int[] lengthsFreeBytes
private final byte[][] freeBytes
public void <init> ()
public void clear ()
private static int findBestFit (int, int[])
private static int findShorter (int, int[])
private void clearTempPoints ()
public javax.vecmath.Point3f[] allocTempPoints (int)
public void freeTempPoints (javax.vecmath.Point3f[])
private void clearTempScreens ()
public javax.vecmath.Point3i[] allocTempScreens (int)
public void freeTempScreens (javax.vecmath.Point3i[])
public byte[] allocTempBytes (int)
public void freeTempBytes (byte[])
}
org/jmol/util/TextFormat.class
<Unknown>
package org.jmol.util
public org.jmol.util.TextFormat extends java.lang.Object {
private static final java.text.DecimalFormat[] formatters
private static final String[] formattingStrings
private static final Boolean[] useNumberLocalization
public void <init> ()
public static void setUseNumberLocalization (boolean)
public static java.lang.String formatDecimal (float, int)
public static java.lang.String format (float, int, int, boolean, boolean)
public static java.lang.String format (double, int, int, boolean, boolean)
public static java.lang.String format (java.lang.String, int, int, boolean, boolean)
public static java.lang.String formatString (java.lang.String, java.lang.String, java.lang.String)
public static java.lang.String formatString (java.lang.String, java.lang.String, float)
public static java.lang.String formatString (java.lang.String, java.lang.String, int)
public static java.lang.String sprintf (java.lang.String, java.lang.Object[])
private static java.lang.String formatString (java.lang.String, java.lang.String, java.lang.String, float, double, boolean)
public static java.lang.String formatCheck (java.lang.String)
private static java.lang.String fdup (java.lang.String, int, int)
public static java.lang.String[] split (java.lang.String, java.lang.String)
public static java.lang.String replaceAllCharacters (java.lang.String, java.lang.String, java.lang.String)
public static java.lang.String replaceAllCharacters (java.lang.String, java.lang.String, char)
public static java.lang.String simpleReplace (java.lang.String, java.lang.String, java.lang.String)
public static java.lang.String trim (java.lang.String, java.lang.String)
public static java.lang.String[] split (java.lang.String, char)
public static void lFill (java.lang.StringBuffer, java.lang.String, java.lang.String)
public static void rFill (java.lang.StringBuffer, java.lang.String, java.lang.String)
public static java.lang.String safeTruncate (float, int)
public static boolean isWild (java.lang.String)
public static boolean isMatch (java.lang.String, java.lang.String, boolean, boolean)
public static java.lang.String join (java.lang.String[], char, int)
static void <clinit> ()
}
org/jmol/util/ZipUtil.class
<Unknown>
package org.jmol.util
public org.jmol.util.ZipUtil extends java.lang.Object {
public void <init> ()
public static boolean isZipFile (java.lang.String)
public static boolean isZipFile (java.io.InputStream) throws java.lang.Exception
public static boolean isZipFile (byte[]) throws java.lang.Exception
public static java.util.zip.ZipInputStream getStream (java.io.InputStream)
public static void getAllData (java.io.InputStream, java.lang.String[], java.lang.String, java.lang.String, java.util.Hashtable)
public static java.lang.String getBinaryStringForBytes (byte[])
public static java.lang.Object getZipFileContents (java.io.InputStream, java.lang.String[], int, boolean)
public static byte[] getZipFileContentsAsBytes (java.io.InputStream, java.lang.String[], int)
public static java.lang.String getZipDirectoryAsStringAndClose (java.io.InputStream)
public static java.lang.String[] getZipDirectoryAndClose (java.io.InputStream, boolean)
private static java.lang.String[] getZipDirectoryOrErrorAndClose (java.io.InputStream, boolean) throws java.io.IOException
public static java.lang.String getZipEntryAsString (java.util.zip.ZipInputStream) throws java.io.IOException
public static byte[] getZipEntryAsBytes (java.util.zip.ZipInputStream) throws java.io.IOException
public static byte[] getStreamAsBytes (java.io.BufferedInputStream) throws java.io.IOException
}
org/jmol/viewer/AnimationManager$AnimationThread.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.AnimationManager$AnimationThread extends java.lang.Thread implements java.lang.Runnable {
final int framePointer
final int framePointer2
int intThread
private final org.jmol.viewer.AnimationManager this$0
void <init> (org.jmol.viewer.AnimationManager, int, int, int)
public void run ()
}
org/jmol/viewer/AnimationManager.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.AnimationManager extends java.lang.Object {
org.jmol.viewer.Viewer viewer
int currentModelIndex
int backgroundModelIndex
private java.util.BitSet bsVisibleFrames
org.jmol.viewer.AnimationManager$AnimationThread animationThread
boolean inMotion
int firstModelIndex
int lastModelIndex
int frameStep
int animationDirection
int currentDirection
int animationFps
static final int ANIMATION_ONCE
static final int ANIMATION_LOOP
static final int ANIMATION_PALINDROME
int animationReplayMode
float firstFrameDelay
float lastFrameDelay
int firstFrameDelayMs
int lastFrameDelayMs
boolean animationOn
boolean animationPaused
int intAnimThread
void <init> (org.jmol.viewer.Viewer)
void setCurrentModelIndex (int)
void setCurrentModelIndex (int, boolean)
private void setStatusFrameChanged ()
void setBackgroundModelIndex (int)
java.util.BitSet getVisibleFramesBitSet ()
private void setFrameRangeVisible ()
void setInMotion (boolean)
void initializePointers (int)
void clear ()
void clearAnimation ()
java.util.Hashtable getAnimationInfo ()
java.lang.String getState (java.lang.StringBuffer)
void setAnimationDirection (int)
void setAnimationFps (int)
void setAnimationReplayMode (int, float, float)
void setAnimationRange (int, int)
private void animationOn (boolean)
void setAnimationOn (boolean)
void setAnimationOff (boolean)
void pauseAnimation ()
void reverseAnimation ()
void resumeAnimation ()
boolean setAnimationNext ()
void setAnimationLast ()
void rewindAnimation ()
boolean setAnimationPrevious ()
boolean setAnimationRelative (int)
java.lang.String getAnimationModeName ()
}
org/jmol/viewer/ColorManager.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.ColorManager extends java.lang.Object {
private org.jmol.viewer.Viewer viewer
private org.jmol.g3d.Graphics3D g3d
private int[] argbsCpk
private int[] altArgbsCpk
private float colorHi
private float colorLo
private float[] colorData
private int palette
private boolean isDefaultColorRasmol
short colixRubberband
short colixBackgroundContrast
void <init> (org.jmol.viewer.Viewer, org.jmol.g3d.Graphics3D)
void clear ()
boolean getDefaultColorRasmol ()
void resetElementColors ()
void setDefaultColors (java.lang.String)
void setRubberbandArgb (int)
void setColixBackgroundContrast (int)
short getColixBondPalette (org.jmol.modelset.Bond, byte)
short getColixAtomPalette (org.jmol.modelset.Atom, byte)
private short getPropertyColix (int)
private static int getJmolOrRasmolArgb (int, int)
void setElementArgb (int, int)
int setColorScheme (java.lang.String, boolean)
float[] getCurrentColorRange ()
void setCurrentColorRange (float[], java.util.BitSet, java.lang.String)
void setCurrentColorRange (float, float)
static java.lang.String getState (java.lang.StringBuffer)
static void setUserScale (int[])
int[] getColorSchemeArray (java.lang.String)
java.lang.String getColorSchemeList (java.lang.String, boolean)
short getColixForPropertyValue (float)
private static void flushCaches ()
static void setSpecular (boolean)
static boolean getSpecular ()
static void setSpecularPercent (int)
static int getSpecularPercent ()
static void setSpecularPower (int)
static void setDiffusePercent (int)
static int getDiffusePercent ()
static void setAmbientPercent (int)
static int getAmbientPercent ()
}
org/jmol/viewer/DataManager.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.DataManager extends java.lang.Object {
private java.util.Hashtable dataValues
int[] userVdwMars
float[] userVdws
int defaultVdw
java.util.BitSet bsUserVdws
void <init> ()
void clear ()
void setData (org.jmol.viewer.Viewer, java.lang.String, java.lang.Object[], int, int, int, int, int)
java.lang.Object[] getData (java.lang.String)
float[] getDataFloat (java.lang.String)
float getDataFloat (java.lang.String, int)
float[][] getDataFloat2D (java.lang.String)
float[][][] getDataFloat3D (java.lang.String)
protected void deleteModelAtoms (int, int, java.util.BitSet)
void getDataState (java.lang.StringBuffer, java.lang.StringBuffer, org.jmol.modelset.Atom[], int, java.lang.String)
public void setUserVdw (int)
public void setDefaultVdw (java.lang.String)
public java.lang.String getDefaultVdw (int, java.util.BitSet)
}
org/jmol/viewer/FileManager$DOMReaderThread.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.FileManager$DOMReaderThread extends java.lang.Object implements java.lang.Runnable {
String errorMessage
Object aDOMNode
Object atomSetCollection
private final org.jmol.viewer.FileManager this$0
void <init> (org.jmol.viewer.FileManager, java.lang.Object)
public void run ()
}
org/jmol/viewer/FileManager$FileReaderThread.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.FileManager$FileReaderThread extends java.lang.Object implements java.lang.Runnable {
String errorMessage
String fullPathNameInThread
String nameAsGivenInThread
String fileTypeInThread
Object atomSetCollection
java.io.BufferedReader reader
java.util.Hashtable htParams
private final org.jmol.viewer.FileManager this$0
void <init> (org.jmol.viewer.FileManager, java.lang.String, java.lang.String, java.lang.String, java.io.BufferedReader, java.util.Hashtable)
public void run ()
private void createAtomSetCollection (java.lang.String, java.util.zip.ZipInputStream)
private void createAtomSetCollection ()
}
org/jmol/viewer/FileManager$FilesReaderThread.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.FileManager$FilesReaderThread extends java.lang.Object implements java.lang.Runnable org.jmol.api.JmolFileReaderInterface {
String errorMessage
private String[] fullPathNamesInThread
private String[] namesAsGivenInThread
private String[] fileTypesInThread
Object atomSetCollection
private java.io.Reader[] stringReaders
private java.util.Hashtable[] htParamsSet
private java.util.Hashtable htParams
private final org.jmol.viewer.FileManager this$0
void <init> (org.jmol.viewer.FileManager, java.lang.String[], java.lang.String[], java.lang.String[], java.io.Reader[], java.util.Hashtable)
public void run ()
private void createAtomSetCollection ()
public java.io.BufferedReader getBufferedReader (int)
}
org/jmol/viewer/FileManager.class
<Unknown>
package org.jmol.viewer
public org.jmol.viewer.FileManager extends java.lang.Object {
protected org.jmol.viewer.Viewer viewer
private String openErrorMessage
private java.net.URL appletDocumentBase
private java.net.URL appletCodeBase
private String appletProxy
private String nameAsGiven
private String fullPathName
private String fileName
private String fileType
private String inlineData
private String loadScript
org.jmol.viewer.FileManager$FileReaderThread fileReaderThread
org.jmol.viewer.FileManager$FilesReaderThread filesReaderThread
private org.jmol.viewer.FileManager$DOMReaderThread aDOMReaderThread
private static final int URL_LOCAL
private static final String[] urlPrefixes
private static final String[] urlPrefixPairs
java.lang.String getInlineData (int)
void <init> (org.jmol.viewer.Viewer)
java.lang.String getState (java.lang.StringBuffer)
java.lang.String getFileTypeName (java.lang.String)
void clear ()
java.lang.String getLoadScript ()
private void setLoadScript (java.lang.String, boolean)
void addLoadScript (java.lang.String)
void createAtomSetCollectionFromFile (java.lang.String, java.util.Hashtable, java.lang.String, boolean)
void createAtomSetCollectionFromFiles (java.lang.String, java.lang.String[], java.lang.String, boolean, java.util.Hashtable)
void createAtomSetCollectionFromString (java.lang.String, java.util.Hashtable, boolean)
void createAtomSeCollectionFromStrings (java.lang.String[], java.util.Hashtable, boolean)
void createAtomSetCollectionFromDOM (java.lang.Object)
void createAtomSetCollectionFromReader (java.lang.String, java.lang.String, java.io.Reader)
static boolean isGzip (java.io.InputStream) throws java.lang.Exception
public java.lang.Object getFileAsBytes (java.lang.String)
boolean getFileDataOrErrorAsString (java.lang.String[], int, boolean)
java.lang.Object getFileAsImage (java.lang.String, java.util.Hashtable)
private java.lang.String getFileDataAsSections (java.lang.String[], java.util.Hashtable)
private java.lang.String getFileDataAsSections (java.lang.String, java.lang.String, java.util.Hashtable)
java.lang.Object getAtomSetCollectionOrError ()
void deallocateReaderThreads ()
java.lang.String getFullPathName ()
void setFileInfo (java.lang.String[])
java.lang.String[] getFileInfo ()
java.lang.String getFileName ()
java.lang.String getAppletDocumentBase ()
void setAppletContext (java.net.URL, java.net.URL, java.lang.String)
void setAppletProxy (java.lang.String)
private static int urlTypeIndex (java.lang.String)
private void setNames (java.lang.String[])
static java.lang.String shortNameOf (java.lang.String)
private java.lang.String[] classifyName (java.lang.String, boolean)
java.lang.String getDefaultDirectory (java.lang.String)
private java.lang.String fixPath (java.lang.String)
public java.lang.String getFullPath (java.lang.String, boolean)
public static java.lang.String getLocalUrl (java.io.File)
public static java.io.File getLocalDirectory (org.jmol.api.JmolViewer, boolean)
public static void setLocalPath (org.jmol.api.JmolViewer, java.lang.String, boolean)
public static java.lang.String setLocalPathForWritingFile (org.jmol.api.JmolViewer, java.lang.String)
private static java.lang.String addDirectory (java.lang.String, java.lang.String)
java.lang.Object getInputStreamOrErrorMessageFromName (java.lang.String, boolean)
public static java.lang.Object getInputStream (java.lang.String, boolean, java.net.URL, java.lang.String)
public static java.io.BufferedReader getBufferedReaderForString (java.lang.String)
java.lang.Object getBufferedReaderOrErrorMessageFromName (java.lang.String, java.lang.String[], boolean, boolean)
java.lang.Object getUnzippedBufferedReaderOrErrorMessageFromName (java.lang.String, boolean, boolean, boolean, boolean)
java.lang.String[] getZipDirectory (java.lang.String, boolean)
java.lang.String getZipDirectoryAsString (java.lang.String)
static void <clinit> ()
}
org/jmol/viewer/Jmol.properties
org/jmol/viewer/JmolConstants.class
<Unknown>
package org.jmol.viewer
public final org.jmol.viewer.JmolConstants extends java.lang.Object {
public static final String copyright
public static final String version
public static final String cvsDate
public static final String date
public static final boolean officialRelease
public static final String CLASSBASE_OPTIONS
public static final String DEFAULT_HELP_PATH
public static final String EMBEDDED_SCRIPT_TAG
public static final String SCRIPT_EDITOR_IGNORE
public static final int CALLBACK_ANIMFRAME
public static final int CALLBACK_ECHO
public static final int CALLBACK_ERROR
public static final int CALLBACK_EVAL
public static final int CALLBACK_HOVER
public static final int CALLBACK_LOADSTRUCT
public static final int CALLBACK_MEASURE
public static final int CALLBACK_MESSAGE
public static final int CALLBACK_MINIMIZATION
public static final int CALLBACK_PICK
public static final int CALLBACK_RESIZE
public static final int CALLBACK_SCRIPT
public static final int CALLBACK_SYNC
public static final int CALLBACK_COUNT
public static final int CALLBACK_SET_MESH_CREATOR
private static final String[] callbackNames
public static final int INFO_A
public static final int INFO_B
public static final int INFO_C
public static final int INFO_ALPHA
public static final int INFO_BETA
public static final int INFO_GAMMA
public static final int JMOL_DATA_RAMACHANDRAN
public static final int JMOL_DATA_QUATERNION
public static final int JMOL_DATA_OTHER
public static final String EXPORT_DRIVER_LIST
public static final int DRAW_MULTIPLE
public static final int DRAW_NONE
public static final int DRAW_POINT
public static final int DRAW_LINE
public static final int DRAW_TRIANGLE
public static final int DRAW_PLANE
public static final int DRAW_CYLINDER
public static final int DRAW_ARROW
public static final int DRAW_CIRCLE
public static final int DRAW_CURVE
public static final int DRAW_CIRCULARPLANE
public static final int DRAW_ARC
public static final int DRAW_LINE_SEGMENT
public static final javax.vecmath.Vector3f center
public static final javax.vecmath.Vector3f axisX
public static final javax.vecmath.Vector3f axisY
public static final javax.vecmath.Vector3f axisZ
public static final javax.vecmath.Vector3f axisNX
public static final javax.vecmath.Vector3f axisNY
public static final javax.vecmath.Vector3f axisNZ
public static final javax.vecmath.Vector3f[] unitAxisVectors
public static final int XY_ZTOP
public static final int DEFAULT_PERCENT_VDW_ATOM
public static final float DEFAULT_BOND_RADIUS
public static final short DEFAULT_BOND_MILLIANGSTROM_RADIUS
public static final float DEFAULT_BOND_TOLERANCE
public static final float DEFAULT_MIN_BOND_DISTANCE
public static final int CONNECT_DELETE_BONDS
public static final int CONNECT_MODIFY_ONLY
public static final int CONNECT_CREATE_ONLY
public static final int CONNECT_MODIFY_OR_CREATE
public static final int CONNECT_AUTO_BOND
public static final int CONNECT_IDENTIFY_ONLY
public static final float DEFAULT_MAX_CONNECT_DISTANCE
public static final float DEFAULT_MIN_CONNECT_DISTANCE
private static final String[] connectOperationStrings
public static final int MOUSE_NONE
public static final int MOUSE_ROTATE
public static final int MOUSE_ZOOM
public static final int MOUSE_XLATE
public static final int MOUSE_PICK
public static final int MOUSE_DELETE
public static final int MOUSE_MEASURE
public static final int MOUSE_ROTATE_Z
public static final int MOUSE_SLAB_PLANE
public static final int MOUSE_POPUP_MENU
public static final byte MULTIBOND_NEVER
public static final byte MULTIBOND_WIREFRAME
public static final byte MULTIBOND_NOTSMALL
public static final byte MULTIBOND_ALWAYS
public static final short madMultipleBondSmallMaximum
public static final int AXES_MODE_BOUNDBOX
public static final int AXES_MODE_MOLECULAR
public static final int AXES_MODE_UNITCELL
public static final int PICKING_OFF
public static final int PICKING_IDENT
public static final int PICKING_LABEL
public static final int PICKING_CENTER
public static final int PICKING_DRAW
public static final int PICKING_SPIN
public static final int PICKING_SELECT_ATOM
public static final int PICKING_SELECT_GROUP
public static final int PICKING_SELECT_CHAIN
public static final int PICKING_SELECT_MOLECULE
public static final int PICKING_SELECT_SITE
public static final int PICKING_SELECT_MODEL
public static final int PICKING_SELECT_ELEMENT
public static final int PICKING_MEASURE
public static final int PICKING_MEASURE_DISTANCE
public static final int PICKING_MEASURE_ANGLE
public static final int PICKING_MEASURE_TORSION
public static final int PICKING_NAVIGATE
private static final String[] pickingModeNames
public static final int PICKINGSTYLE_SELECT_JMOL
public static final int PICKINGSTYLE_SELECT_CHIME
public static final int PICKINGSTYLE_SELECT_RASMOL
public static final int PICKINGSTYLE_SELECT_PFAAT
public static final int PICKINGSTYLE_SELECT_DRAG
public static final int PICKINGSTYLE_MEASURE_ON
public static final int PICKINGSTYLE_MEASURE_OFF
private static final String[] pickingStyleNames
public static final short BOND_ORDER_ANY
public static final short BOND_ORDER_NULL
public static final short BOND_HBOND_SHIFT
public static final short BOND_NEW
public static final short BOND_HYDROGEN_MASK
public static final short BOND_H_REGULAR
public static final short BOND_H_CALC_MASK
public static final short BOND_H_CALC
public static final short BOND_H_PLUS_2
public static final short BOND_H_PLUS_3
public static final short BOND_H_PLUS_4
public static final short BOND_H_PLUS_5
public static final short BOND_H_MINUS_3
public static final short BOND_H_MINUS_4
public static final short BOND_H_NUCLEOTIDE
public static final int[] argbsHbondType
public static final short BOND_STEREO_MASK
public static final short BOND_STEREO_NEAR
public static final short BOND_STEREO_FAR
public static final short BOND_AROMATIC_MASK
public static final short BOND_AROMATIC_SINGLE
public static final short BOND_AROMATIC_DOUBLE
public static final short BOND_AROMATIC
public static final short BOND_SULFUR_MASK
public static final short BOND_PARTIAL_MASK
public static final short BOND_PARTIAL01
public static final short BOND_PARTIAL12
public static final short BOND_PARTIAL23
public static final short BOND_PARTIAL32
public static final short BOND_COVALENT_MASK
public static final short BOND_COVALENT_SINGLE
public static final short BOND_COVALENT_DOUBLE
public static final short BOND_COVALENT_TRIPLE
public static final short BOND_COVALENT_QUADRUPLE
public static final short BOND_ORDER_UNSPECIFIED
private static final String[] bondOrderNames
private static final String[] bondOrderNumbers
private static final short[] bondOrderValues
public static final float ANGSTROMS_PER_BOHR
public static final int FRONTLIT
public static final int BACKLIT
public static final int FULLYLIT
private static final String[] elementSymbols
public static final int elementNumberMax
private static java.util.Hashtable htElementMap
private static final String[] elementNames
private static final String naturalIsotopes
private static final short[] altElementNumbers
private static final String[] altElementSymbols
private static final String[] altElementNames
public static final int[] altArgbsCpk
public static final int firstIsotope
public static final int altElementMax
public static final int VDW_JMOL
public static final int VDW_BABEL
public static final int VDW_RASMOL
public static final int VDW_USER
static final String[] vdwLabels
public static final short[] vanderwaalsMars
private static final short[] covalentMars
public static final int FORMAL_CHARGE_MIN
public static final int FORMAL_CHARGE_MAX
private static final short[] cationLookupTable
private static final short[] anionLookupTable
static java.util.BitSet bsCations
static java.util.BitSet bsAnions
public static final int MAXIMUM_AUTO_BOND_COUNT
public static final byte PALETTE_VOLATILE
public static final byte PALETTE_STATIC
public static final byte PALETTE_UNKNOWN
public static final byte PALETTE_NONE
public static final byte PALETTE_CPK
public static final byte PALETTE_PARTIAL_CHARGE
public static final byte PALETTE_FORMAL_CHARGE
public static final byte PALETTE_TEMP
public static final byte PALETTE_FIXEDTEMP
public static final byte PALETTE_SURFACE
public static final byte PALETTE_STRUCTURE
public static final byte PALETTE_AMINO
public static final byte PALETTE_SHAPELY
public static final byte PALETTE_CHAIN
public static final byte PALETTE_GROUP
public static final byte PALETTE_MONOMER
public static final byte PALETTE_MOLECULE
public static final byte PALETTE_ALTLOC
public static final byte PALETTE_INSERTION
public static final byte PALETTE_JMOL
public static final byte PALETTE_RASMOL
public static final byte PALETTE_TYPE
public static final byte PALETTE_ENERGY
public static final byte PALETTE_PROPERTY
public static final byte PALETTE_VARIABLE
public static final byte PALETTE_STRAIGHTNESS
private static final String[] paletteNames
private static final byte[] paletteIDs
private static final int paletteCount
public static final int[] argbsCpk
public static final int[] argbsCpkRasmol
public static final byte PROTEIN_STRUCTURE_NONE
public static final byte PROTEIN_STRUCTURE_TURN
public static final byte PROTEIN_STRUCTURE_SHEET
public static final byte PROTEIN_STRUCTURE_HELIX
public static final byte PROTEIN_STRUCTURE_DNA
public static final byte PROTEIN_STRUCTURE_RNA
public static final String[] proteinStructureNames
public static final int[] argbsStructure
public static final int[] argbsAmino
public static final int argbShapelyBackbone
public static final int argbShapelySpecial
public static final int argbShapelyDefault
public static final int[] argbsChainAtom
public static final int[] argbsChainHetero
public static final short FORMAL_CHARGE_COLIX_RED
public static final short FORMAL_CHARGE_COLIX_WHITE
public static final short FORMAL_CHARGE_COLIX_BLUE
public static final int FORMAL_CHARGE_RANGE_SIZE
public static final int[] argbsFormalCharge
public static final int FORMAL_CHARGE_INDEX_WHITE
public static final int FORMAL_CHARGE_INDEX_MAX
public static final short PARTIAL_CHARGE_COLIX_RED
public static final short PARTIAL_CHARGE_COLIX_WHITE
public static final short PARTIAL_CHARGE_COLIX_BLUE
public static final int PARTIAL_CHARGE_RANGE_SIZE
public static final int[] argbsRwbScale
public static final int[] argbsRoygbScale
public static final int[] argbsIsosurfacePositive
public static final int[] argbsIsosurfaceNegative
public static final String[] specialAtomNames
public static final int ATOMID_MAX
public static final byte ATOMID_AMINO_NITROGEN
public static final byte ATOMID_ALPHA_CARBON
public static final byte ATOMID_CARBONYL_CARBON
public static final byte ATOMID_CARBONYL_OXYGEN
public static final byte ATOMID_O1
public static final int ATOMID_ALPHA_ONLY_MASK
public static final int ATOMID_PROTEIN_MASK
public static final byte ATOMID_O5_PRIME
public static final byte ATOMID_C3_PRIME
public static final byte ATOMID_O3_PRIME
public static final int ATOMID_NUCLEIC_MASK
public static final byte ATOMID_NUCLEIC_PHOSPHORUS
public static final int ATOMID_PHOSPHORUS_ONLY_MASK
public static final int ATOMID_DISTINGUISHING_ATOM_MAX
public static final byte ATOMID_N1
public static final byte ATOMID_C2
public static final byte ATOMID_N3
public static final byte ATOMID_C4
public static final byte ATOMID_C5
public static final byte ATOMID_C6
public static final byte ATOMID_O2
public static final byte ATOMID_N7
public static final byte ATOMID_C8
public static final byte ATOMID_N9
public static final byte ATOMID_N4
public static final byte ATOMID_N2
public static final byte ATOMID_N6
public static final byte ATOMID_C5M
public static final byte ATOMID_O6
public static final byte ATOMID_O4
public static final byte ATOMID_S4
public static final byte ATOMID_C7
private static final int ATOMID_BACKBONE_MIN
public static final byte ATOMID_TERMINATING_OXT
public static final byte ATOMID_H5T_TERMINUS
public static final byte ATOMID_O5T_TERMINUS
public static final byte ATOMID_O1P
public static final byte ATOMID_OP1
public static final byte ATOMID_O2P
public static final byte ATOMID_OP2
public static final byte ATOMID_O2_PRIME
public static final byte ATOMID_H3T_TERMINUS
public static final byte ATOMID_HO3_PRIME
public static final byte ATOMID_HO5_PRIME
public static final int GROUPID_PROLINE
public static final int GROUPID_AMINO_MAX
private static final int GROUPID_WATER
private static final int GROUPID_SULPHATE
public static final String[] predefinedGroup3Names
public static final int[] argbsShapely
private static final String allCarbohydrates
public static final String group3List
public static final int group3Count
public static final char[] predefinedGroup1Names
public static String[] predefinedVariable
public static String[] predefinedStatic
public static final String DEFAULT_FONTFACE
public static final String DEFAULT_FONTSTYLE
public static final int LABEL_MINIMUM_FONTSIZE
public static final int LABEL_MAXIMUM_FONTSIZE
public static final int LABEL_DEFAULT_FONTSIZE
public static final int LABEL_DEFAULT_X_OFFSET
public static final int LABEL_DEFAULT_Y_OFFSET
public static final int MEASURE_DEFAULT_FONTSIZE
public static final int AXES_DEFAULT_FONTSIZE
public static final int SHAPE_BALLS
public static final int SHAPE_STICKS
public static final int SHAPE_HSTICKS
public static final int SHAPE_SSSTICKS
public static final int SHAPE_LABELS
public static final int SHAPE_MEASURES
public static final int SHAPE_DOTS
public static final int SHAPE_STARS
public static final int SHAPE_HALOS
public static final int SHAPE_MIN_SECONDARY
public static final int SHAPE_BACKBONE
public static final int SHAPE_TRACE
public static final int SHAPE_CARTOON
public static final int SHAPE_STRANDS
public static final int SHAPE_MESHRIBBON
public static final int SHAPE_RIBBONS
public static final int SHAPE_ROCKETS
public static final int SHAPE_MAX_SECONDARY
public static final int SHAPE_MIN_SPECIAL
public static final int SHAPE_DIPOLES
public static final int SHAPE_VECTORS
public static final int SHAPE_GEOSURFACE
public static final int SHAPE_ELLIPSOIDS
public static final int SHAPE_MAX_SIZE_ZERO_ON_RESTRICT
public static final int SHAPE_POLYHEDRA
public static final int SHAPE_MIN_HAS_ID
public static final int SHAPE_MIN_MESH_COLLECTION
public static final int SHAPE_DRAW
public static final int SHAPE_MAX_SPECIAL
public static final int SHAPE_MIN_SURFACE
public static final int SHAPE_ISOSURFACE
public static final int SHAPE_LCAOCARTOON
public static final int SHAPE_MO
public static final int SHAPE_PMESH
public static final int SHAPE_MAX_SURFACE
public static final int SHAPE_MAX_MESH_COLLECTION
public static final int SHAPE_ECHO
public static final int SHAPE_MAX_HAS_ID
public static final int SHAPE_AXES
public static final int SHAPE_BBCAGE
public static final int SHAPE_UCCAGE
public static final int SHAPE_HOVER
public static final int SHAPE_FRANK
public static final int SHAPE_MAX
public static final String[] shapeClassBases
public static final int[] shapeToks
public static final int ATOM_IN_FRAME
public static final int ATOM_SLABBED
public static final String PREVIOUS_MESH_ID
public static final int CARTOON_VISIBILITY_FLAG
public static final int ALPHA_CARBON_VISIBILITY_FLAG
static final int STEREO_UNKNOWN
static final int STEREO_NONE
static final int STEREO_DOUBLE
static final int STEREO_REDCYAN
static final int STEREO_REDBLUE
static final int STEREO_REDGREEN
static final int STEREO_CUSTOM
private static final String[] stereoModes
private static final String[][] shellOrder
public static final int SHELL_S
public static final int SHELL_P
public static final int SHELL_SP
public static final int SHELL_L
public static final int SHELL_D_CARTESIAN
public static final int SHELL_D_SPHERICAL
public static final int SHELL_F_CARTESIAN
public static final int SHELL_F_SPHERICAL
private static final String[] quantumShellTags
private static final int[] quantumShellIDs
public static final String LOAD_ATOM_DATA_TYPES
static Class class$org$jmol$viewer$JmolConstants
public void <init> ()
public static java.lang.String getCallbackName (int)
public static int getCallbackId (java.lang.String)
public static java.lang.String getDrawTypeName (int)
public static int connectOperationFromString (java.lang.String)
public static java.lang.String connectOperationName (int)
public static final java.lang.String getPickingModeName (int)
public static final int getPickingMode (java.lang.String)
public static final java.lang.String getPickingStyleName (int)
public static final int getPickingStyle (java.lang.String)
public static int getArgbHbondType (short)
static final short getBondOrderFromString (java.lang.String)
static final short getPartialBondOrderFromInteger (int)
public static final short getPartialBondOrder (int)
public static final int getPartialBondDotted (int)
static final short getBondOrderFromFloat (float)
public static final java.lang.String getBondOrderNameFromOrder (short)
public static final java.lang.String getBondOrderNumberFromOrder (short)
public static final short elementNumberFromSymbol (java.lang.String)
public static final java.lang.String elementSymbolFromNumber (int)
public static final java.lang.String elementNameFromNumber (int)
public static final java.lang.String altElementNameFromIndex (int)
public static final short altElementNumberFromIndex (int)
public static final java.lang.String altElementSymbolFromIndex (int)
public static final java.lang.String altIsotopeSymbolFromIndex (int)
public static final int altElementIndexFromNumber (int)
public static final boolean isNaturalIsotope (java.lang.String)
public static int getVdwType (java.lang.String)
public static int getVanderwaalsMar (int, int)
public static short getBondingMar (int, int)
public static short getBondingMar (int, int, short[])
public static byte pidOf (java.lang.Object)
public static boolean isPaletteVariable (byte)
public static final byte getPaletteID (java.lang.String)
public static final java.lang.String getPaletteName (byte)
public static final java.lang.String getProteinStructureName (int)
public static final boolean checkCarbohydrate (java.lang.String)
private static final java.lang.String getGroup3List ()
public static final boolean isHetero (java.lang.String)
public static final boolean isShapeSecondary (int)
static final int shapeTokenIndex (int)
public static final java.lang.String getShapeClassName (int)
public static final int getShapeVisibilityFlag (int)
static int getStereoMode (java.lang.String)
static java.lang.String getStereoModeName (int)
public static final java.lang.String[] getShellOrder (int)
public static final int getQuantumShellTagID (java.lang.String)
public static final int getQuantumShellTagIDSpherical (java.lang.String)
public static final java.lang.String getQuantumShellTag (int)
public static final java.lang.String canonicalizeQuantumSubshellTag (java.lang.String)
public static final int getQuantumSubshellTagID (int, java.lang.String)
public static final java.lang.String getQuantumSubshellTag (int, int)
static int modelValue (java.lang.String)
static java.lang.Class class$ (java.lang.String)
static void <clinit> ()
}
org/jmol/viewer/ModelManager.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.ModelManager extends java.lang.Object {
private final org.jmol.viewer.Viewer viewer
private org.jmol.modelset.ModelLoader modelLoader
private String fullPathName
private String fileName
void <init> (org.jmol.viewer.Viewer)
org.jmol.modelset.ModelSet zap ()
java.lang.String getModelSetFileName ()
java.lang.String getModelSetPathName ()
org.jmol.modelset.ModelSet createModelSet (java.lang.String, java.lang.String, java.lang.Object, boolean)
private static java.lang.String reduceFilename (java.lang.String)
}
org/jmol/viewer/MonitorInputStream.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.MonitorInputStream extends java.io.FilterInputStream {
int length
int position
int markPosition
int readEventCount
void <init> (java.io.InputStream, int)
public int read () throws java.io.IOException
public int read (byte[]) throws java.io.IOException
public int read (byte[], int, int) throws java.io.IOException
public long skip (long) throws java.io.IOException
public void mark (int)
public void reset () throws java.io.IOException
int getPosition ()
int getLength ()
int getPercentageRead ()
}
org/jmol/viewer/MouseManager$HoverWatcher.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.MouseManager$HoverWatcher extends java.lang.Object implements java.lang.Runnable {
private final org.jmol.viewer.MouseManager this$0
void <init> (org.jmol.viewer.MouseManager)
public void run ()
}
org/jmol/viewer/MouseManager.class
<Unknown>
package org.jmol.viewer
public abstract org.jmol.viewer.MouseManager extends java.lang.Object implements java.awt.event.KeyListener {
protected org.jmol.viewer.Viewer viewer
protected Thread hoverWatcherThread
private int previousDragX
private int previousDragY
protected int xCurrent
protected int yCurrent
protected long timeCurrent
private boolean drawMode
private boolean labelMode
private boolean dragSelectedMode
private boolean measuresEnabled
private org.jmol.modelset.MeasurementPending measurementPending
private boolean hoverActive
private boolean rubberbandSelectionMode
private int xAnchor
private int yAnchor
private final java.awt.Rectangle rectRubber
private int previousClickX
private int previousClickY
private int previousClickModifiers
private int previousClickCount
private long previousClickTime
private int previousPressedX
private int previousPressedY
private int previousPressedModifiers
private long previousPressedTime
private int pressedCount
protected int mouseMovedX
protected int mouseMovedY
protected long mouseMovedTime
private String keyBuffer
boolean isAltKeyReleased
private boolean keyProcessing
static final long MAX_DOUBLE_CLICK_MILLIS
static final int LEFT
static final int MIDDLE
static final int ALT
static final int RIGHT
static final int CTRL
public static final int SHIFT
static final int MIDDLE_RIGHT
static final int LEFT_MIDDLE_RIGHT
static final int CTRL_SHIFT
static final int CTRL_ALT
static final int CTRL_LEFT
static final int CTRL_RIGHT
static final int CTRL_MIDDLE
static final int CTRL_ALT_LEFT
static final int CTRL_ALT_RIGHT
public static final int ALT_LEFT
public static final int ALT_SHIFT_LEFT
public static final int SHIFT_LEFT
static final int CTRL_SHIFT_LEFT
static final int CTRL_ALT_SHIFT_LEFT
static final int SHIFT_MIDDLE
static final int CTRL_SHIFT_MIDDLE
static final int SHIFT_RIGHT
static final int CTRL_SHIFT_RIGHT
static final int CTRL_ALT_SHIFT_RIGHT
private static final int BUTTON_MODIFIER_MASK
static final float wheelClickFractionUp
static final float wheelClickFractionDown
int mouseMovedModifiers
abstract boolean handleOldJvm10Event (java.awt.Event)
void <init> (java.awt.Component, org.jmol.viewer.Viewer)
void clear ()
synchronized void startHoverWatcher (boolean)
void removeMouseListeners11 ()
void removeMouseListeners14 ()
void setModeMouse (int)
private void clearKeyBuffer ()
private void addKeyBuffer (char)
private void sendKeyBuffer ()
public void keyTyped (java.awt.event.KeyEvent)
public void keyPressed (java.awt.event.KeyEvent)
public void keyReleased (java.awt.event.KeyEvent)
protected void processKeyEvent (java.awt.event.KeyEvent)
java.awt.Rectangle getRubberBand ()
private void calcRectRubberBand ()
void mouseMoved (long, int, int, int)
void mouseWheel (long, int, int)
void mousePressed (long, int, int, int, boolean)
void mouseEntered (long, int, int)
void mouseExited (long, int, int)
void mouseReleased (long, int, int, int)
void clearClickCount ()
void mouseClicked (long, int, int, int, int)
void setMouseMode ()
private void checkPointOrAtomClicked (int, int, int, int)
void mouseDragged (long, int, int, int)
void checkMotion ()
private int addToMeasurement (int, org.jmol.util.Point3fi, boolean)
private void enterMeasurementMode ()
private void exitMeasurementMode ()
private void toggleMeasurement ()
void hoverOn (int)
void hoverOff ()
}
org/jmol/viewer/MouseManager10.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.MouseManager10 extends org.jmol.viewer.MouseManager {
int xWhenPressed
int yWhenPressed
int modifiersWhenPressed10
void <init> (java.awt.Component, org.jmol.viewer.Viewer)
private int applyLeftMouse (int)
boolean handleOldJvm10Event (java.awt.Event)
}
org/jmol/viewer/MouseManager11.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.MouseManager11 extends org.jmol.viewer.MouseManager implements java.awt.event.MouseListener java.awt.event.MouseMotionListener {
void <init> (java.awt.Component, org.jmol.viewer.Viewer)
void removeMouseListeners11 ()
boolean handleOldJvm10Event (java.awt.Event)
public void mouseClicked (java.awt.event.MouseEvent)
public void mouseEntered (java.awt.event.MouseEvent)
public void mouseExited (java.awt.event.MouseEvent)
public void mousePressed (java.awt.event.MouseEvent)
public void mouseReleased (java.awt.event.MouseEvent)
public void mouseDragged (java.awt.event.MouseEvent)
public void mouseMoved (java.awt.event.MouseEvent)
}
org/jmol/viewer/MouseManager14.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.MouseManager14 extends org.jmol.viewer.MouseManager11 implements java.awt.event.MouseWheelListener {
void <init> (java.awt.Component, org.jmol.viewer.Viewer)
void removeMouseListeners14 ()
public void mouseWheelMoved (java.awt.event.MouseWheelEvent)
}
org/jmol/viewer/MouseWrapper11.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.MouseWrapper11 extends java.lang.Object {
void <init> ()
static org.jmol.viewer.MouseManager alloc (java.awt.Component, org.jmol.viewer.Viewer)
}
org/jmol/viewer/MouseWrapper14.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.MouseWrapper14 extends java.lang.Object {
void <init> ()
static org.jmol.viewer.MouseManager alloc (java.awt.Component, org.jmol.viewer.Viewer)
}
org/jmol/viewer/PickingManager.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.PickingManager extends java.lang.Object {
private org.jmol.viewer.Viewer viewer
private int pickingMode
private int pickingStyleSelect
private int pickingStyleMeasure
private int pickingStyle
private org.jmol.modelset.MeasurementPending measurementQueued
void <init> (org.jmol.viewer.Viewer)
void clear ()
void setPickingMode (int)
int getPickingMode ()
private void resetMeasurement ()
void setPickingStyle (int)
int getPickingStyle ()
void atomsPicked (java.util.BitSet, int)
private void pickSelected (java.lang.String, int, boolean)
void atomPicked (int, org.jmol.util.Point3fi, int, boolean)
private int queueAtom (int, org.jmol.util.Point3fi)
private void applyMouseStyle (java.lang.String, boolean, boolean, boolean)
}
org/jmol/viewer/PropertyManager.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.PropertyManager extends java.lang.Object {
private static final String atomExpression
private static final String[] propertyTypes
private static final int PROP_APPLET_INFO
private static final int PROP_FILENAME
private static final int PROP_FILEHEADER
static final int PROP_FILECONTENTS_PATH
private static final int PROP_FILECONTENTS
private static final int PROP_ANIMATION_INFO
private static final int PROP_MODEL_INFO
private static final int PROP_SHAPE_INFO
private static final int PROP_MEASUREMENT_INFO
private static final int PROP_CENTER_INFO
private static final int PROP_ORIENTATION_INFO
private static final int PROP_TRANSFORM_INFO
private static final int PROP_ATOM_LIST
private static final int PROP_ATOM_INFO
private static final int PROP_BOND_INFO
private static final int PROP_CHAIN_INFO
private static final int PROP_POLYMER_INFO
private static final int PROP_MOLECULE_INFO
private static final int PROP_STATE_INFO
private static final int PROP_EXTRACT_MODEL
private static final int PROP_JMOL_STATUS
private static final int PROP_JMOL_VIEWER
private static final int PROP_MESSAGE_QUEUE
private static final int PROP_AUXILIARY_INFO
private static final int PROP_BOUNDBOX_INFO
private static final int PROP_DATA_INFO
private static final int PROP_IMAGE
private static final int PROP_EVALUATE
private static final int PROP_MENU
private static final int PROP_MINIMIZATION_INFO
private static final int PROP_POINTGROUP_INFO
private static final int PROP_FILE_INFO
private static final int PROP_ERROR_MESSAGE
private static final int PROP_COUNT
private static final String[] readableTypes
void <init> ()
static int getPropertyNumber (java.lang.String)
static java.lang.String getDefaultParam (int)
static boolean acceptsStringParameter (java.lang.String)
static java.lang.Object getProperty (org.jmol.viewer.Viewer, java.lang.String, java.lang.String, java.lang.Object)
static java.lang.Object extractProperty (java.lang.Object, org.jmol.viewer.ScriptVariable[], int)
private static java.lang.String getPropertyName (int)
private static java.lang.String getParamType (int)
private static boolean isReadableAsString (java.lang.String)
private static java.lang.Object getPropertyAsObject (org.jmol.viewer.Viewer, java.lang.String, java.lang.Object, java.lang.String)
static java.lang.Object getFileInfo (java.lang.Object, java.lang.String)
static void <clinit> ()
}
org/jmol/viewer/RepaintManager.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.RepaintManager extends java.lang.Object {
private org.jmol.viewer.Viewer viewer
private int holdRepaint
boolean repaintPending
private boolean repaintInterrupted
private boolean logTime
private org.jmol.shape.ShapeRenderer[] renderers
void <init> (org.jmol.viewer.Viewer)
void clear ()
void pushHoldRepaint ()
void popHoldRepaint ()
boolean refresh ()
synchronized void requestRepaintAndWait ()
private void repaintDisplay ()
synchronized void cancelRendering ()
synchronized void repaintDone ()
void render (org.jmol.g3d.Graphics3D, org.jmol.modelset.ModelSet)
private void render1 (org.jmol.g3d.Graphics3D, org.jmol.modelset.ModelSet)
void clear (int)
private org.jmol.shape.ShapeRenderer getRenderer (int, org.jmol.g3d.Graphics3D)
private org.jmol.shape.ShapeRenderer allocateRenderer (int, org.jmol.g3d.Graphics3D)
java.lang.String generateOutput (java.lang.String, org.jmol.g3d.Graphics3D, org.jmol.modelset.ModelSet, java.lang.String)
private org.jmol.shape.ShapeRenderer getGenerator (int, org.jmol.g3d.Graphics3D)
}
org/jmol/viewer/ScriptCompilationTokenParser.class
<Unknown>
package org.jmol.viewer
abstract org.jmol.viewer.ScriptCompilationTokenParser extends java.lang.Object {
protected String script
protected short lineCurrent
protected int iCommand
protected int ichCurrentCommand
protected int ichComment
protected int ichEnd
protected int ichToken
protected org.jmol.viewer.Token theToken
protected org.jmol.viewer.Token lastFlowCommand
protected org.jmol.viewer.Token tokenCommand
protected org.jmol.viewer.Token lastToken
protected org.jmol.viewer.Token tokenAndEquals
protected int theTok
protected int nTokens
protected int tokCommand
protected int ptNewSetModifier
protected boolean isNewSet
protected boolean logMessages
protected org.jmol.viewer.Token[] atokenInfix
protected int itokenInfix
protected boolean isSetBrace
protected boolean isMathExpressionCommand
protected boolean isSetOrDefine
private java.util.Vector ltokenPostfix
protected boolean isEmbeddedExpression
protected boolean isCommaAsOrAllowed
private Object theValue
boolean haveString
private boolean residueSpecCodeGenerated
protected String errorMessage
protected String errorMessageUntranslated
protected String errorLine
protected String errorType
protected static final int ERROR_badArgumentCount
protected static final int ERROR_badContext
protected static final int ERROR_commandExpected
protected static final int ERROR_endOfCommandUnexpected
protected static final int ERROR_invalidExpressionToken
protected static final int ERROR_missingEnd
protected static final int ERROR_tokenExpected
protected static final int ERROR_tokenUnexpected
protected static final int ERROR_unrecognizedParameter
protected static final int ERROR_unrecognizedToken
private static final int ERROR_coordinateExpected
private static final int ERROR_endOfExpressionExpected
private static final int ERROR_identifierOrResidueSpecificationExpected
private static final int ERROR_invalidAtomSpecification
private static final int ERROR_invalidChainSpecification
private static final int ERROR_invalidModelSpecification
private static final int ERROR_numberExpected
private static final int ERROR_numberOrVariableNameExpected
private static final int ERROR_residueSpecificationExpected
private static final int ERROR_unrecognizedExpressionToken
void <init> ()
protected boolean compileExpressions ()
protected boolean compileExpression ()
private boolean isExpressionNext ()
protected static boolean tokenAttr (org.jmol.viewer.Token, int)
private boolean moreTokens ()
private int tokAt (int)
private int tokPeek ()
private boolean tokPeek (int)
private int intPeek ()
private java.lang.Object valuePeek ()
private org.jmol.viewer.Token tokenNext ()
private boolean tokenNext (int)
private boolean returnToken ()
private org.jmol.viewer.Token getToken ()
private boolean isToken (int)
private boolean getNumericalToken ()
private float floatValue ()
private boolean addTokenToPostfix (int, java.lang.Object)
private boolean addTokenToPostfix (int, int, java.lang.Object)
private boolean addTokenToPostfix (org.jmol.viewer.Token)
private boolean addNextToken ()
private boolean addNextTokenIf (int)
private boolean addSubstituteTokenIf (int, org.jmol.viewer.Token)
private boolean clauseOr (boolean)
private boolean clauseAnd ()
private boolean clauseNot ()
private boolean clausePrimitive ()
private boolean checkForCoordinate (boolean)
private boolean checkForItemSelector ()
private boolean clauseWithin ()
private boolean clauseConnected ()
private boolean clauseSubstructure ()
private boolean clauseItemSelector ()
private boolean clauseComparator (boolean)
private boolean clauseCell ()
private boolean clauseDefine ()
private boolean generateResidueSpecCode (org.jmol.viewer.Token)
private boolean clauseResidueSpec ()
private boolean clauseResNameSpec ()
private boolean clauseSequenceSpec ()
private org.jmol.viewer.Token getSequenceCode (boolean)
private boolean clauseChainSpec (int)
private boolean isSpecTerminator (int)
private boolean clauseAlternateSpec ()
private boolean clauseModelSpec ()
private boolean clauseAtomSpec ()
static java.lang.String errorString (int, java.lang.String, java.lang.String, boolean)
protected boolean commandExpected ()
protected boolean error (int)
protected boolean error (int, java.lang.String)
protected boolean error (int, java.lang.String, java.lang.String)
protected boolean error (java.lang.String, java.lang.String)
}
org/jmol/viewer/ScriptCompiler.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.ScriptCompiler extends org.jmol.viewer.ScriptCompilationTokenParser {
private static final String LOAD_TYPES
private org.jmol.viewer.Viewer viewer
private String filename
private boolean isSilent
private java.util.Hashtable contextVariables
private org.jmol.viewer.Token[][] aatokenCompiled
private short[] lineNumbers
private int[][] lineIndices
private int lnLength
private boolean preDefining
private boolean isShowScriptOutput
private boolean isCheckOnly
private boolean haveComments
String scriptExtensions
private org.jmol.viewer.ScriptFunction thisFunction
private org.jmol.viewer.ScriptFlowContext flowContext
private java.util.Vector ltoken
private java.util.Vector lltoken
private java.util.Vector vBraces
private int ichBrace
private int cchToken
private int cchScript
private int nSemiSkip
private int parenCount
private int braceCount
private int setBraceCount
private int bracketCount
private int ptSemi
private int forPoint3
private int setEqualPt
private int iBrace
private boolean iHaveQuotedString
private boolean isEndOfCommand
private boolean needRightParen
private boolean endOfLine
private String comment
private static final int OK
private static final int OK2
private static final int CONTINUE
private static final int EOL
private static final int ERROR
private int tokLastMath
private boolean isShowCommand
char chFirst
void <init> (org.jmol.viewer.Viewer)
org.jmol.viewer.ScriptContext parseScriptForTokens (java.lang.String)
private org.jmol.viewer.ScriptContext parseScript (boolean)
org.jmol.viewer.ScriptContext compile (java.lang.String, java.lang.String, boolean, boolean, boolean, boolean)
private void addContextVariable (java.lang.String)
private boolean isContextVariable (java.lang.String)
private java.lang.String cleanScriptComments (java.lang.String)
private void addTokenToPrefix (org.jmol.viewer.Token)
private boolean compile0 (boolean)
private void setAaTokenCompiled ()
private boolean lookingAtLeadingWhitespace ()
private boolean isLineContinuation (int, boolean)
private boolean lookingAtMathContinuation (int)
private boolean lookingAtEndOfLine ()
private int nCharNewLine (int)
private boolean lookingAtEndOfStatement ()
private int lookingAtComment ()
private int processTokenList (short, boolean)
private boolean compileCommand ()
private java.lang.String getPrefixToken ()
private int checkSpecialParameterSyntax ()
private int parseKnownToken (java.lang.String)
private int parseCommandParameter (java.lang.String)
private boolean checkFlowStartBrace (boolean)
private int checkFlowEndBrace ()
private int forceFlowEnd (org.jmol.viewer.Token)
private boolean checkFlowCommand (java.lang.String)
private boolean checkFlowEnd (int, java.lang.String, int)
private boolean getData (java.lang.String)
private int incrementLineCount (java.lang.String)
private static boolean isSpaceOrTab (char)
private boolean eol (char)
static boolean eol (char, int)
private boolean lookingAtBraceSyntax ()
private boolean lookingAtString (boolean)
java.lang.String getUnescapedStringLiteral ()
static int getHexitValue (char)
private boolean lookingAtLoadFormat ()
private boolean lookingAtImpliedString ()
static int ichMathTerminator (java.lang.String, int, int)
private float lookingAtExponential ()
private boolean lookingAtDecimal ()
private boolean lookingAtSeqcode ()
private boolean lookingAtInteger ()
java.util.BitSet lookingAtBitset ()
private boolean lookingAtObjectID (boolean)
private boolean lookingAtLookupToken (int)
private boolean charToken ()
private int ERROR (int)
private int ERROR (int, java.lang.String)
private boolean handleError ()
}
org/jmol/viewer/ScriptContext.class
<Unknown>
package org.jmol.viewer
public org.jmol.viewer.ScriptContext extends java.lang.Object {
public String fullpath
public String filename
public String functionName
public String script
public short[] lineNumbers
public int[][] lineIndices
public org.jmol.viewer.Token[][] aatoken
public org.jmol.viewer.Token[] statement
public int statementLength
public int pc
public int pcEnd
public int lineEnd
public int iToken
public StringBuffer outputBuffer
public java.util.Hashtable contextVariables
public boolean isStateScript
public String errorMessage
public String errorMessageUntranslated
public int iCommandError
public String errorType
public org.jmol.viewer.ScriptContext[] stack
public int scriptLevel
public boolean isSyntaxCheck
public boolean executionStepping
public boolean executionPaused
public String scriptExtensions
public String contextPath
void <init> ()
}
org/jmol/viewer/ScriptEvaluator$ScriptException.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.ScriptEvaluator$ScriptException extends java.lang.Exception {
private String message
private String untranslated
private final org.jmol.viewer.ScriptEvaluator this$0
void <init> (org.jmol.viewer.ScriptEvaluator, java.lang.String, java.lang.String)
protected java.lang.String getErrorMessageUntranslated ()
public java.lang.String toString ()
}
org/jmol/viewer/ScriptEvaluator.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.ScriptEvaluator extends java.lang.Object {
private boolean tQuiet
protected boolean isSyntaxCheck
private boolean isCmdLine_C_Option
protected boolean isCmdLine_c_or_C_Option
private boolean historyDisabled
protected boolean logMessages
private boolean debugScript
private boolean interruptExecution
private boolean executionPaused
private boolean executionStepping
private boolean isExecuting
private long timeBeginExecution
private long timeEndExecution
private static final String EXPRESSION_KEY
private static final int scriptLevelMax
private Thread currentThread
protected org.jmol.viewer.Viewer viewer
protected org.jmol.viewer.ScriptCompiler compiler
private java.util.Hashtable definedAtomSets
private StringBuffer outputBuffer
private org.jmol.viewer.ScriptContext[] stack
private String contextPath
private String filename
private String functionName
private boolean isStateScript
private int scriptLevel
private int scriptReportingLevel
private int commandHistoryLevelMax
private org.jmol.viewer.Token[][] aatoken
private short[] lineNumbers
private int[][] lineIndices
private java.util.Hashtable contextVariables
private String script
protected int pc
private String thisCommand
private String fullCommand
private org.jmol.viewer.Token[] statement
private int statementLength
private int iToken
private int lineEnd
private int pcEnd
private String scriptExtensions
private boolean error
private String errorMessage
protected String errorMessageUntranslated
protected String errorType
protected int iCommandError
private boolean ignoreError
static final int ERROR_axisExpected
static final int ERROR_backgroundModelError
static final int ERROR_badArgumentCount
static final int ERROR_badMillerIndices
static final int ERROR_badRGBColor
static final int ERROR_booleanExpected
static final int ERROR_booleanOrNumberExpected
static final int ERROR_booleanOrWhateverExpected
static final int ERROR_colorExpected
static final int ERROR_colorOrPaletteRequired
static final int ERROR_commandExpected
static final int ERROR_coordinateOrNameOrExpressionRequired
static final int ERROR_drawObjectNotDefined
static final int ERROR_endOfStatementUnexpected
static final int ERROR_expressionExpected
static final int ERROR_expressionOrIntegerExpected
static final int ERROR_filenameExpected
static final int ERROR_fileNotFoundException
static final int ERROR_incompatibleArguments
static final int ERROR_insufficientArguments
static final int ERROR_integerExpected
static final int ERROR_integerOutOfRange
static final int ERROR_invalidArgument
static final int ERROR_invalidParameterOrder
static final int ERROR_keywordExpected
static final int ERROR_moCoefficients
static final int ERROR_moIndex
static final int ERROR_moModelError
static final int ERROR_moOccupancy
static final int ERROR_moOnlyOne
static final int ERROR_multipleModelsNotOK
static final int ERROR_noData
static final int ERROR_noPartialCharges
static final int ERROR_noUnitCell
static final int ERROR_numberExpected
static final int ERROR_numberMustBe
static final int ERROR_numberOutOfRange
static final int ERROR_objectNameExpected
static final int ERROR_planeExpected
static final int ERROR_propertyNameExpected
static final int ERROR_spaceGroupNotFound
static final int ERROR_stringExpected
static final int ERROR_stringOrIdentifierExpected
static final int ERROR_tooManyPoints
static final int ERROR_tooManyScriptLevels
static final int ERROR_unrecognizedAtomProperty
static final int ERROR_unrecognizedBondProperty
static final int ERROR_unrecognizedCommand
static final int ERROR_unrecognizedExpression
static final int ERROR_unrecognizedObject
static final int ERROR_unrecognizedParameter
static final int ERROR_unrecognizedParameterWarning
static final int ERROR_unrecognizedShowParameter
static final int ERROR_what
static final int ERROR_writeWhat
private org.jmol.viewer.Token[] tempStatement
private boolean isBondSet
private Object expressionResult
private int theTok
private org.jmol.viewer.Token theToken
private boolean coordinatesAreFractional
private Object[] data
void <init> (org.jmol.viewer.Viewer)
public boolean compileScriptString (java.lang.String, boolean)
public boolean compileScriptFile (java.lang.String, boolean)
public void evaluateCompiledScript (boolean, boolean, boolean, boolean)
public void runScript (java.lang.String, java.lang.StringBuffer) throws org.jmol.viewer.ScriptEvaluator$ScriptException
public org.jmol.viewer.ScriptContext checkScriptSilent (java.lang.String)
void setDebugging ()
int getExecutionWalltime ()
void haltExecution ()
void pauseExecution ()
void stepPausedExecution ()
void resumePausedExecution ()
boolean isScriptExecuting ()
boolean isExecutionPaused ()
boolean isExecutionStepping ()
java.lang.String getNextStatement ()
private java.lang.String getCommand (int, boolean, boolean)
private void logDebugScript (int)
static java.lang.Object evaluateExpression (org.jmol.viewer.Viewer, java.lang.Object)
static java.util.BitSet getAtomBitSet (org.jmol.viewer.ScriptEvaluator, java.lang.Object)
static java.util.Vector getAtomBitSetVector (org.jmol.viewer.ScriptEvaluator, int, java.lang.Object)
private java.lang.Object parameterExpression (int, int, java.lang.String, boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private java.lang.Object parameterExpression (int, int, java.lang.String, boolean, int, boolean, java.util.Hashtable, java.lang.String) throws org.jmol.viewer.ScriptEvaluator$ScriptException
java.lang.Object bitsetVariableVector (java.lang.Object)
java.lang.Object getBitsetIdent (java.util.BitSet, java.lang.String, java.lang.Object, boolean, int, boolean)
private org.jmol.viewer.ScriptVariable getBitsetPropertySelector (int, boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
protected java.lang.Object getBitsetProperty (java.util.BitSet, int, javax.vecmath.Point3f, javax.vecmath.Point4f, java.lang.Object, java.lang.Object, boolean, int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void setBitsetProperty (java.util.BitSet, int, int, float, org.jmol.viewer.Token) throws org.jmol.viewer.ScriptEvaluator$ScriptException
java.lang.String getScript ()
private boolean compileScript (java.lang.String, java.lang.String, boolean)
private int setScriptExtensions ()
private void runScript (java.lang.String) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean compileScriptFileInternal (java.lang.String)
private java.lang.Object getParameter (java.lang.String, boolean)
private java.lang.String getParameterEscaped (java.lang.String)
private java.lang.String getStringParameter (java.lang.String, boolean)
private java.lang.Object getNumericParameter (java.lang.String)
private org.jmol.viewer.ScriptVariable getContextVariableAsVariable (java.lang.String)
private java.lang.Object getStringObjectAsVariable (java.lang.String, java.lang.String)
private boolean loadFunction (java.lang.String, java.util.Vector)
protected org.jmol.viewer.ScriptVariable getFunctionReturn (java.lang.String, java.util.Vector, org.jmol.viewer.ScriptVariable) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void clearDefinedVariableAtomSets ()
private void defineSets ()
private void defineAtomSet (java.lang.String)
private java.util.BitSet lookupIdentifierValue (java.lang.String) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private java.util.BitSet lookupValue (java.lang.String, boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
void deleteAtomsInVariables (java.util.BitSet)
private boolean setStatement (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void clearState (boolean)
private void pushContext (org.jmol.viewer.ScriptFunction) throws org.jmol.viewer.ScriptEvaluator$ScriptException
org.jmol.viewer.ScriptContext getScriptContext ()
private void getScriptContext (org.jmol.viewer.ScriptContext, boolean)
private void popContext ()
private java.lang.String getContext (boolean)
private int getLinenumber (org.jmol.viewer.ScriptContext)
private java.lang.String getScriptID (org.jmol.viewer.ScriptContext)
java.lang.String getErrorMessage ()
java.lang.String getErrorMessageUntranslated ()
private void setErrorMessage (java.lang.String)
private void planeExpected () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void integerOutOfRange (int, int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void numberOutOfRange (float, float) throws org.jmol.viewer.ScriptEvaluator$ScriptException
void error (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
void error (int, java.lang.String) throws org.jmol.viewer.ScriptEvaluator$ScriptException
void error (int, java.lang.String, java.lang.String) throws org.jmol.viewer.ScriptEvaluator$ScriptException
void error (int, java.lang.String, java.lang.String, java.lang.String) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void warning (int, java.lang.String, java.lang.String) throws org.jmol.viewer.ScriptEvaluator$ScriptException
void error (int, java.lang.String, java.lang.String, java.lang.String, boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
void evalError (java.lang.String, java.lang.String) throws org.jmol.viewer.ScriptEvaluator$ScriptException
static java.lang.String errorString (int, java.lang.String, java.lang.String, java.lang.String, boolean)
java.lang.String contextTrace ()
static java.lang.String setErrorLineMessage (java.lang.String, java.lang.String, int, int, java.lang.String)
public java.lang.String toString ()
private java.lang.String statementAsString (org.jmol.viewer.Token[], int)
private void setShapeProperty (int, java.lang.String, java.lang.Object)
private void setShapeSize (int, int)
private void setShapeSize (int, int, float)
private void setBooleanProperty (java.lang.String, boolean)
private boolean setIntProperty (java.lang.String, int)
private boolean setFloatProperty (java.lang.String, float)
private void setStringProperty (java.lang.String, java.lang.String)
private void showString (java.lang.String)
private void scriptStatusOrBuffer (java.lang.String)
private java.util.BitSet expression (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private java.util.BitSet expression (org.jmol.viewer.Token[], int, int, boolean, boolean, boolean, boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private java.util.BitSet compareFloat (int, float[], int, float)
private java.util.BitSet compareString (int, int, java.lang.String) throws org.jmol.viewer.ScriptEvaluator$ScriptException
protected java.util.BitSet compareInt (int, float[], int, int)
private boolean compareString (int, java.lang.String, java.lang.String) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private static boolean compareInt (int, int, int)
private static boolean compareFloat (int, float, float)
private java.util.BitSet getAtomBits (int, java.lang.Object)
private static int getSeqCode (org.jmol.viewer.Token)
private void checkLength (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void checkLength (int, int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private int checkLength23 () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void checkLength34 () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private org.jmol.viewer.Token getToken (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private int tokAt (int)
private int tokAt (int, org.jmol.viewer.Token[])
private org.jmol.viewer.Token tokenAt (int, org.jmol.viewer.Token[])
private boolean checkToken (int)
private int modelNumberParameter (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private java.lang.String optParameterAsString (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private java.lang.String parameterAsString (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private int intParameter (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private int intParameter (int, int, int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean isFloatParameter (int)
private float floatParameter (int, float, float) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private float floatParameter (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private float[] floatParameterSet (int, int, int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private java.lang.String stringParameter (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private java.lang.String objectNameParameter (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private float radiusParameter (int, float) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean booleanParameter (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private javax.vecmath.Point3f atomCenterOrCoordinateParameter (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean isCenterParameter (int)
private javax.vecmath.Point3f centerParameter (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private javax.vecmath.Point4f planeParameter (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private javax.vecmath.Point4f hklParameter (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private int getMadParameter () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private int getSetAxesTypeMad (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean isColorParam (int)
private int getArgbParam (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private int getArgbParamLast (int, boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private int getArgbParam (int, boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
static int colorPtToInt (javax.vecmath.Point3f)
private int getColorTriad (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean isPoint3f (int)
private javax.vecmath.Point3f getPoint3f (int, boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private javax.vecmath.Point4f getPoint4f (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private java.lang.Object getPointOrPlane (int, boolean, boolean, boolean, boolean, int, int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private javax.vecmath.Point3f xypParameter (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private int intSetting (int, int, int, int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private int intSetting (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private float floatSetting (int, float, float) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private float floatSetting (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private java.lang.String stringSetting (int, boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private org.jmol.viewer.ScriptVariable tokenSetting (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean isCommandDisplayable (int)
private boolean checkContinue ()
private void instructionDispatchLoop (boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean flowControl (int, boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean ifCmd () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void returnCmd () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void help () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void move () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void moveto () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void navigate () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void bondorder () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void console () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void centerAt () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void stereo () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void connect (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private float getTranslucentLevel (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void getProperty () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void background (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void center (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private java.lang.String setObjectProperty () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void color () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean changeElementColor (java.lang.String, int)
private void colorObject (int, int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void colorShape (int, int, boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void setShapeTranslucency (int, java.lang.String, java.lang.String, float, java.util.BitSet)
private void cd () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void data () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void define () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void echo (int, boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void message () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void print () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean pause () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void label (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void hover () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void load () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private java.lang.String getFullPathName () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void dataFrame (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void monitor () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void refresh ()
private void reset () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void restrict () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void restrictSelected (boolean, boolean)
private void rotate (boolean, boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private javax.vecmath.Point3f getObjectCenter (java.lang.String, int)
private javax.vecmath.Vector3f getDrawObjectAxis (java.lang.String)
private void script (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void function () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void sync () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void history (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void display (boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void delete () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void minimize () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void select (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void subset () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void invertSelected () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void translateSelected () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void translate () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void zap (boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void zoom (boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private float getZoom (int, java.util.BitSet, float) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void gotocmd () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void delay () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void delay (long)
private void slab (boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void ellipsoid () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private java.lang.String getShapeNameParameter (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private java.lang.String setShapeId (int, int, boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void setAtomShapeSize (int, int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void structure () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void wireframe () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void ssbond () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void hbond (boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void configuration () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void vector () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void dipole () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void animationMode () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void vibration () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void animationDirection () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void calculate () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void pointGroup () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void dots (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void proteinShape (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void animation () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void file () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void frame (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
java.util.BitSet bitSetForModelFileNumber (int)
private void frameControl (int, boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private int getShapeType (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void font (int, float) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void set () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void setVariable (int, int, java.lang.String, boolean, int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean setParameter (java.lang.String, int, boolean, boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void axes (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void boundbox (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void unitcell (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void frank (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void setUserColors () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void setBondmode () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void selectionHalo (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void setEcho () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean setLabel (java.lang.String) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void setMonitor () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean setMeasurementUnits (java.lang.String) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void setProperty () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void setSpin (java.lang.String, int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void setNav (java.lang.String, int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void setSsbond () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void setHbond () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void setPicking () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void setPickingStyle () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void save () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void restore () throws org.jmol.viewer.ScriptEvaluator$ScriptException
java.lang.String write (org.jmol.viewer.Token[]) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void show () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private java.lang.String getIsosurfaceJvxl ()
private java.lang.String getMoJvxl (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private java.lang.String extractCommandOption (java.lang.String)
private void draw () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void polyhedra () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void lcaoCartoon () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean mo (boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private java.lang.String setColorOptions (int, int, int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private int moOffset (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void setMoData (int, int, int, int, java.lang.String) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private java.lang.String initIsosurface (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private java.lang.String getNextComment ()
private boolean listIsosurface (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void isosurface (int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean setMeshDisplayProperty (int, int, int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
static org.jmol.util.Quaternion getAtomQuaternion (org.jmol.viewer.Viewer, java.util.BitSet)
}
org/jmol/viewer/ScriptFlowContext.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.ScriptFlowContext extends java.lang.Object {
private org.jmol.viewer.ScriptCompiler compiler
org.jmol.viewer.Token token
private int pt0
org.jmol.viewer.ScriptFunction function
private org.jmol.viewer.ScriptFlowContext parent
int lineStart
int commandStart
int ptLine
int ptCommand
boolean forceEndIf
String ident
void <init> (org.jmol.viewer.ScriptCompiler, org.jmol.viewer.Token, int, org.jmol.viewer.ScriptFlowContext)
org.jmol.viewer.ScriptFlowContext getBreakableContext (int)
boolean checkForceEndIf (int)
int getPt0 ()
int setPt0 (int)
public void setLine ()
public java.lang.String toString ()
org.jmol.viewer.ScriptFlowContext getParent ()
java.lang.String path ()
void setFunction (org.jmol.viewer.ScriptFunction)
}
org/jmol/viewer/ScriptFunction.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.ScriptFunction extends java.lang.Object {
int pt0
int chpt0
int cmdpt0
String name
String script
org.jmol.viewer.Token[][] aatoken
short[] lineNumbers
int[][] lineIndices
int nParameters
java.util.Vector names
java.util.Hashtable variables
org.jmol.viewer.ScriptVariable returnValue
public boolean isVariable (java.lang.String)
void <init> (java.lang.String)
void setVariables (java.util.Hashtable, java.util.Vector)
public void unsetVariables (java.util.Hashtable, java.util.Vector)
void addVariable (java.lang.String, boolean)
static void setFunction (org.jmol.viewer.ScriptFunction, java.lang.String, int, int, short[], int[][], java.util.Vector)
private void setScript (java.lang.String)
public java.lang.String getSignature ()
public java.lang.String toString ()
}
org/jmol/viewer/ScriptManager$CommandWatcher.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.ScriptManager$CommandWatcher extends java.lang.Object implements java.lang.Runnable {
private final org.jmol.viewer.ScriptManager this$0
void <init> (org.jmol.viewer.ScriptManager)
public void run ()
}
org/jmol/viewer/ScriptManager$ScriptQueueRunnable.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.ScriptManager$ScriptQueueRunnable extends java.lang.Object implements java.lang.Runnable {
boolean startedByCommandThread
int pt
private final org.jmol.viewer.ScriptManager this$0
public void <init> (org.jmol.viewer.ScriptManager, boolean, int)
public void run ()
public void stop ()
private boolean runNextScript ()
private void runScript (java.lang.String, java.lang.String, java.lang.String, boolean, boolean)
}
org/jmol/viewer/ScriptManager.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.ScriptManager extends java.lang.Object {
org.jmol.viewer.Viewer viewer
Thread[] queueThreads
boolean[] scriptQueueRunning
java.util.Vector scriptQueue
boolean useQueue
Thread commandWatcherThread
boolean useCommandWatcherThread
static final String SCRIPT_COMPLETED
void <init> (org.jmol.viewer.Viewer)
void clear ()
public void setQueue (boolean)
public java.lang.String addScript (java.lang.String)
public java.lang.String addScript (java.lang.String, boolean, boolean)
public java.lang.Object addScript (java.lang.String, java.lang.String, java.lang.String, boolean, boolean)
public int getScriptCount ()
public void clearQueue ()
public void waitForQueue ()
public synchronized void flushQueue (java.lang.String)
void startScriptQueue (boolean)
java.util.Vector getScriptItem (boolean, boolean)
synchronized void startCommandWatcher (boolean)
void interruptQueueThreads ()
}
org/jmol/viewer/ScriptMathProcessor.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.ScriptMathProcessor extends java.lang.Object {
private boolean isSyntaxCheck
private boolean logMessages
private org.jmol.viewer.ScriptEvaluator eval
private org.jmol.viewer.Viewer viewer
private org.jmol.viewer.Token[] oStack
private org.jmol.viewer.ScriptVariable[] xStack
private char[] ifStack
private int ifPt
private int oPt
private int xPt
private int parenCount
private int squareCount
private int braceCount
private boolean wasX
private int incrementX
private boolean isArrayItem
private boolean asVector
private int ptid
private int ptx
private boolean skipping
void <init> (org.jmol.viewer.ScriptEvaluator, boolean, boolean)
org.jmol.viewer.ScriptVariable getResult (boolean, java.lang.String) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private void putX (org.jmol.viewer.ScriptVariable)
private void putOp (org.jmol.viewer.Token)
private void putIf (char)
boolean addX (org.jmol.viewer.ScriptVariable)
boolean addX (java.lang.Object)
boolean addXNum (org.jmol.viewer.ScriptVariable) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean addX (boolean)
private boolean addX (int)
private boolean addX (float)
private static boolean isOpFunc (org.jmol.viewer.Token)
boolean addOp (org.jmol.viewer.Token) throws org.jmol.viewer.ScriptEvaluator$ScriptException
boolean addOp (org.jmol.viewer.Token, boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean doBitsetSelect ()
void dumpStacks (java.lang.String)
private org.jmol.viewer.ScriptVariable getX () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean evaluateFunction () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean evaluateSymop (org.jmol.viewer.ScriptVariable[], boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean evaluateBin (org.jmol.viewer.ScriptVariable[]) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean evaluateHelix (org.jmol.viewer.ScriptVariable[]) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean evaluateDistance (org.jmol.viewer.ScriptVariable[], int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private javax.vecmath.Point3f ptValue (org.jmol.viewer.ScriptVariable) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private javax.vecmath.Point4f planeValue (org.jmol.viewer.Token)
private boolean evaluateMeasure (org.jmol.viewer.ScriptVariable[], boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean evaluateUserFunction (java.lang.String, org.jmol.viewer.ScriptVariable[], int, boolean) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean evaluateFind (org.jmol.viewer.ScriptVariable[]) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean evaluateGetProperty (org.jmol.viewer.ScriptVariable[])
private boolean evaluatePoint (org.jmol.viewer.ScriptVariable[])
private boolean evaluatePlane (org.jmol.viewer.ScriptVariable[]) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean evaluateReplace (org.jmol.viewer.ScriptVariable[]) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean evaluateString (int, org.jmol.viewer.ScriptVariable[]) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean evaluateList (int, org.jmol.viewer.ScriptVariable[]) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean evaluateArray (org.jmol.viewer.ScriptVariable[])
private boolean evaluateMath (org.jmol.viewer.ScriptVariable[], int)
private boolean evaluateRandom (org.jmol.viewer.ScriptVariable[])
private boolean evaluateCross (org.jmol.viewer.ScriptVariable[])
private boolean evaluateLoad (org.jmol.viewer.ScriptVariable[], int)
private boolean evaluateWrite (org.jmol.viewer.ScriptVariable[]) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean evaluateScript (org.jmol.viewer.ScriptVariable[], int) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean evaluateData (org.jmol.viewer.ScriptVariable[])
private boolean evaluateLabel (int, org.jmol.viewer.ScriptVariable[]) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean evaluateWithin (org.jmol.viewer.ScriptVariable[])
private boolean evaluateConnected (org.jmol.viewer.ScriptVariable[])
private boolean evaluateSubstructure (org.jmol.viewer.ScriptVariable[]) throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean operate () throws org.jmol.viewer.ScriptEvaluator$ScriptException
private boolean evaluateBoundBox (org.jmol.viewer.ScriptVariable)
private boolean evaluatePointOrBitsetOperation (org.jmol.viewer.Token, org.jmol.viewer.ScriptVariable) throws org.jmol.viewer.ScriptEvaluator$ScriptException
}
org/jmol/viewer/ScriptVariable.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.ScriptVariable extends org.jmol.viewer.Token {
private static final org.jmol.viewer.ScriptVariable vT
private static final org.jmol.viewer.ScriptVariable vF
static org.jmol.viewer.ScriptVariable vAll
int index
String name
private static final int FLAG_CANINCREMENT
private static final int FLAG_LOCALVAR
int flags
static final javax.vecmath.Point3f pt0
void <init> ()
void <init> (int)
void <init> (int, int, java.lang.Object)
void <init> (int, java.lang.Object)
void <init> (int, int)
void <init> (java.util.BitSet, int)
void <init> (org.jmol.viewer.Token)
static org.jmol.viewer.ScriptVariable getVariable (java.lang.Object)
org.jmol.viewer.ScriptVariable set (org.jmol.viewer.ScriptVariable)
org.jmol.viewer.ScriptVariable setName (java.lang.String)
org.jmol.viewer.ScriptVariable setGlobal ()
boolean canIncrement ()
boolean increment (int)
static org.jmol.viewer.ScriptVariable getVariableSelected (int, java.lang.Object)
boolean asBoolean ()
int asInt ()
float asFloat ()
java.lang.String asString ()
java.lang.Object getValAsObj ()
static final org.jmol.viewer.ScriptVariable intVariable (int)
static java.lang.Object oValue (org.jmol.viewer.ScriptVariable)
static java.lang.Object nValue (org.jmol.viewer.Token)
static boolean bValue (org.jmol.viewer.Token)
static int iValue (org.jmol.viewer.Token)
static float fValue (org.jmol.viewer.Token)
static float toFloat (java.lang.String)
static java.lang.String sValue (org.jmol.viewer.Token)
static java.lang.String sValue (org.jmol.viewer.ScriptVariable)
static int sizeOf (org.jmol.viewer.Token)
static java.lang.String typeOf (org.jmol.viewer.ScriptVariable)
static java.lang.String[] concatList (org.jmol.viewer.ScriptVariable, org.jmol.viewer.ScriptVariable)
static java.util.BitSet bsSelect (org.jmol.viewer.Token)
static java.util.BitSet bsSelect (org.jmol.viewer.ScriptVariable)
static java.util.BitSet bsSelect (org.jmol.viewer.Token, int)
static org.jmol.viewer.ScriptVariable selectItem (org.jmol.viewer.ScriptVariable)
static org.jmol.viewer.Token selectItem (org.jmol.viewer.Token)
static org.jmol.viewer.ScriptVariable selectItem (org.jmol.viewer.ScriptVariable, int)
static org.jmol.viewer.Token selectItem (org.jmol.viewer.Token, int)
static org.jmol.viewer.ScriptVariable tValue (java.lang.String)
boolean setSelectedValue (int, org.jmol.viewer.ScriptVariable)
java.lang.String escape ()
static java.lang.Object unescapePointOrBitsetAsVariable (java.lang.String)
static org.jmol.viewer.ScriptVariable getBoolean (boolean)
static java.lang.Object sprintf (java.lang.String, org.jmol.viewer.ScriptVariable)
private static java.lang.String sprintf (java.lang.String, org.jmol.viewer.ScriptVariable, java.lang.Object[], int[], float[], double[], boolean, boolean)
static java.lang.String sprintf (org.jmol.viewer.ScriptVariable[])
public java.lang.String toString ()
static void <clinit> ()
}
org/jmol/viewer/SelectionManager.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.SelectionManager extends java.lang.Object {
private org.jmol.viewer.Viewer viewer
private org.jmol.api.JmolSelectionListener[] listeners
final java.util.BitSet bsSelection
java.util.BitSet bsSubset
java.util.BitSet bsDeleted
private static final int TRUE
private static final int FALSE
private static final int UNKNOWN
private int empty
private boolean hideNotSelected
private final java.util.BitSet bsHidden
void <init> (org.jmol.viewer.Viewer)
void clear ()
void hide (java.util.BitSet, boolean)
void display (java.util.BitSet, java.util.BitSet, boolean)
java.util.BitSet getHiddenSet ()
boolean getHideNotSelected ()
void setHideNotSelected (boolean)
boolean isSelected (int)
void select (java.util.BitSet, boolean)
void selectAll (boolean)
void clearSelection (boolean)
void setSelectionSet (java.util.BitSet)
void setSelectionSubset (java.util.BitSet)
boolean isInSelectionSubset (int)
void invertSelection ()
private void excludeSelectionSet (java.util.BitSet)
int getSelectionCount ()
void addListener (org.jmol.api.JmolSelectionListener)
private void selectionChanged (boolean)
java.lang.String getState (java.lang.StringBuffer)
public int deleteAtoms (java.util.BitSet)
java.util.BitSet getDeletedAtoms ()
}
org/jmol/viewer/StateManager$Connection.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.StateManager$Connection extends java.lang.Object {
int atomIndex1
int atomIndex2
short mad
short colix
short order
int shapeVisibilityFlags
void <init> (int, int, short, short, short, int)
}
org/jmol/viewer/StateManager$Connections.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.StateManager$Connections extends java.lang.Object {
String saveName
int bondCount
org.jmol.viewer.StateManager$Connection[] connections
private final org.jmol.viewer.StateManager this$0
void <init> (org.jmol.viewer.StateManager)
void restore ()
}
org/jmol/viewer/StateManager$GlobalSettings.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.StateManager$GlobalSettings extends java.lang.Object {
java.util.Hashtable htUserVariables
int ambientPercent
int diffusePercent
boolean specular
int specularExponent
int specularPercent
int specularPower
boolean allowEmbeddedScripts
boolean appendNew
String appletProxy
boolean applySymmetryToBonds
String atomTypes
boolean autoBond
boolean autoLoadOrientation
short bondRadiusMilliAngstroms
float bondTolerance
String defaultLoadScript
String defaultDirectory
boolean forceAutoBond
char inlineNewlineChar
String loadFormat
float minBondDistance
boolean pdbGetHeader
boolean pdbSequential
int percentVdwAtom
boolean smartAromatic
boolean zeroBasedXyzRasmol
private final javax.vecmath.Point3f ptDefaultLattice
boolean allowRotateSelected
boolean perspectiveDepth
float visualRange
boolean solventOn
String defaultAngleLabel
String defaultDistanceLabel
String defaultTorsionLabel
boolean justifyMeasurements
boolean measureAllModels
int minimizationSteps
boolean minimizationRefresh
float minimizationCriterion
boolean antialiasDisplay
boolean antialiasImages
boolean imageState
boolean antialiasTranslucent
boolean displayCellParameters
boolean dotsSelectedOnly
boolean dotSurface
int dotDensity
boolean dynamicMeasurements
boolean greyscaleRendering
boolean isosurfacePropertySmoothing
boolean showHiddenSelectionHalos
boolean allowKeyStrokes
boolean showKeyStrokes
boolean showMeasurements
boolean zoomLarge
String backgroundImageFileName
boolean bondModeOr
boolean hbondsBackbone
float hbondsAngleMinimum
float hbondsDistanceMaximum
boolean hbondsSolid
byte modeMultipleBond
boolean showHydrogens
boolean showMultipleBonds
boolean ssbondsBackbone
boolean cartoonRockets
boolean chainCaseSensitive
int hermiteLevel
boolean highResolutionFlag
boolean rangeSelected
boolean rasmolHydrogenSetting
boolean rasmolHeteroSetting
int ribbonAspectRatio
boolean ribbonBorder
boolean rocketBarrels
float sheetSmoothing
boolean traceAlpha
int animationFps
boolean autoFps
boolean axesOrientationRasmol
int axesMode
float axesScale
float cameraDepth
String dataSeparator
boolean debugScript
float defaultDrawArrowScale
float defaultTranslucent
int delayMaximumMs
float dipoleScale
boolean disablePopupMenu
boolean drawHover
boolean drawPicking
boolean bondPicking
boolean atomPicking
String helpPath
boolean fontScaling
boolean fontCaching
int helixStep
boolean hideNameInPopup
int hoverDelayMs
float loadAtomDataTolerance
boolean measurementLabels
boolean messageStyleChime
int pickingSpinRate
String pickLabel
float pointGroupDistanceTolerance
float pointGroupLinearTolerance
String propertyColorScheme
String quaternionFrame
float solventProbeRadius
int scriptDelay
boolean selectAllModels
boolean statusReporting
int strandCountForStrands
int strandCountForMeshRibbon
boolean useMinimizationThread
boolean useNumberLocalization
float vectorScale
float vibrationPeriod
float vibrationScale
boolean wireframeRotation
boolean hideNavigationPoint
boolean navigationMode
boolean navigateSurface
boolean navigationPeriodic
float navigationSpeed
boolean showNavigationPointAlways
String stereoState
int[] objColors
boolean[] objStateOn
int[] objMad
boolean ellipsoidAxes
boolean ellipsoidDots
boolean ellipsoidArcs
boolean ellipsoidFill
boolean ellipsoidBall
int ellipsoidDotCount
float ellipsoidAxisDiameter
boolean testFlag1
boolean testFlag2
boolean testFlag3
boolean testFlag4
private String measureDistanceUnits
java.util.Hashtable htParameterValues
java.util.Hashtable htPropertyFlags
java.util.Hashtable htPropertyFlagsRemoved
private final org.jmol.viewer.StateManager this$0
void <init> (org.jmol.viewer.StateManager)
void clear ()
java.lang.String getLoadState ()
void setDefaultLattice (javax.vecmath.Point3f)
javax.vecmath.Point3f getDefaultLattice ()
java.lang.String getWindowState (java.lang.StringBuffer)
java.lang.String getSpecularState ()
void setMeasureDistanceUnits (java.lang.String)
java.lang.String getMeasureDistanceUnits ()
boolean isJmolVariable (java.lang.String)
private void resetParameterStringValue (java.lang.String, org.jmol.viewer.StateManager$GlobalSettings)
void setParameterValue (java.lang.String, boolean)
void setParameterValue (java.lang.String, int)
void setParameterValue (java.lang.String, float)
void setParameterValue (java.lang.String, java.lang.String)
void removeJmolParameter (java.lang.String)
org.jmol.viewer.ScriptVariable setUserVariable (java.lang.String, org.jmol.viewer.ScriptVariable)
void unsetUserVariable (java.lang.String)
void removeUserVariable (java.lang.String)
org.jmol.viewer.ScriptVariable getUserVariable (java.lang.String)
java.lang.String getParameterEscaped (java.lang.String, int)
java.lang.Object getParameter (java.lang.String)
org.jmol.viewer.ScriptVariable getOrSetNewVariable (java.lang.String, boolean)
java.lang.Object getParameter (java.lang.String, boolean)
java.lang.String getAllSettings (java.lang.String)
java.lang.String getState (java.lang.StringBuffer)
private boolean doReportProperty (java.lang.String)
void registerAllValues (org.jmol.viewer.StateManager$GlobalSettings)
java.lang.String getVariableList ()
}
org/jmol/viewer/StateManager$Orientation.class
<Unknown>
package org.jmol.viewer
public org.jmol.viewer.StateManager$Orientation extends java.lang.Object {
String saveName
javax.vecmath.Matrix3f rotationMatrix
float xTrans
float yTrans
float zoom
float rotationRadius
javax.vecmath.Point3f center
javax.vecmath.Point3f navCenter
float xNav
float yNav
float navDepth
boolean windowCenteredFlag
boolean navigationMode
boolean navigateSurface
String moveToText
private final org.jmol.viewer.StateManager this$0
void <init> (org.jmol.viewer.StateManager, boolean)
public java.lang.String getMoveToText ()
public void restore (float, boolean)
}
org/jmol/viewer/StateManager.class
<Unknown>
package org.jmol.viewer
public org.jmol.viewer.StateManager extends java.lang.Object {
public static final int OBJ_BACKGROUND
public static final int OBJ_AXIS1
public static final int OBJ_AXIS2
public static final int OBJ_AXIS3
public static final int OBJ_BOUNDBOX
public static final int OBJ_UNITCELL
public static final int OBJ_FRANK
public static final int OBJ_MAX
private static final String objectNameList
org.jmol.viewer.Viewer viewer
java.util.Hashtable saved
String lastOrientation
String lastConnections
String lastSelected
String lastState
String lastShape
String lastCoordinates
private static final java.util.Hashtable staticFunctions
private java.util.Hashtable localFunctions
protected static final String unreportedProperties
static java.lang.String getVariableList (java.util.Hashtable, int)
static int getObjectIdFromName (java.lang.String)
static java.lang.String getObjectNameFromId (int)
void <init> (org.jmol.viewer.Viewer)
org.jmol.viewer.StateManager$GlobalSettings getGlobalSettings (org.jmol.viewer.StateManager$GlobalSettings)
void clear ()
void setCrystallographicDefaults ()
private void setCommonDefaults ()
void setJmolDefaults ()
void setRasMolDefaults ()
java.lang.String getStandardLabelFormat ()
java.lang.String listSavedStates ()
private void deleteSaved (java.lang.String)
void saveSelection (java.lang.String, java.util.BitSet)
boolean restoreSelection (java.lang.String)
void saveState (java.lang.String)
java.lang.String getSavedState (java.lang.String)
void saveStructure (java.lang.String)
java.lang.String getSavedStructure (java.lang.String)
void saveCoordinates (java.lang.String, java.util.BitSet)
java.lang.String getSavedCoordinates (java.lang.String)
org.jmol.viewer.StateManager$Orientation getOrientation ()
void saveOrientation (java.lang.String)
boolean restoreOrientation (java.lang.String, float, boolean)
void saveBonds (java.lang.String)
boolean restoreBonds (java.lang.String)
static boolean isMeasurementUnit (java.lang.String)
public java.util.Hashtable getFunctions (boolean)
java.lang.String getFunctionCalls (java.lang.String)
public void clearFunctions ()
private static boolean isGlobalFunction (java.lang.String)
boolean isFunction (java.lang.String)
void addFunction (org.jmol.viewer.ScriptFunction)
org.jmol.viewer.ScriptFunction getFunction (java.lang.String)
public static void setStateInfo (java.util.Hashtable, int, int, java.lang.String)
public static java.lang.String varClip (java.lang.String, java.lang.String, int)
public static java.lang.String getCommands (java.util.Hashtable)
public static java.lang.String getCommands (java.util.Hashtable, java.util.Hashtable, int)
public static java.lang.String getCommands (java.util.Hashtable, java.util.Hashtable, int, java.lang.String)
public static java.lang.String getCommands (java.util.Hashtable, java.lang.StringBuffer, java.lang.String, int, java.lang.String)
public static void appendCmd (java.lang.StringBuffer, java.lang.String)
static void <clinit> ()
}
org/jmol/viewer/StatusManager.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.StatusManager extends java.lang.Object {
private boolean allowStatusReporting
private org.jmol.viewer.Viewer viewer
private org.jmol.api.JmolStatusListener jmolStatusListener
private org.jmol.api.JmolCallbackListener jmolCallbackListener
private String statusList
private java.util.Hashtable messageQueue
private int statusPtr
private static int MAXIMUM_QUEUE_LENGTH
private boolean asVector
private String[] jmolScriptCallbacks
private int minSyncRepeatMs
boolean syncingScripts
boolean syncingMouse
boolean drivingSync
boolean isSynced
boolean syncDisabled
boolean stereoSync
static final int SYNC_OFF
static final int SYNC_DRIVER
static final int SYNC_SLAVE
static final int SYNC_DISABLE
static final int SYNC_ENABLE
static final int SYNC_STEREO
void <init> (org.jmol.viewer.Viewer)
void setAllowStatusReporting (boolean)
java.lang.String getStatusList ()
java.util.Hashtable getMessageQueue ()
private boolean recordStatus (java.lang.String)
private synchronized void setStatusChanged (java.lang.String, int, java.lang.Object, boolean)
synchronized java.lang.Object getStatusChanged (java.lang.String)
private synchronized boolean resetMessageQueue (java.lang.String)
synchronized void setJmolStatusListener (org.jmol.api.JmolStatusListener, org.jmol.api.JmolCallbackListener)
synchronized void setJmolCallbackListener (org.jmol.api.JmolCallbackListener)
private java.lang.String jmolScriptCallback (int)
synchronized void setCallbackFunction (java.lang.String, java.lang.String)
private boolean notifyEnabled (int)
synchronized void setStatusAtomPicked (int, java.lang.String)
synchronized void setStatusResized (int, int)
synchronized void setStatusAtomHovered (int, java.lang.String)
synchronized void setFileLoadStatus (java.lang.String, java.lang.String, java.lang.String, java.lang.String, int, boolean)
synchronized void setStatusFrameChanged (int, int, int, int, int)
synchronized void setScriptEcho (java.lang.String, boolean)
synchronized void setStatusMeasuring (java.lang.String, int, java.lang.String)
synchronized void notifyError (java.lang.String, java.lang.String, java.lang.String)
synchronized void notifyMinimizationStatus (java.lang.String, java.lang.Integer, java.lang.Float, java.lang.Float)
synchronized void setScriptStatus (java.lang.String, java.lang.String, int, java.lang.String)
private void processScript (java.lang.Object[])
boolean doSync ()
synchronized void setSync (java.lang.String)
void setSyncDriver (int)
void syncSend (java.lang.String, java.lang.String)
int getSyncMode ()
synchronized void showUrl (java.lang.String)
synchronized void clearConsole ()
float[][] functionXY (java.lang.String, int, int)
float[][][] functionXYZ (java.lang.String, int, int, int)
java.lang.String jsEval (java.lang.String)
java.lang.String createImage (java.lang.String[], java.lang.String, java.lang.Object, int)
java.util.Hashtable getRegistryInfo ()
java.lang.String dialogAsk (java.lang.String, java.lang.String)
static void <clinit> ()
}
org/jmol/viewer/Token.class
<Unknown>
package org.jmol.viewer
public org.jmol.viewer.Token extends java.lang.Object {
public int tok
public Object value
public int intValue
static final int nada
public static final int identifier
static final int integer
static final int decimal
public static final int string
static final int seqcode
public static final int list
public static final int point3f
public static final int point4f
private static final int keyword
static final int listf
static final String[] astrType
public static final int command
static final int atomExpressionCommand
static final int implicitStringCommand
static final int mathExpressionCommand
static final int flowCommand
static final int noeval
static final int noArgs
static final int defaultON
static final int expression
static final int predefinedset
public static final int atomproperty
public static final int strproperty
public static final int intproperty
public static final int floatproperty
public static final int PROPERTYFLAGS
static final int mathproperty
static final int mathfunc
static final int mathop
static final int comparator
static final int setparam
static final int misc
static final int center
static final int define
public static final int delete
static final int display
static final int hide
static final int restrict
static final int subset
static final int zap
static final int print
static final int returncmd
static final int set
static final int var
static final int echo
static final int help
static final int hover
static final int message
static final int pause
static final int elseif
static final int elsecmd
static final int endifcmd
static final int whilecmd
static final int breakcmd
static final int continuecmd
static final int end
static final int animation
public static final int axes
static final int backbone
static final int background
static final int bondorder
static final int calculate
static final int cartoon
static final int cd
static final int centerAt
static final int configuration
public static final int connect
static final int console
static final int delay
static final int depth
static final int dipole
public static final int dots
public static final int draw
static final int ellipsoid
static final int exit
static final int font
static final int frame
static final int frank
static final int geosurface
static final int gotocmd
static final int halo
static final int hbond
static final int history
static final int initialize
static final int invertSelected
static final int isosurface
static final int lcaocartoon
static final int loop
static final int meshRibbon
static final int minimize
static final int mo
public static final int monitor
static final int move
public static final int moveto
static final int navigate
static final int pmesh
static final int polyhedra
static final int quit
static final int ramachandran
static final int refresh
static final int reset
static final int restore
static final int resume
static final int ribbon
static final int rocket
static final int rotate
static final int rotateSelected
static final int save
static final int selectionHalo
static final int show
static final int slab
static final int spin
static final int ssbond
static final int star
static final int step
static final int stereo
static final int strands
static final int sync
static final int trace
static final int translate
static final int translateSelected
public static final int unitcell
static final int vector
public static final int vibration
public static final int wireframe
static final int zoom
static final int zoomTo
static final int expressionBegin
static final int expressionEnd
static final int all
public static final int branch
static final int coord
static final int dollarsign
static final int period
public static final int isaromatic
static final int leftbrace
static final int none
public static final int off
public static final int on
static final int rightbrace
static final int semicolon
public static final int spec_alternate
public static final int spec_atom
public static final int spec_chain
public static final int spec_model
static final int spec_model2
public static final int spec_name_pattern
public static final int spec_resid
public static final int spec_seqcode
public static final int spec_seqcode_range
static final int amino
public static final int dna
public static final int hetero
public static final int hydrogen
public static final int nucleic
public static final int protein
public static final int purine
public static final int pyrimidine
public static final int rna
public static final int selected
static final int solvent
public static final int sidechain
static final int surface
static final int thismodel
public static final int carbohydrate
static final int clickable
static final int displayed
static final int hidden
public static final int specialposition
static final int visible
static final int leftparen
static final int rightparen
static final int opIf
static final int colon
static final int comma
static final int leftsquare
static final int rightsquare
static final int opOr
static final int opXor
static final int opToggle
static final int opAnd
static final int opNot
static final int opGT
static final int opGE
static final int opLE
static final int opLT
public static final int opEQ
static final int opNE
static final int minus
static final int plus
static final int divide
static final int times
public static final int percent
static final int leftdivide
static final int unaryMinus
static final int minusMinus
static final int plusPlus
static final int propselector
static final int andequals
public static final int min
public static final int max
public static final int average
public static final int stddev
public static final int sum2
public static final int allfloat
static final int minmaxmask
static final int settable
public static final int atoms
public static final int bonds
static final int length
static final int lines
public static final int reverse
static final int size
public static final int sort
public static final int type
public static final int boundbox
public static final int xyz
public static final int fracXyz
public static final int unitXyz
public static final int vibXyz
public static final int occupancy
public static final int radius
public static final int structure
public static final int atomType
public static final int atomName
public static final int altloc
public static final int chain
public static final int element
public static final int group
public static final int group1
public static final int sequence
public static final int identify
public static final int insertion
public static final int strucid
public static final int symbol
public static final int symmetry
public static final int atomno
public static final int atomID
public static final int atomIndex
public static final int bondcount
public static final int cell
public static final int color
public static final int elemno
public static final int formalCharge
public static final int groupID
public static final int groupindex
public static final int model
public static final int modelindex
public static final int molecule
public static final int polymerLength
public static final int resno
public static final int site
public static final int strucno
public static final int valence
public static final int adpmax
public static final int adpmin
public static final int atomX
public static final int atomY
public static final int atomZ
public static final int covalent
public static final int fracX
public static final int fracY
public static final int fracZ
public static final int ionic
public static final int partialCharge
public static final int phi
public static final int psi
public static final int property
public static final int spacefill
public static final int straightness
public static final int surfacedistance
public static final int temperature
public static final int unitX
public static final int unitY
public static final int unitZ
public static final int vanderwaals
public static final int vibX
public static final int vibY
public static final int vibZ
public static final int array
public static final int format
public static final int label
static final int function
static final int getproperty
static final int write
static final int now
static final int substructure
static final int javascript
static final int acos
static final int sin
static final int cos
static final int sqrt
public static final int file
static final int forcmd
static final int ifcmd
static final int abs
static final int div
static final int dot
static final int join
static final int mul
static final int split
static final int sub
static final int trim
public static final int cross
static final int load
static final int random
static final int script
static final int add
static final int distance
static final int replace
static final int find
static final int select
static final int bin
public static final int symop
public static final int angle
public static final int data
public static final int helix
static final int plane
public static final int point
static final int quaternion
static final int axisangle
static final int within
public static final int connected
public static final int ambient
static final int bondmode
static final int fontsize
static final int picking
static final int specular
static final int specpercent
static final int specpower
static final int specexponent
static final int transparent
static final int defaultColors
static final int scale3d
static final int diffuse
static final int pickingStyle
static final int absolute
public static final int axis
static final int babel
static final int back
public static final int backlit
public static final int bitset
static final int bondset
static final int bottom
static final int clear
static final int clipboard
static final int constraint
public static final int contourlines
static final int direction
static final int displacement
static final int dotted
public static final int fill
static final int fixedtemp
public static final int front
public static final int frontlit
public static final int frontonly
public static final int fullylit
static final int hkl
static final int image
public static final int info
static final int jmol
static final int last
static final int left
static final int mep
public static final int mesh
static final int mode
static final int monomer
static final int next
public static final int nocontourlines
public static final int nodots
public static final int nofill
public static final int nomesh
static final int normal
public static final int notfrontonly
public static final int notriangles
static final int only
static final int opaque
static final int orientation
static final int pdbheader
static final int play
static final int playrev
static final int pointgroup
static final int polymer
static final int prev
static final int range
static final int rasmol
public static final int residue
static final int rewind
static final int right
static final int rotation
static final int rubberband
static final int sasurface
static final int scale
static final int shape
static final int shapely
public static final int sheet
static final int solid
static final int spacegroup
static final int state
static final int top
static final int torsion
static final int transform
static final int translation
public static final int translucent
public static final int triangles
static final int url
static final int user
static final int qw
static final org.jmol.viewer.Token tokenOn
static final org.jmol.viewer.Token tokenOff
static final org.jmol.viewer.Token tokenAll
static final org.jmol.viewer.Token tokenIf
public static final org.jmol.viewer.Token tokenAnd
public static final org.jmol.viewer.Token tokenOr
public static final org.jmol.viewer.Token tokenOpIf
public static final org.jmol.viewer.Token tokenComma
static final org.jmol.viewer.Token tokenPlus
static final org.jmol.viewer.Token tokenMinus
static final org.jmol.viewer.Token tokenTimes
static final org.jmol.viewer.Token tokenDivide
public static final org.jmol.viewer.Token tokenLeftParen
public static final org.jmol.viewer.Token tokenRightParen
static final org.jmol.viewer.Token tokenArray
static final org.jmol.viewer.Token tokenArraySelector
public static final org.jmol.viewer.Token tokenExpressionBegin
public static final org.jmol.viewer.Token tokenExpressionEnd
static final org.jmol.viewer.Token tokenCoordinateBegin
static final org.jmol.viewer.Token tokenCoordinateEnd
static final org.jmol.viewer.Token tokenColon
static final org.jmol.viewer.Token tokenSet
static final org.jmol.viewer.Token tokenSetArray
static final org.jmol.viewer.Token tokenSetProperty
static final org.jmol.viewer.Token tokenSetVar
static final org.jmol.viewer.Token tokenEquals
private static final Object[] arrayPairs
private static java.util.Hashtable map
public void <init> ()
public void <init> (int, int, java.lang.Object)
public void <init> (int)
public void <init> (int, int)
public void <init> (int, java.lang.Object)
public static final org.jmol.viewer.Token intToken (int)
public static boolean tokAttr (int, int)
public static boolean tokAttrOr (int, int, int)
static int getPrecedence (int)
static int getMaxMathParams (int)
public static void addToken (java.lang.String, org.jmol.viewer.Token)
public static org.jmol.viewer.Token getTokenFromName (java.lang.String)
public static java.lang.String nameOf (int)
public java.lang.String toString ()
public static java.lang.String getCommandSet (java.lang.String)
static java.lang.String[] getTokensLike (java.lang.String)
public static int getSettableTokFromString (java.lang.String)
public static java.lang.String completeCommand (java.lang.String, int)
static void <clinit> ()
}
org/jmol/viewer/TransformManager$SpinThread.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.TransformManager$SpinThread extends java.lang.Thread implements java.lang.Runnable {
float endDegrees
float nDegrees
java.util.BitSet bsAtoms
boolean isNav
private final org.jmol.viewer.TransformManager this$0
void <init> (org.jmol.viewer.TransformManager, float, java.util.BitSet, boolean)
public void run ()
}
org/jmol/viewer/TransformManager$VibrationThread.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.TransformManager$VibrationThread extends java.lang.Thread implements java.lang.Runnable {
private final org.jmol.viewer.TransformManager this$0
void <init> (org.jmol.viewer.TransformManager)
public void run ()
}
org/jmol/viewer/TransformManager.class
<Unknown>
package org.jmol.viewer
abstract org.jmol.viewer.TransformManager extends java.lang.Object {
org.jmol.viewer.Viewer viewer
static final float twoPI
static final float radiansPerDegree
static final float degreesPerRadian
protected int perspectiveModel
protected float cameraScaleFactor
protected float referencePlaneOffset
protected float modelCenterOffset
protected float modelRadius
protected float modelRadiusPixels
protected final javax.vecmath.Point3f navigationCenter
protected final javax.vecmath.Point3f navigationOffset
protected final javax.vecmath.Point3f navigationShiftXY
protected final javax.vecmath.Matrix4f matrixTemp
protected final javax.vecmath.Vector3f vectorTemp
protected boolean haveNotifiedNaN
float spinX
float spinY
float spinZ
float spinFps
protected float navX
protected float navY
protected float navZ
protected float navFps
boolean isSpinInternal
boolean isSpinFixed
boolean isSpinSelected
protected final javax.vecmath.Point3f fixedRotationOffset
protected final javax.vecmath.Point3f fixedRotationCenter
private final javax.vecmath.Point3f rotationCenterDefault
private float rotationRadiusDefault
protected final javax.vecmath.AxisAngle4f fixedRotationAxis
protected final javax.vecmath.AxisAngle4f internalRotationAxis
private final javax.vecmath.Point3f internalRotationCenter
private float internalRotationAngle
protected final javax.vecmath.Matrix3f matrixRotate
private final javax.vecmath.Matrix3f matrixTemp3
private final javax.vecmath.Matrix4f matrixTemp4
private final javax.vecmath.AxisAngle4f axisangleT
private final javax.vecmath.Vector3f vectorT
private final javax.vecmath.Vector3f vectorT2
protected final javax.vecmath.Point3f pointT
private final javax.vecmath.Point3f pointT2
static final int MAXIMUM_ZOOM_PERCENTAGE
static final int MAXIMUM_ZOOM_PERSPECTIVE_DEPTH
private boolean rotateMolecule
javax.vecmath.Vector3f rotationAxis
float rotationRate
protected final javax.vecmath.Point3f fixedTranslation
float xTranslationFraction
float yTranslationFraction
protected float prevZoomSetting
protected float previousX
protected float previousY
boolean zoomEnabled
float zoomPercent
float zoomPercentSetting
float zoomRatio
boolean slabEnabled
boolean internalSlab
boolean zShadeEnabled
int slabPercentSetting
int depthPercentSetting
int slabValue
int depthValue
int zSlabValue
int zDepthValue
javax.vecmath.Point4f slabPlane
javax.vecmath.Point4f depthPlane
protected boolean perspectiveDepth
protected boolean scale3D
protected float cameraDepth
protected float cameraDepthSetting
protected float visualRange
protected float cameraDistance
int width
int height
int screenPixelCount
float scalePixelsPerAngstrom
float scaleDefaultPixelsPerAngstrom
float scale3DAngstromsPerInch
protected boolean antialias
private boolean useZoomLarge
int screenWidth
int screenHeight
protected final javax.vecmath.Matrix4f matrixTransform
protected final javax.vecmath.Point3f point3fScreenTemp
protected final javax.vecmath.Point3i point3iScreenTemp
private final javax.vecmath.Point3f point3fVibrationTemp
protected boolean navigating
protected boolean isNavigationMode
protected final javax.vecmath.Point3f ptTest1
protected final javax.vecmath.Point3f ptTest2
protected final javax.vecmath.Point3f ptTest3
protected final javax.vecmath.AxisAngle4f aaTest1
protected final javax.vecmath.AxisAngle4f aaMoveTo
protected final javax.vecmath.AxisAngle4f aaStep
protected final javax.vecmath.AxisAngle4f aaTotal
protected final javax.vecmath.Matrix3f matrixStart
private final javax.vecmath.Matrix3f matrixStartInv
protected final javax.vecmath.Matrix3f matrixStep
protected final javax.vecmath.Matrix3f matrixTest
protected final javax.vecmath.Matrix3f matrixEnd
protected final javax.vecmath.Vector3f aaStepCenter
protected final javax.vecmath.Vector3f aaStepNavCenter
protected boolean spinOn
protected boolean navOn
private org.jmol.viewer.TransformManager$SpinThread spinThread
boolean vibrationOn
private float vibrationPeriod
public int vibrationPeriodMs
private float vibrationAmplitude
private float vibrationRadians
private float vibrationScale
private org.jmol.viewer.TransformManager$VibrationThread vibrationThread
static final int DEFAULT_STEREO_DEGREES
int stereoMode
int[] stereoColors
float stereoDegrees
float stereoRadians
boolean stereoFrame
protected final javax.vecmath.Matrix3f matrixStereo
boolean windowCentered
javax.vecmath.Point3f[] frameOffsets
final javax.vecmath.Point3f frameOffset
protected abstract void calcCameraFactors ()
protected abstract float getPerspectiveFactor (float)
abstract void adjustTemporaryScreenPoint ()
void <init> ()
void <init> (org.jmol.viewer.Viewer)
void <init> (org.jmol.viewer.Viewer, int, int)
void setViewer (org.jmol.viewer.Viewer, int, int)
org.jmol.viewer.TransformManager getNavigationManager (org.jmol.viewer.Viewer, int, int)
void homePosition ()
void clear ()
java.lang.String getState (java.lang.StringBuffer)
java.lang.String getSpinState (boolean)
void setRotateMolecule (boolean)
private void setFixedRotationCenter (javax.vecmath.Point3f)
void setRotationPointXY (javax.vecmath.Point3f)
float setRotateInternal (javax.vecmath.Point3f, javax.vecmath.Vector3f, float)
float setRotateFixed (javax.vecmath.Point3f, javax.vecmath.Vector3f, float)
void rotateXYBy (int, int, java.util.BitSet)
void rotateZBy (int)
void rotateFront ()
void rotateX (float)
void rotateY (float)
void rotateZ (float)
private void applyRotation (javax.vecmath.Matrix3f, boolean, java.util.BitSet)
synchronized void rotateXRadians (float, java.util.BitSet)
synchronized void rotateYRadians (float, java.util.BitSet)
synchronized void rotateZRadians (float)
protected void rotateAxisAngle (javax.vecmath.Vector3f, float)
synchronized void rotateAxisAngle (javax.vecmath.AxisAngle4f, java.util.BitSet)
void rotateAxisAngleAtCenter (javax.vecmath.Point3f, javax.vecmath.Vector3f, float, float, boolean, java.util.BitSet)
synchronized void rotateAxisAngleRadiansFixed (float, java.util.BitSet)
void rotateAboutPointsInternal (javax.vecmath.Point3f, javax.vecmath.Point3f, float, float, boolean, boolean, java.util.BitSet)
synchronized void rotateAxisAngleRadiansInternal (float, java.util.BitSet)
void getNewFixedRotationCenter ()
void setTranslationFractions ()
void translateXYBy (int, int)
int percentToPixels (char, float)
int angstromsToPixels (float)
void translateToXPercent (float)
void translateToYPercent (float)
void translateToZPercent (float)
float getTranslationXPercent ()
float getTranslationYPercent ()
float getTranslationZPercent ()
java.lang.String getTranslationScript ()
java.lang.String getOrientationText (int)
java.util.Hashtable getOrientationInfo ()
void getAxisAngle (javax.vecmath.AxisAngle4f)
java.lang.String getTransformText ()
javax.vecmath.Matrix3f getMatrixRotate ()
void setRotation (javax.vecmath.Matrix3f)
void getRotation (javax.vecmath.Matrix3f)
protected void zoomBy (int)
float getZoomPercentFloat ()
void zoomToPercent (float)
void translateZBy (int)
void zoomByFactor (float)
void zoomByPercent (float)
void setZoomEnabled (boolean)
void setScaleAngstromsPerInch (float)
void setSlabEnabled (boolean)
void setZShadeEnabled (boolean)
void slabReset ()
int getSlabPercentSetting ()
void slabByPercentagePoints (int)
void depthByPercentagePoints (int)
void slabDepthByPercentagePoints (int)
void slabToPercent (int)
void depthToPercent (int)
void slabInternal (javax.vecmath.Point4f, boolean)
void setSlabDepthInternal (boolean)
javax.vecmath.Point4f getSlabDepthPlane (boolean)
boolean checkInternalSlab (javax.vecmath.Point3f)
void setPerspectiveDepth (boolean)
boolean getPerspectiveDepth ()
void setCameraDepthPercent (float)
void setVisualRange (float)
javax.vecmath.Matrix4f getUnscaledTransformMatrix ()
void setScreenParameters (int, int, boolean, boolean, boolean, boolean)
void setAntialias (boolean)
private float defaultScaleToScreen (float)
void scaleFitToScreen (boolean)
void scaleFitToScreen (boolean, boolean, boolean, boolean)
short scaleToScreen (int, int)
float unscaleToScreen (int, int)
float scaleToPerspective (int, float)
javax.vecmath.Matrix4f getMatrixtransform ()
void setNavigationMode (boolean)
boolean isNavigating ()
synchronized void finalizeTransformParameters ()
float getZoomSetting ()
protected void calcSlabAndDepthValues ()
int zValueFromPercent (int)
protected synchronized void calcTransformMatrix ()
void rotatePoint (javax.vecmath.Point3f, javax.vecmath.Point3f)
void transformPoints (int, javax.vecmath.Point3f[], javax.vecmath.Point3i[])
void transformPoint (javax.vecmath.Point3f, javax.vecmath.Point3i)
void transformPointNoClip (javax.vecmath.Point3f, javax.vecmath.Point3f)
synchronized javax.vecmath.Point3i transformPoint (javax.vecmath.Point3f)
private javax.vecmath.Point3i transformScreenPoint (javax.vecmath.Point3f)
synchronized javax.vecmath.Point3f transformPointNoClip (javax.vecmath.Point3f)
javax.vecmath.Point3i transformPoint (javax.vecmath.Point3f, javax.vecmath.Vector3f)
void transformPoint (javax.vecmath.Point3f, javax.vecmath.Point3f)
void transformVector (javax.vecmath.Vector3f, javax.vecmath.Vector3f)
void unTransformPoint (javax.vecmath.Point3f, javax.vecmath.Point3f)
protected void matrixUnTransform (javax.vecmath.Point3f, javax.vecmath.Point3f)
void move (javax.vecmath.Vector3f, float, javax.vecmath.Vector3f, float, float, int)
boolean isInPosition (javax.vecmath.Vector3f, float)
void moveTo (float, javax.vecmath.Point3f, javax.vecmath.Tuple3f, float, float, float, float, float, javax.vecmath.Point3f, float, float, float)
void moveTo (float, javax.vecmath.Point3f, javax.vecmath.Matrix3f, float, float, float, float, javax.vecmath.Point3f, float, float, float)
org.jmol.util.Quaternion getRotationQuaternion ()
java.lang.String getRotationText ()
java.lang.String getMoveToText (float, boolean)
private java.lang.String getCenterText ()
private java.lang.String getRotateXyzText ()
private void addZoomTranslationNavigationText (java.lang.StringBuffer)
private java.lang.String getRotateZyzText (boolean)
private static void truncate0 (java.lang.StringBuffer, float)
private static void truncate2 (java.lang.StringBuffer, float)
void setSpinXYZ (float, float, float)
void setSpinFps (int)
void setNavXYZ (float, float, float)
protected void setNavFps (int)
private void clearSpin ()
boolean getSpinOn ()
boolean getNavOn ()
void setSpinOn (boolean)
private void setSpinOn (boolean, float, java.util.BitSet)
protected void setNavOn (boolean)
void setVibrationScale (float)
protected void setNavigationOffsetRelative (boolean)
void setVibrationPeriod (float)
protected void setVibrationT (float)
boolean isVibrationOn ()
private void setVibrationOn (boolean)
private void clearVibration ()
void setStereoMode (int[])
void setStereoMode (int)
void setStereoDegrees (float)
synchronized javax.vecmath.Matrix3f getStereoRotationMatrix (boolean)
boolean isWindowCentered ()
void setWindowCentered (boolean)
javax.vecmath.Point3f getRotationCenter ()
float getRotationRadius ()
float setRotationRadius (float, boolean)
private void setRotationCenterAndRadiusXYZ (javax.vecmath.Point3f, boolean)
private void setRotationCenterAndRadiusXYZ (java.lang.String, javax.vecmath.Point3f)
void setNewRotationCenter (javax.vecmath.Point3f, boolean)
private void moveRotationCenter (javax.vecmath.Point3f, boolean)
void setCenter ()
void setCenterAt (java.lang.String, javax.vecmath.Point3f)
boolean canNavigate ()
synchronized void navigate (int, int)
void navigate (float, javax.vecmath.Point3f)
void navigate (float, javax.vecmath.Vector3f, float)
void navigate (float, javax.vecmath.Point3f[], float[], int, int)
void navigate (float, javax.vecmath.Point3f[][])
void navTranslate (float, javax.vecmath.Point3f)
void navTranslatePercent (float, float, float)
protected void calcNavigationPoint ()
protected void resetNavigationPoint (boolean)
protected java.lang.String getNavigationState ()
void setNavigationDepthPercent (float, float)
javax.vecmath.Point3f getNavigationCenter ()
javax.vecmath.Point3f getNavigationOffset ()
float getNavigationDepthPercent ()
float getNavigationOffsetPercent (char)
void setNavigationSlabOffsetPercent (float)
java.lang.String getNavigationText (boolean)
void setFrameOffset (int)
void setFrameOffsets (javax.vecmath.Point3f[])
void navigateSurface (float, java.lang.String)
}
org/jmol/viewer/TransformManager10.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.TransformManager10 extends org.jmol.viewer.TransformManager {
void <init> (org.jmol.viewer.Viewer)
void <init> (org.jmol.viewer.Viewer, int, int)
protected void calcCameraFactors ()
protected float getPerspectiveFactor (float)
protected void adjustTemporaryScreenPoint ()
}
org/jmol/viewer/TransformManager11.class
<Unknown>
package org.jmol.viewer
org.jmol.viewer.TransformManager11 extends org.jmol.viewer.TransformManager {
private float navigationSlabOffset
private float zoomFactor
private static final int NAV_MODE_IGNORE
private static final int NAV_MODE_ZOOMED
private static final int NAV_MODE_NONE
private static final int NAV_MODE_RESET
private static final int NAV_MODE_NEWXY
private static final int NAV_MODE_NEWXYZ
private static final int NAV_MODE_NEWZ
private int navMode
float navigationDepth
private int nHits
private int multiplier
void <init> ()
void <init> (org.jmol.viewer.Viewer)
protected void setNavFps (int)
void <init> (org.jmol.viewer.Viewer, int, int)
protected void calcCameraFactors ()
protected float getPerspectiveFactor (float)
protected void adjustTemporaryScreenPoint ()
void setScreenParameters (int, int, boolean, boolean, boolean, boolean)
protected void calcNavigationPoint ()
private float getNavPtHeight ()
protected void calcNavigationSlabAndDepth ()
private void newNavigationCenter ()
boolean canNavigate ()
protected void resetNavigationPoint (boolean)
protected void setNavigationOffsetRelative (boolean)
synchronized void navigate (int, int)
private void navigateSurface (int)
void navigate (float, javax.vecmath.Point3f)
void navigate (float, javax.vecmath.Vector3f, float)
void setNavigationDepthPercent (float, float)
void navTranslate (float, javax.vecmath.Point3f)
void navTranslatePercent (float, float, float)
private void navigateTo (float, javax.vecmath.Vector3f, float, javax.vecmath.Point3f, float, float, float)
void navigate (float, javax.vecmath.Point3f[][])
void navigate (float, javax.vecmath.Point3f[], float[], int, int)
private void navigate (float, javax.vecmath.Point3f[][], javax.vecmath.Point3f[], float[], int, int)
void navigateSurface (float, java.lang.String)
void alignZX (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f)
javax.vecmath.Point3f getNavigationCenter ()
float getNavigationDepthPercent ()
void setNavigationSlabOffsetPercent (float)
private float getNavigationSlabOffsetPercent ()
javax.vecmath.Point3f getNavigationOffset ()
private void setNavigationDepthPercent (float)
private void calcNavigationDepthPercent ()
float getNavigationOffsetPercent (char)
protected java.lang.String getNavigationText (boolean)
protected java.lang.String getNavigationState ()
}
org/jmol/viewer/Viewer.class
<Unknown>
package org.jmol.viewer
public org.jmol.viewer.Viewer extends org.jmol.api.JmolViewer implements org.jmol.atomdata.AtomDataServer {
private java.awt.Component display
private org.jmol.g3d.Graphics3D g3d
private org.jmol.api.JmolAdapter modelAdapter
private org.jmol.util.CommandHistory commandHistory
private org.jmol.viewer.ColorManager colorManager
org.jmol.viewer.ScriptCompiler compiler
java.util.Hashtable definedAtomSets
private org.jmol.api.MinimizerInterface minimizer
private org.jmol.api.SmilesMatcherInterface smilesMatcher
private org.jmol.api.SymmetryInterface symmetry
org.jmol.viewer.ScriptEvaluator eval
private org.jmol.viewer.AnimationManager animationManager
private org.jmol.viewer.DataManager dataManager
private org.jmol.viewer.FileManager fileManager
private org.jmol.viewer.ModelManager modelManager
private org.jmol.modelset.ModelSet modelSet
public org.jmol.viewer.MouseManager mouseManager
private org.jmol.viewer.PickingManager pickingManager
private org.jmol.viewer.RepaintManager repaintManager
private org.jmol.viewer.ScriptManager scriptManager
private org.jmol.viewer.SelectionManager selectionManager
private org.jmol.viewer.StateManager stateManager
private org.jmol.viewer.StateManager$GlobalSettings global
private org.jmol.viewer.StatusManager statusManager
private org.jmol.util.TempArray tempManager
private org.jmol.viewer.TransformManager transformManager
private String strJavaVendor
private String strJavaVersion
private String strOSName
private String htmlName
private String fullName
private String syncId
private String appletDocumentBase
private String appletCodeBase
private boolean jvm11orGreater
private boolean jvm12orGreater
private boolean jvm14orGreater
private boolean isSilent
private boolean isApplet
private boolean isPreviewOnly
boolean autoExit
boolean haveDisplay
private boolean isPrintOnly
private boolean mustRender
private boolean isCmdLine_c_or_C_Option
private boolean listCommands
private boolean isCmdLine_C_Option
private boolean useCommandThread
private boolean isSignedApplet
private boolean isDataOnly
private boolean mouseEnabled
private boolean noneSelected
private static final int FILE_STATUS_NOT_LOADED
private static final int FILE_STATUS_ZAPPED
private static final int FILE_STATUS_CREATING_MODELSET
private static final int FILE_STATUS_MODELSET_CREATED
private static final int FILE_STATUS_MODELS_DELETED
static final String STATE_VERSION_STAMP
public static Object testData
public static Object testData2
java.util.BitSet bsFrameOffsets
javax.vecmath.Point3f[] frameOffsets
boolean wasInMotion
int motionEventNumber
private boolean refreshing
private boolean axesAreTainted
final java.awt.Dimension dimScreen
private int maximumSize
private float imageFontScaling
private boolean antialiasDisplay
String interruptScript
int scriptIndex
boolean isScriptQueued
int hoverAtomIndex
String hoverText
public static final int CURSOR_DEFAULT
public static final int CURSOR_HAND
public static final int CURSOR_CROSSHAIR
public static final int CURSOR_MOVE
public static final int CURSOR_WAIT
private int currentCursor
int prevFrame
private String language
boolean frankOn
private boolean scriptEditorVisible
org.jmol.api.JmolAppConsoleInterface appConsole
org.jmol.api.JmolScriptEditorInterface scriptEditor
org.jmol.popup.JmolPopup jmolpopup
String menuStructure
boolean isTainted
private boolean creatingImage
public static final String SYNC_GRAPHICS_MESSAGE
public static final String SYNC_NO_GRAPHICS_MESSAGE
private String errorMessage
private String errorMessageUntranslated
private int currentShapeID
private String currentShapeState
protected void finalize () throws java.lang.Throwable
public org.jmol.api.JmolAdapter getModelAdapter ()
org.jmol.api.MinimizerInterface getMinimizer (boolean)
org.jmol.api.SmilesMatcherInterface getSmilesMatcher ()
public org.jmol.api.SymmetryInterface getSymmetry ()
public java.lang.Object getSymmetryInfo (java.util.BitSet, java.lang.String, int, javax.vecmath.Point3f, java.lang.String, int)
private void clearModelDependentObjects ()
org.jmol.viewer.StateManager$GlobalSettings getGlobalSettings ()
public void <init> (java.awt.Component, org.jmol.api.JmolAdapter)
public static org.jmol.api.JmolViewer allocateViewer (java.awt.Component, org.jmol.api.JmolAdapter, java.lang.String, java.net.URL, java.net.URL, java.lang.String, org.jmol.api.JmolStatusListener)
public static org.jmol.api.JmolViewer allocateViewer (java.awt.Component, org.jmol.api.JmolAdapter)
public boolean isApplet ()
boolean isPreviewOnly ()
public void setAppletContext (java.lang.String, java.net.URL, java.net.URL, java.lang.String)
public boolean isDataOnly ()
public static java.lang.String getJmolVersion ()
public java.lang.String getExportDriverList ()
private static int getJmolVersionInt ()
java.lang.String getHtmlName ()
boolean mustRenderFlag ()
static int getLogLevel ()
public java.awt.Component getDisplay ()
public boolean handleOldJvm10Event (java.awt.Event)
void reset ()
public void homePosition ()
java.util.Hashtable getAppletInfo ()
void initialize ()
java.lang.String listSavedStates ()
public void saveOrientation (java.lang.String)
public boolean restoreOrientation (java.lang.String, float)
public void restoreRotation (java.lang.String, float)
void saveModelOrientation ()
public org.jmol.viewer.StateManager$Orientation getOrientation ()
void restoreModelOrientation (int)
void restoreModelRotation (int)
void saveBonds (java.lang.String)
boolean restoreBonds (java.lang.String)
void saveState (java.lang.String)
public java.lang.String getSavedState (java.lang.String)
void saveStructure (java.lang.String)
java.lang.String getSavedStructure (java.lang.String)
public void saveCoordinates (java.lang.String, java.util.BitSet)
java.lang.String getSavedCoordinates (java.lang.String)
void saveSelection (java.lang.String)
boolean restoreSelection (java.lang.String)
public javax.vecmath.Matrix4f getMatrixtransform ()
org.jmol.util.Quaternion getRotationQuaternion ()
public float getRotationRadius ()
void setRotationRadius (float, boolean)
public javax.vecmath.Point3f getRotationCenter ()
void setCenterAt (java.lang.String, javax.vecmath.Point3f)
void setCenterBitSet (java.util.BitSet, boolean)
void setNewRotationCenter (javax.vecmath.Point3f)
public javax.vecmath.Point3f getNavigationCenter ()
public float getNavigationDepthPercent ()
void navigate (int, int)
public javax.vecmath.Point3f getNavigationOffset ()
float getNavigationOffsetPercent (char)
public boolean isNavigating ()
boolean isInPosition (javax.vecmath.Vector3f, float)
void move (javax.vecmath.Vector3f, float, javax.vecmath.Vector3f, float, float, int)
void moveTo (float, javax.vecmath.Point3f, javax.vecmath.Vector3f, float, float, float, float, float, javax.vecmath.Point3f, float, float, float)
void moveTo (float, javax.vecmath.Point3f, javax.vecmath.Matrix3f, float, float, float, float, javax.vecmath.Point3f, float, float, float)
private void moveUpdate (float)
java.lang.String getMoveToText (float)
void navigate (float, javax.vecmath.Point3f[], float[], int, int)
public void navigate (float, javax.vecmath.Point3f)
void navigate (float, javax.vecmath.Point3f[][])
void navigateSurface (float, java.lang.String)
public void navigate (float, javax.vecmath.Vector3f, float)
void navTranslate (float, javax.vecmath.Point3f)
void navTranslatePercent (float, float, float)
public void setMouseEnabled (boolean)
void zoomBy (int)
void zoomByFactor (float)
void rotateXYBy (int, int)
void rotateZBy (int)
void rotateMolecule (int, int)
void translateXYBy (int, int)
public void rotateFront ()
public void rotateX (float)
public void rotateY (float)
public void rotateZ (float)
public void rotateX (int)
public void rotateY (int)
void translate (char, float, char)
public float getTranslationXPercent ()
public float getTranslationYPercent ()
float getTranslationZPercent ()
public java.lang.String getTranslationScript ()
public int getZoomPercent ()
float getZoomSetting ()
public float getZoomPercentFloat ()
float getMaxZoomPercent ()
void slabReset ()
boolean getZoomEnabled ()
public boolean getSlabEnabled ()
void slabByPixels (int)
void depthByPixels (int)
void slabDepthByPixels (int)
void slabToPercent (int)
void slabInternal (javax.vecmath.Point4f, boolean)
void depthToPercent (int)
void setSlabDepthInternal (boolean)
public int zValueFromPercent (int)
public javax.vecmath.Matrix4f getUnscaledTransformMatrix ()
void finalizeTransformParameters ()
public void rotatePoint (javax.vecmath.Point3f, javax.vecmath.Point3f)
public javax.vecmath.Point3i transformPoint (javax.vecmath.Point3f)
public javax.vecmath.Point3i transformPoint (javax.vecmath.Point3f, javax.vecmath.Vector3f)
public void transformPoint (javax.vecmath.Point3f, javax.vecmath.Point3i)
public void transformPointNoClip (javax.vecmath.Point3f, javax.vecmath.Point3f)
public void transformPoint (javax.vecmath.Point3f, javax.vecmath.Point3f)
public void transformPoints (javax.vecmath.Point3f[], javax.vecmath.Point3i[])
public void transformVector (javax.vecmath.Vector3f, javax.vecmath.Vector3f)
public void unTransformPoint (javax.vecmath.Point3f, javax.vecmath.Point3f)
public float getScalePixelsPerAngstrom (boolean)
public short scaleToScreen (int, int)
public float unscaleToScreen (int, int)
public float scaleToPerspective (int, float)
void setSpin (java.lang.String, int)
java.lang.String getSpinState ()
void setSpinOn (boolean)
boolean getSpinOn ()
void setNavOn (boolean)
boolean getNavOn ()
void setNavXYZ (float, float, float)
public java.lang.String getOrientationText (int)
java.util.Hashtable getOrientationInfo ()
javax.vecmath.Matrix3f getMatrixRotate ()
public void getAxisAngle (javax.vecmath.AxisAngle4f)
java.lang.String getTransformText ()
void getRotation (javax.vecmath.Matrix3f)
private void setDefaultColors (java.lang.String)
float getDefaultTranslucent ()
public int getColixArgb (short)
void setRubberbandArgb (int)
public short getColixRubberband ()
void setElementArgb (int, int)
public float getVectorScale ()
public void setVectorScale (float)
public float getDefaultDrawArrowScale ()
public void setDefaultDrawArrowScale (float)
float getVibrationScale ()
float getVibrationPeriod ()
public boolean isVibrationOn ()
public void setVibrationScale (float)
void setVibrationOff ()
public void setVibrationPeriod (float)
void setObjectColor (java.lang.String, java.lang.String)
void setObjectArgb (java.lang.String, int)
void setBackgroundImage (java.lang.String, java.awt.Image)
int getObjectArgb (int)
public short getObjectColix (int)
public java.lang.String getObjectState (java.lang.String)
public void setColorBackground (java.lang.String)
public int getBackgroundArgb ()
void setObjectMad (int, java.lang.String, int)
public int getObjectMad (int)
public void setPropertyColorScheme (java.lang.String, boolean)
public java.lang.String getPropertyColorScheme ()
public short getColixBackgroundContrast ()
java.lang.String getSpecularState ()
private static void setSpecular (boolean)
boolean getSpecular ()
private static void setSpecularPower (int)
private static void setSpecularExponent (int)
private static void setAmbientPercent (int)
static int getAmbientPercent ()
private static void setDiffusePercent (int)
static int getDiffusePercent ()
private static void setSpecularPercent (int)
static int getSpecularPercent ()
public short getColixAtomPalette (org.jmol.modelset.Atom, byte)
public short getColixBondPalette (org.jmol.modelset.Bond, byte)
public int[] getColorSchemeArray (java.lang.String)
public java.lang.String getColorSchemeList (java.lang.String, boolean)
public static void setUserScale (int[])
public short getColixForPropertyValue (float)
javax.vecmath.Point3f getColorPointForPropertyValue (float)
void select (java.util.BitSet, boolean)
void selectBonds (java.util.BitSet)
void hide (java.util.BitSet, boolean)
void display (java.util.BitSet, boolean)
java.util.BitSet getHiddenSet ()
public boolean isSelected (int)
boolean isInSelectionSubset (int)
void reportSelection (java.lang.String)
public javax.vecmath.Point3f getAtomSetCenter (java.util.BitSet)
private void clearAtomSets ()
public void selectAll ()
void setNoneSelected (boolean)
java.lang.Boolean getNoneSelected ()
public void clearSelection ()
public void setSelectionSet (java.util.BitSet)
void setSelectionSubset (java.util.BitSet)
public java.util.BitSet getSelectionSubset ()
void invertSelection ()
public java.util.BitSet getSelectionSet ()
public int getSelectionCount ()
void setFormalCharges (int)
public void addSelectionListener (org.jmol.api.JmolSelectionListener)
public void removeSelectionListener (org.jmol.api.JmolSelectionListener)
java.util.BitSet getAtomBitSet (java.lang.Object)
java.util.Vector getAtomBitSetVector (java.lang.Object)
public void setModeMouse (int)
java.awt.Rectangle getRubberBandSelection ()
public int getCursorX ()
public int getCursorY ()
java.lang.String getDefaultDirectory ()
public java.io.BufferedInputStream getBufferedInputStream (java.lang.String)
java.lang.Object getBufferedReaderOrErrorMessageFromName (java.lang.String, java.lang.String[], boolean)
void addLoadScript (java.lang.String)
private java.util.Hashtable setLoadParameters (java.util.Hashtable)
public java.lang.String openFile (java.lang.String)
public void openFileAsynchronously (java.lang.String)
void openFile (java.lang.String, java.util.Hashtable, java.lang.String, boolean)
public java.lang.String openFiles (java.lang.String, java.lang.String[])
java.lang.String openFiles (java.lang.String, java.lang.String[], java.lang.String, boolean, java.util.Hashtable)
public java.lang.String openStringInline (java.lang.String)
private java.lang.String createModelSetInline (java.lang.String, java.util.Hashtable, boolean, boolean)
private java.lang.String openStringsInline (java.lang.String[], java.util.Hashtable, boolean)
public char getInlineChar ()
public java.lang.String loadInline (java.lang.String)
public java.lang.String loadInline (java.lang.String, boolean)
public java.lang.String loadInline (java.lang.String, char)
java.lang.String loadInline (java.lang.String, char, boolean)
java.lang.String getDataSeparator ()
public java.lang.String loadInline (java.lang.String[])
public java.lang.String loadInline (java.lang.String[], boolean)
public boolean getApplySymmetryToBonds ()
void setApplySymmetryToBonds (boolean)
void setAtomData (int, java.lang.String, java.lang.String)
public java.lang.String openDOM (java.lang.Object)
public java.lang.String openReader (java.lang.String, java.lang.String, java.io.Reader)
java.lang.String createModelSetAndReturnError (boolean)
java.lang.String loadAtomDataAndReturnError (int)
private java.lang.String createAtomDataSet (int, java.lang.Object)
void deallocateReaderThreads ()
public void openClientFile (java.lang.String, java.lang.String, java.lang.Object)
private java.lang.String createModelSet (java.lang.String, java.lang.String, java.lang.Object, boolean)
public java.lang.Object getCurrentFileAsBytes ()
public java.lang.Object getFileAsBytes (java.lang.String)
public java.lang.String getCurrentFileAsString ()
public java.lang.String getFullPathName ()
public java.lang.String getFileName ()
public java.lang.String getFileAsString (java.lang.String)
public java.lang.String getFileAsString (java.lang.String, int, boolean)
public java.lang.String getFullPath (java.lang.String)
public boolean getFileAsString (java.lang.String[], int, boolean)
java.lang.String[] getFileInfo ()
void setFileInfo (java.lang.String[])
public void autoCalculate (int)
int getSurfaceDistanceMax ()
public void calculateStraightness ()
public javax.vecmath.Point3f[] calculateSurface (java.util.BitSet, float)
void calculateStructures (java.util.BitSet)
public org.jmol.modelset.AtomIndexIterator getWithinModelIterator (org.jmol.modelset.Atom, float)
public org.jmol.modelset.AtomIndexIterator getWithinAtomSetIterator (int, float, java.util.BitSet, boolean, boolean)
public void fillAtomData (org.jmol.atomdata.AtomData, int)
org.jmol.modelset.ModelCollection$StateScript addStateScript (java.lang.String, boolean, boolean)
org.jmol.modelset.ModelCollection$StateScript addStateScript (java.lang.String, java.util.BitSet, java.util.BitSet, java.util.BitSet, java.lang.String, boolean, boolean)
public boolean getEchoStateActive ()
void setEchoStateActive (boolean)
public void zap (boolean, boolean)
private void zap (java.lang.String)
void echoMessage (java.lang.String)
public java.lang.String getMinimizationInfo ()
public boolean useMinimizationThread ()
private void initializeModel ()
public java.lang.String getModelSetName ()
public java.lang.String getModelSetFileName ()
public java.lang.String getUnitCellInfoText ()
public java.util.Hashtable getSpaceGroupInfo (java.lang.String)
void getPolymerPointsAndVectors (java.util.BitSet, java.util.Vector)
public java.lang.String getModelSetProperty (java.lang.String)
public java.lang.Object getModelSetAuxiliaryInfo (java.lang.String)
public java.lang.String getModelSetPathName ()
public java.lang.String getModelSetTypeName ()
public boolean haveFrame ()
boolean haveModelSet ()
void clearBfactorRange ()
public java.lang.String getHybridizationAndAxes (int, javax.vecmath.Vector3f, javax.vecmath.Vector3f, java.lang.String, boolean)
public java.util.BitSet getModelAtomBitSet (int, boolean)
public java.util.BitSet getModelBitSet (java.util.BitSet, boolean)
public java.lang.String getClientAtomStringProperty (java.lang.Object, java.lang.String)
public org.jmol.modelset.ModelSet getModelSet ()
public java.lang.String getBoundBoxCommand (boolean)
void setBoundBox (javax.vecmath.Point3f, javax.vecmath.Point3f, boolean)
public javax.vecmath.Point3f getBoundBoxCenter ()
javax.vecmath.Point3f getAverageAtomPoint ()
void calcBoundBoxDimensions (java.util.BitSet)
org.jmol.modelset.BoxInfo getBoxInfo (java.util.BitSet)
float calcRotationRadius (javax.vecmath.Point3f)
public float calcRotationRadius (java.util.BitSet)
public javax.vecmath.Vector3f getBoundBoxCornerVector ()
java.util.Hashtable getBoundBoxInfo ()
public java.util.BitSet getBoundBoxModels ()
public int getBoundBoxCenterX ()
public int getBoundBoxCenterY ()
public int getModelCount ()
java.lang.String getModelInfoAsString ()
java.lang.String getSymmetryInfoAsString ()
public java.util.Properties getModelSetProperties ()
public java.util.Hashtable getModelSetAuxiliaryInfo ()
public int getModelNumber (int)
public int getModelFileNumber (int)
public java.lang.String getModelNumberDotted (int)
public java.lang.String getModelName (int)
public java.util.Properties getModelProperties (int)
public java.lang.String getModelProperty (int, java.lang.String)
public java.lang.String getModelFileInfo ()
java.lang.String getModelFileInfoAll ()
public java.util.Hashtable getModelAuxiliaryInfo (int)
public java.lang.Object getModelAuxiliaryInfo (int, java.lang.String)
int getModelNumberIndex (int, boolean, boolean)
boolean modelSetHasVibrationVectors ()
public boolean modelHasVibrationVectors (int)
public int getChainCount ()
public int getChainCountInModel (int)
public int getChainCountInModel (int, boolean)
public int getGroupCount ()
public int getGroupCountInModel (int)
public int getPolymerCount ()
public int getPolymerCountInModel (int)
public int getAtomCount ()
public int getAtomCountInModel (int)
public int getBondCount ()
public int getBondCountInModel (int)
java.util.BitSet getBondsForSelectedAtoms (java.util.BitSet)
boolean frankClicked (int, int)
public int findNearestAtomIndex (int, int)
void selectRectangle (java.awt.Rectangle, int)
void toCartesian (javax.vecmath.Point3f)
void toUnitCell (javax.vecmath.Point3f, javax.vecmath.Point3f)
void toFractional (javax.vecmath.Point3f)
public void setCenterSelected ()
public void setBondTolerance (float)
public float getBondTolerance ()
public void setMinBondDistance (float)
public float getMinBondDistance ()
int[] getAtomIndices (java.util.BitSet)
public java.util.BitSet getAtomBits (int, java.lang.Object)
java.util.BitSet getSequenceBits (java.lang.String, java.util.BitSet)
java.util.BitSet getAtomsWithin (float, javax.vecmath.Point3f)
java.util.BitSet getAtomsWithin (float, javax.vecmath.Point4f)
java.util.BitSet getAtomsWithin (float, java.util.BitSet, boolean)
java.util.BitSet getAtomsConnected (float, float, int, java.util.BitSet)
java.util.BitSet getBranchBitSet (int, int)
int getAtomIndexFromAtomNumber (int)
public java.util.BitSet getElementsPresentBitSet (int)
public java.util.Hashtable getHeteroList (int)
java.util.BitSet getVisibleSet ()
java.util.BitSet getClickableSet ()
void calcSelectedGroupsCount ()
void calcSelectedMonomersCount ()
void calcSelectedMoleculesCount ()
java.lang.String getFileHeader ()
java.lang.Object getFileData ()
public java.util.Hashtable getCifData (int)
java.lang.String getPDBHeader ()
public java.util.Hashtable getModelInfo (java.lang.Object)
public java.util.Hashtable getAuxiliaryInfo (java.lang.Object)
public java.util.Hashtable getShapeInfo ()
int getShapeIdFromObjectName (java.lang.String)
java.util.Vector getAllAtomInfo (java.lang.Object)
java.util.Vector getAllBondInfo (java.lang.Object)
java.util.Vector getMoleculeInfo (java.lang.Object)
public java.lang.String getChimeInfo (int)
public java.util.Hashtable getAllChainInfo (java.lang.Object)
public java.util.Hashtable getAllPolymerInfo (java.lang.Object)
public java.lang.String getStateInfo ()
public java.lang.String getStateInfo (java.lang.String)
public java.lang.String getStructureState ()
java.lang.String getProteinStructureState ()
public java.lang.String getCoordinateState (java.util.BitSet)
void setCurrentColorRange (java.lang.String)
void setCurrentColorRange (float[], java.util.BitSet)
public void setCurrentColorRange (float, float)
public float[] getCurrentColorRange ()
public void setData (java.lang.String, java.lang.Object[], int, int, int, int, int)
java.lang.Object[] getData (java.lang.String)
public float[] getDataFloat (java.lang.String)
float[][] getDataFloat2D (java.lang.String)
public float[][][] getDataFloat3D (java.lang.String)
public float getDataFloat (java.lang.String, int)
public java.lang.String getAltLocListInModel (int)
public java.util.BitSet setConformation ()
public java.util.BitSet setConformation (int)
int autoHbond (java.util.BitSet)
int autoHbond (java.util.BitSet, java.util.BitSet, java.util.BitSet, float, float)
public boolean hasCalculatedHBonds (java.util.BitSet)
public boolean havePartialCharges ()
public org.jmol.api.SymmetryInterface getCurrentUnitCell ()
void setCurrentUnitCellOffset (int)
void setCurrentUnitCellOffset (javax.vecmath.Point3f)
public java.lang.String getDefaultMeasurementLabel (int)
public int getMeasurementCount ()
public java.lang.String getMeasurementStringValue (int)
java.util.Vector getMeasurementInfo ()
public java.lang.String getMeasurementInfoAsString ()
public int[] getMeasurementCountPlusIndices (int)
void setPendingMeasurement (org.jmol.modelset.MeasurementPending)
org.jmol.modelset.MeasurementPending getPendingMeasurement ()
void clearAllMeasurements ()
public void clearMeasurements ()
public boolean getJustifyMeasurements ()
void setMeasurementFormats (java.lang.String)
void defineMeasurement (java.util.Vector, float[], boolean, boolean, boolean, boolean, boolean, java.lang.String)
public void deleteMeasurement (int)
void deleteMeasurement (int[])
public void showMeasurement (int[], boolean)
void hideMeasurements (boolean)
void toggleMeasurement (int[], java.lang.String)
void setAnimationDirection (int)
void reverseAnimation ()
int getAnimationDirection ()
java.util.Hashtable getAnimationInfo ()
public void setAnimationFps (int)
public int getAnimationFps ()
void setAnimationReplayMode (int, float, float)
int getAnimationReplayMode ()
void setAnimationOn (boolean)
void resumeAnimation ()
void pauseAnimation ()
void setAnimationRange (int, int)
public java.util.BitSet getVisibleFramesBitSet ()
boolean isAnimationOn ()
void setAnimationNext ()
void setAnimationPrevious ()
void setAnimationLast ()
void rewindAnimation ()
void setCurrentModelIndex (int)
void setTrajectory (int)
public void setTrajectory (java.util.BitSet)
boolean isTrajectory (int)
public java.util.BitSet getBitSetTrajectories ()
java.lang.String getTrajectoryInfo ()
void setFrameOffset (int)
public void setFrameOffsets (java.util.BitSet)
public java.util.BitSet getFrameOffsets ()
public void setCurrentModelIndex (int, boolean)
public int getCurrentModelIndex ()
public int getDisplayModelIndex ()
boolean haveFileSet ()
void setBackgroundModelIndex (int)
public int getBackgroundModelIndex ()
void setFrameVariables (int, int)
public int getMotionEventNumber ()
void setInMotion (boolean)
public boolean getInMotion ()
public void pushHoldRepaint ()
void pushHoldRepaint (java.lang.String)
public void popHoldRepaint ()
void popHoldRepaint (java.lang.String)
void setRefreshing (boolean)
boolean getRefreshing ()
public void refresh (int, java.lang.String)
void requestRepaintAndWait ()
void setSync ()
public void viewerNotifyRepaintDone ()
public boolean areAxesTainted ()
private void setMaximumSize (int)
public void setScreenDimension (java.awt.Dimension)
public float getImageFontScaling ()
private void resizeImage (int, int, boolean, boolean, boolean)
public int getScreenWidth ()
public int getScreenHeight ()
public int getScreenDim ()
public java.lang.String generateOutput (java.lang.String, java.lang.String, int, int)
public void renderScreenImage (java.awt.Graphics, java.awt.Graphics, java.awt.Dimension, java.awt.Rectangle)
public void renderScreenImage (java.awt.Graphics, java.awt.Dimension, java.awt.Rectangle)
private java.awt.Image getImage (boolean)
private void render ()
private java.awt.Image getStereoImage (int)
private void render1 (java.awt.Graphics, java.awt.Image, int, int)
public java.awt.Image getScreenImage ()
public java.lang.Object getImageAs (java.lang.String, int, int, int, java.lang.String, java.io.OutputStream)
public void releaseScreenImage ()
boolean getAllowEmbeddedScripts ()
public java.lang.String evalFile (java.lang.String)
public java.lang.String script (java.lang.String)
java.lang.String getInterruptScript ()
public java.lang.String evalString (java.lang.String)
public java.lang.String evalStringQuiet (java.lang.String)
java.lang.String evalStringQuiet (java.lang.String, boolean, boolean)
private java.lang.String checkScriptExecution (java.lang.String)
boolean usingScriptQueue ()
public void clearScriptQueue ()
public boolean checkResume (java.lang.String)
public boolean checkStepping (java.lang.String)
public boolean checkHalt (java.lang.String)
public java.lang.String scriptWait (java.lang.String)
public java.lang.Object scriptWaitStatus (java.lang.String, java.lang.String)
public java.lang.Object evalStringWaitStatus (java.lang.String, java.lang.String, java.lang.String)
synchronized java.lang.Object evalStringWaitStatus (java.lang.String, java.lang.String, java.lang.String, boolean, boolean, boolean)
void exitJmol ()
private java.lang.Object scriptCheck (java.lang.String, boolean)
public synchronized java.lang.Object scriptCheck (java.lang.String)
public boolean isScriptExecuting ()
public void haltScriptExecution ()
public void resumeScriptExecution ()
public void stepScriptExecution ()
public void pauseScriptExecution ()
java.lang.String getDefaultLoadScript ()
java.lang.String getLoadFormat ()
public java.lang.String getStandardLabelFormat ()
public int getRibbonAspectRatio ()
public float getSheetSmoothing ()
public boolean getSsbondsBackbone ()
public boolean getHbondsBackbone ()
public boolean getHbondsSolid ()
public void setMarBond (short)
void hoverOn (int, int)
int getHoverDelay ()
public void hoverOn (int, int, java.lang.String)
void hoverOff ()
void setLabel (java.lang.String)
void togglePickingLabel (java.util.BitSet)
java.util.BitSet getBitSetSelection ()
public void clearShapes ()
public void loadShape (int)
void setShapeSize (int, int, float)
public void setShapeSize (int, int, java.util.BitSet)
public void setShapeSize (int, int, float, java.util.BitSet)
public void setShapeProperty (int, java.lang.String, java.lang.Object)
void setShapeProperty (int, java.lang.String, java.lang.Object, java.util.BitSet)
void setShapePropertyArgb (int, java.lang.String, int)
public java.lang.Object getShapeProperty (int, java.lang.String)
public boolean getShapeProperty (int, java.lang.String, java.lang.Object[])
java.lang.Object getShapeProperty (int, java.lang.String, int)
int getShapePropertyAsInt (int, java.lang.String)
short getColix (java.lang.Object)
boolean getRasmolHydrogenSetting ()
boolean getRasmolHeteroSetting ()
boolean getDebugScript ()
public void setDebugScript (boolean)
void atomPicked (int, org.jmol.util.Point3fi, int, boolean)
void clearClickCount ()
public void setCursor (int)
private void setPickingMode (java.lang.String)
public int getPickingMode ()
public boolean getDrawPicking ()
public boolean getBondPicking ()
private boolean getAtomPicking ()
private void setPickingStyle (java.lang.String)
int getPickingStyle ()
public boolean getDrawHover ()
public java.lang.String getAtomInfo (int)
public java.lang.String getAtomInfoXYZ (int, boolean)
public void setJmolCallbackListener (org.jmol.api.JmolCallbackListener)
public void setJmolStatusListener (org.jmol.api.JmolStatusListener)
public java.util.Hashtable getMessageQueue ()
java.lang.Object getStatusChanged (java.lang.String)
void popupMenu (int, int)
java.lang.String getMenu (java.lang.String)
void setMenu (java.lang.String, boolean)
void setStatusFrameChanged (int)
public void scriptEcho (java.lang.String)
void notifyError (java.lang.String, java.lang.String, java.lang.String)
java.lang.String jsEval (java.lang.String)
public void setStatusAtomHovered (int, java.lang.String)
private void setFileLoadStatus (int, java.lang.String, java.lang.String, java.lang.String, java.lang.String)
public void setStatusMeasuring (java.lang.String, int, java.lang.String)
public void notifyMinimizationStatus ()
public void setStatusAtomPicked (int, java.lang.String)
public void setStatusResized (int, int)
void scriptStatus (java.lang.String)
void scriptStatus (java.lang.String, java.lang.String)
void scriptStatus (java.lang.String, java.lang.String, int, java.lang.String)
private java.lang.String getModelTitle (int)
private java.lang.String getModelFileName (int)
public java.lang.String dialogAsk (java.lang.String, java.lang.String)
int getScriptDelay ()
public void showUrl (java.lang.String)
public void setMeshCreator (java.lang.Object)
void showConsole (boolean)
void clearConsole ()
java.lang.Object getParameterEscaped (java.lang.String)
public java.lang.Object getParameter (java.lang.String)
org.jmol.viewer.ScriptVariable getOrSetNewVariable (java.lang.String, boolean)
org.jmol.viewer.ScriptVariable setUserVariable (java.lang.String, org.jmol.viewer.ScriptVariable)
void unsetProperty (java.lang.String)
java.lang.String getVariableList ()
public boolean getBooleanProperty (java.lang.String)
public boolean getBooleanProperty (java.lang.String, boolean)
public void setStringProperty (java.lang.String, java.lang.String)
public java.lang.String getLanguage ()
private void setLanguage (java.lang.String)
private void setPropertyError (java.lang.String)
void removeUserVariable (java.lang.String)
boolean isJmolVariable (java.lang.String)
public void setFloatProperty (java.lang.String, float)
private boolean setFloatProperty (java.lang.String, float, boolean)
public void setIntProperty (java.lang.String, int)
private void setIntProperty (java.lang.String, int, boolean)
int getDelayMaximum ()
public void setBooleanProperty (java.lang.String, boolean)
boolean setBooleanProperty (java.lang.String, boolean, boolean)
public boolean getPdbLoadInfo (int)
boolean getSelectAllModels ()
boolean getMessageStyleChime ()
public boolean getFontCaching ()
public boolean getFontScaling ()
void showParameter (java.lang.String, boolean, int)
public void showString (java.lang.String, boolean)
java.lang.String getAllSettings (java.lang.String)
public boolean getDotSurfaceFlag ()
public boolean getDotsSelectedOnlyFlag ()
public int getDotDensity ()
public boolean isRangeSelected ()
boolean getIsosurfacePropertySmoothing ()
public boolean getWireframeRotation ()
boolean isWindowCentered ()
void setNavigationDepthPercent (float, float)
float getNavigationSpeed ()
public boolean getShowNavigationPoint ()
public void setVisualRange (float)
float getSolventProbeRadius ()
public float getCurrentSolventProbeRadius ()
boolean getSolventOn ()
public boolean getTestFlag1 ()
public boolean getTestFlag2 ()
public boolean getTestFlag3 ()
public boolean getTestFlag4 ()
public void setPerspectiveDepth (boolean)
public void setAxesOrientationRasmol (boolean)
public boolean getAxesOrientationRasmol ()
void setAxesScale (float)
public javax.vecmath.Point3f[] getAxisPoints ()
public float getAxesScale ()
private void setAxesModeMolecular (boolean)
void setAxesModeUnitCell (boolean)
public int getAxesMode ()
public boolean getDisplayCellParameters ()
public boolean getPerspectiveDepth ()
public void setSelectionHalos (boolean)
public boolean getSelectionHaloEnabled ()
public boolean getBondSelectionModeOr ()
public boolean getChainCaseSensitive ()
public boolean getRibbonBorder ()
public boolean getCartoonRocketFlag ()
public boolean getRocketBarrelFlag ()
private void setStrandCount (int, int)
public int getStrandCount (int)
boolean getHideNameInPopup ()
boolean getNavigationPeriodic ()
private void stopAnimationThreads ()
private void setNavigationMode (boolean)
public boolean getNavigationMode ()
public boolean getNavigateSurface ()
public void setTransformManager (org.jmol.viewer.TransformManager)
private void setPerspectiveModel (int)
private void setTransformManagerDefaults ()
public float getCameraDepth ()
boolean getZoomLarge ()
public boolean getTraceAlpha ()
public int getHermiteLevel ()
public boolean getHighResolution ()
java.lang.String getLoadState ()
public void setAutoBond (boolean)
public boolean getAutoBond ()
int[] makeConnections (float, float, short, int, java.util.BitSet, java.util.BitSet, java.util.BitSet, boolean)
public void rebond ()
void setPdbConectBonding (boolean)
boolean getGreyscaleRendering ()
boolean getDisablePopupMenu ()
public boolean getForceAutoBond ()
public void setPercentVdwAtom (int)
public int getPercentVdwAtom ()
public short getDefaultMadAtom ()
public short getMadBond ()
public short getMarBond ()
public byte getModeMultipleBond ()
public boolean getShowMultipleBonds ()
public void setShowHydrogens (boolean)
public boolean getShowHydrogens ()
public boolean getShowHiddenSelectionHalos ()
public void setShowBbcage (boolean)
public boolean getShowBbcage ()
public void setShowUnitCell (boolean)
public boolean getShowUnitCell ()
public void setShowAxes (boolean)
public boolean getShowAxes ()
public void setFrankOn (boolean)
public boolean getShowFrank ()
public boolean isSignedApplet ()
public void setShowMeasurements (boolean)
public boolean getShowMeasurements ()
public boolean getShowMeasurementLabels ()
public boolean getMeasureAllModelsFlag ()
void setMeasureDistanceUnits (java.lang.String)
public java.lang.String getMeasureDistanceUnits ()
public boolean getUseNumberLocalization ()
void setAppendNew (boolean)
public boolean getAppendNew ()
boolean getAutoFps ()
public void setRasmolDefaults ()
public void setJmolDefaults ()
private void setDefaults (java.lang.String)
public boolean getZeroBasedXyzRasmol ()
private void setAntialias (int, boolean)
public javax.vecmath.Point3f[] allocTempPoints (int)
public void freeTempPoints (javax.vecmath.Point3f[])
public javax.vecmath.Point3i[] allocTempScreens (int)
public void freeTempScreens (javax.vecmath.Point3i[])
public byte[] allocTempBytes (int)
public void freeTempBytes (byte[])
org.jmol.g3d.Font3D getFont3D (java.lang.String, java.lang.String, float)
public java.lang.String formatText (java.lang.String)
java.lang.String getElementSymbol (int)
int getElementNumber (int)
public java.lang.String getAtomName (int)
public int getAtomNumber (int)
float getAtomX (int)
float getAtomY (int)
float getAtomZ (int)
public javax.vecmath.Point3f getAtomPoint3f (int)
public float getAtomRadius (int)
public float getAtomVdwRadius (int)
public int getAtomArgb (int)
java.lang.String getAtomChain (int)
public int getAtomModelIndex (int)
java.lang.String getAtomSequenceCode (int)
public float getBondRadius (int)
public short getBondOrder (int)
void assignAromaticBonds ()
public boolean getSmartAromatic ()
void resetAromatic ()
public int getBondArgb1 (int)
public int getBondModelIndex (int)
public int getBondArgb2 (int)
public javax.vecmath.Point3f[] getPolymerLeadMidPoints (int, int)
void setStereoMode (int[], int, float)
public boolean isJvm12orGreater ()
public java.lang.String getOperatingSystemName ()
public java.lang.String getJavaVendor ()
public java.lang.String getJavaVersion ()
public org.jmol.g3d.Graphics3D getGraphics3D ()
public boolean showModelSetDownload ()
public java.lang.Object getProperty (java.lang.String, java.lang.String, java.lang.String)
boolean isScriptEditorVisible ()
public java.lang.Object getProperty (java.lang.String, java.lang.String, java.lang.Object)
void showEditor (java.lang.String[])
java.lang.String getModelExtract (java.lang.Object)
public java.lang.String getHexColorFromIndex (short)
void setModelVisibility ()
void setFrameTitle (int, java.lang.String)
java.lang.String getFrameTitle (int)
void setTainted (boolean)
org.jmol.util.Point3fi checkObjectClicked (int, int, int)
boolean checkObjectHovered (int, int)
void checkObjectDragged (int, int, int, int, int)
void rotateAxisAngleAtCenter (javax.vecmath.Point3f, javax.vecmath.Vector3f, float, float, boolean, java.util.BitSet)
void rotateAboutPointsInternal (javax.vecmath.Point3f, javax.vecmath.Point3f, float, float, boolean, java.util.BitSet)
int getPickingSpinRate ()
public void startSpinningAxis (javax.vecmath.Point3f, javax.vecmath.Point3f, boolean)
public javax.vecmath.Vector3f getModelDipole ()
public javax.vecmath.Vector3f calculateMolecularDipole ()
public float getDipoleScale ()
public void getAtomIdentityInfo (int, java.util.Hashtable)
void setDefaultLattice (javax.vecmath.Point3f)
javax.vecmath.Point3f getDefaultLattice ()
java.util.BitSet getTaintedAtoms (byte)
public void setTaintedAtoms (java.util.BitSet, byte)
public java.lang.String getData (java.lang.String, java.lang.String)
public synchronized java.lang.Object evaluateExpression (java.lang.Object)
java.lang.Object getHelixData (java.util.BitSet, int)
public java.lang.String getPdbData (java.util.BitSet)
java.lang.String getPdbData (int, java.lang.String)
public boolean isJmolDataFrame (int)
public boolean isJmolDataFrame ()
int getJmolDataFrameIndex (int, java.lang.String)
void setJmolDataFrame (java.lang.String, int, int)
void setFrameTitle (java.lang.String)
public java.lang.String getFrameTitle ()
java.lang.String getJmolFrameType (int)
public int getJmolDataSourceFrame (int)
void setAtomProperty (java.util.BitSet, int, int, float, java.lang.String, float[], java.lang.String[])
public void setAtomCoord (int, float, float, float)
void setAtomCoord (java.util.BitSet, int, java.lang.Object)
public void setAtomCoordRelative (int, float, float, float)
void setAtomCoordRelative (javax.vecmath.Point3f)
void setAllowRotateSelected (boolean)
boolean allowRotateSelected ()
void invertSelected (javax.vecmath.Point3f, java.util.BitSet)
void invertSelected (javax.vecmath.Point3f, javax.vecmath.Point4f)
synchronized void moveSelected (int, int, int, int, boolean)
void rotateAtoms (javax.vecmath.Matrix3f, javax.vecmath.Matrix3f, boolean, javax.vecmath.Point3f, boolean, java.util.BitSet)
public void refreshMeasures ()
void setDynamicMeasurements (boolean)
public boolean getDynamicMeasurements ()
public float[][] functionXY (java.lang.String, int, int)
float[][][] functionXYZ (java.lang.String, int, int, int)
void getHelp (java.lang.String)
void addCommand (java.lang.String)
java.lang.String removeCommand ()
public java.lang.String getSetHistory (int)
public void writeTextFile (java.lang.String, java.lang.String)
public java.lang.String clipImage (java.lang.String)
java.lang.String createImage (java.lang.String, java.lang.String, java.lang.Object, int, int, int, java.util.BitSet)
public java.lang.String createImage (java.lang.String, java.lang.String, java.lang.Object, int, int, int)
private void setImageFontScaling (int, int)
private void setSyncTarget (int, boolean)
public void syncScript (java.lang.String, java.lang.String)
void setSyncDriver (int)
public float[] getPartialCharges ()
void setProteinType (byte, java.util.BitSet)
public javax.vecmath.Point3f getBondPoint3f1 (int)
public javax.vecmath.Point3f getBondPoint3f2 (int)
public javax.vecmath.Vector3f getVibrationVector (int)
public int getVanderwaalsMar (int)
public int getVanderwaalsMar (int, int)
void setDefaultVdw (java.lang.String)
java.lang.String getDefaultVdw (int)
public int deleteAtoms (java.util.BitSet, boolean)
public void deleteModelAtoms (int, int, java.util.BitSet)
public java.util.BitSet getDeletedAtoms ()
public char getQuaternionFrame ()
public int getHelixStep ()
java.lang.String calculatePointGroup ()
public java.util.Hashtable getPointGroupInfo (java.lang.Object)
public java.lang.String getPointGroupAsString (boolean, java.lang.String, int, float)
public float getPointGroupTolerance (int)
java.lang.Object getFileAsImage (java.lang.String, java.util.Hashtable)
java.lang.String cd (java.lang.String)
private java.lang.String setErrorMessage (java.lang.String)
private java.lang.String setErrorMessage (java.lang.String, java.lang.String)
public java.lang.String getErrorMessage ()
public java.lang.String getErrorMessageUntranslated ()
public org.jmol.shape.Shape getShape (int)
public void setShapeErrorState (int, java.lang.String)
public java.lang.String getShapeErrorState ()
public void handleError (java.lang.Error, boolean)
float[] getAtomicCharges ()
org.jmol.viewer.ScriptFunction getFunction (java.lang.String)
void addFunction (org.jmol.viewer.ScriptFunction)
public void clearFunctions ()
public boolean isFunction (java.lang.String)
public java.lang.String getFunctionCalls (java.lang.String)
void showMessage (java.lang.String)
public java.lang.String getMoInfo (int)
boolean isRepaintPending ()
}
com/
com/obrador/
javax/
javax/vecmath/
com/obrador/license.txt
javax/vecmath/AxisAngle4d.class
AxisAngle4d.java
package javax.vecmath
public javax.vecmath.AxisAngle4d extends java.lang.Object implements java.io.Serializable {
public double x
public double y
public double z
public double angle
public void <init> (double, double, double, double)
double x
double y
double z
double angle
public void <init> (double[])
double[] a
public void <init> (javax.vecmath.AxisAngle4d)
javax.vecmath.AxisAngle4d a1
public void <init> (javax.vecmath.AxisAngle4f)
javax.vecmath.AxisAngle4f a1
public void <init> ()
public void <init> (javax.vecmath.Vector3d, double)
javax.vecmath.Vector3d axis
double angle
public final void set (javax.vecmath.Vector3d, double)
javax.vecmath.Vector3d axis
double angle
public final void set (double, double, double, double)
double x
double y
double z
double angle
public final void set (double[])
double[] a
public final void set (javax.vecmath.AxisAngle4d)
javax.vecmath.AxisAngle4d a1
public final void set (javax.vecmath.AxisAngle4f)
javax.vecmath.AxisAngle4f a1
public final void get (double[])
double[] a
public final void set (javax.vecmath.Matrix4f)
javax.vecmath.Matrix4f m1
public final void set (javax.vecmath.Matrix4d)
javax.vecmath.Matrix4d m1
public final void set (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public final void set (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public final void set (javax.vecmath.Quat4f)
javax.vecmath.Quat4f q1
public final void set (javax.vecmath.Quat4d)
javax.vecmath.Quat4d q1
private void setFromMat (double, double, double, double, double, double, double, double, double)
double m00
double m01
double m02
double m10
double m11
double m12
double m20
double m21
double m22
double cos
double sin
private void setFromQuat (double, double, double, double)
double x
double y
double z
double w
double sin_a2
public java.lang.String toString ()
public boolean equals (javax.vecmath.AxisAngle4d)
javax.vecmath.AxisAngle4d a1
public boolean equals (java.lang.Object)
Object o1
public boolean epsilonEquals (javax.vecmath.AxisAngle4d, double)
javax.vecmath.AxisAngle4d a1
double epsilon
public int hashCode ()
long xbits
long ybits
long zbits
long abits
}
javax/vecmath/AxisAngle4f.class
AxisAngle4f.java
package javax.vecmath
public javax.vecmath.AxisAngle4f extends java.lang.Object implements java.io.Serializable {
public float x
public float y
public float z
public float angle
public void <init> (float, float, float, float)
float x
float y
float z
float angle
public void <init> (float[])
float[] a
public void <init> (javax.vecmath.AxisAngle4f)
javax.vecmath.AxisAngle4f a1
public void <init> (javax.vecmath.AxisAngle4d)
javax.vecmath.AxisAngle4d a1
public void <init> ()
public void <init> (javax.vecmath.Vector3f, float)
javax.vecmath.Vector3f axis
float angle
public final void set (javax.vecmath.Vector3f, float)
javax.vecmath.Vector3f axis
float angle
public final void set (float, float, float, float)
float x
float y
float z
float angle
public final void set (float[])
float[] a
public final void set (javax.vecmath.AxisAngle4f)
javax.vecmath.AxisAngle4f a1
public final void set (javax.vecmath.AxisAngle4d)
javax.vecmath.AxisAngle4d a1
public final void get (float[])
float[] a
public final void set (javax.vecmath.Matrix4f)
javax.vecmath.Matrix4f m1
public final void set (javax.vecmath.Matrix4d)
javax.vecmath.Matrix4d m1
public final void set (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public final void set (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public final void set (javax.vecmath.Quat4f)
javax.vecmath.Quat4f q1
public final void set (javax.vecmath.Quat4d)
javax.vecmath.Quat4d q1
private void setFromMat (double, double, double, double, double, double, double, double, double)
double m00
double m01
double m02
double m10
double m11
double m12
double m20
double m21
double m22
double cos
double sin
private void setFromQuat (double, double, double, double)
double x
double y
double z
double w
double sin_a2
public java.lang.String toString ()
public boolean equals (javax.vecmath.AxisAngle4f)
javax.vecmath.AxisAngle4f a1
public boolean equals (java.lang.Object)
Object o1
public boolean epsilonEquals (javax.vecmath.AxisAngle4f, float)
javax.vecmath.AxisAngle4f a1
float epsilon
public int hashCode ()
}
javax/vecmath/Matrix3d.class
Matrix3d.java
package javax.vecmath
public javax.vecmath.Matrix3d extends java.lang.Object implements java.io.Serializable {
public double m00
public double m01
public double m02
public double m10
public double m11
public double m12
public double m20
public double m21
public double m22
public void <init> (double, double, double, double, double, double, double, double, double)
double m00
double m01
double m02
double m10
double m11
double m12
double m20
double m21
double m22
public void <init> (double[])
double[] v
public void <init> (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public void <init> (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public void <init> ()
public java.lang.String toString ()
String nl
public final void setIdentity ()
public final void setScale (double)
double scale
public final void setElement (int, int, double)
int row
int column
double value
public final double getElement (int, int)
int row
int column
public final void setRow (int, double, double, double)
int row
double x
double y
double z
public final void setRow (int, javax.vecmath.Vector3d)
int row
javax.vecmath.Vector3d v
public final void setRow (int, double[])
int row
double[] v
public final void getRow (int, double[])
int row
double[] v
public final void getRow (int, javax.vecmath.Vector3d)
int row
javax.vecmath.Vector3d v
public final void setColumn (int, double, double, double)
int column
double x
double y
double z
public final void setColumn (int, javax.vecmath.Vector3d)
int column
javax.vecmath.Vector3d v
public final void setColumn (int, double[])
int column
double[] v
public final void getColumn (int, javax.vecmath.Vector3d)
int column
javax.vecmath.Vector3d v
public final void getColumn (int, double[])
int column
double[] v
public final double getScale ()
public final void add (double)
double scalar
public final void add (double, javax.vecmath.Matrix3d)
double scalar
javax.vecmath.Matrix3d m1
public final void add (javax.vecmath.Matrix3d, javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
javax.vecmath.Matrix3d m2
public final void add (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public final void sub (javax.vecmath.Matrix3d, javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
javax.vecmath.Matrix3d m2
public final void sub (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public final void transpose ()
double tmp
public final void transpose (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public final void set (javax.vecmath.Quat4d)
javax.vecmath.Quat4d q1
public final void set (javax.vecmath.AxisAngle4d)
javax.vecmath.AxisAngle4d a1
public final void set (javax.vecmath.Quat4f)
javax.vecmath.Quat4f q1
public final void set (javax.vecmath.AxisAngle4f)
javax.vecmath.AxisAngle4f a1
public final void set (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public final void set (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public final void set (double[])
double[] m
public final void invert (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public final void invert ()
double s
public final double determinant ()
public final void set (double)
double scale
public final void rotX (double)
double angle
double c
double s
public final void rotY (double)
double angle
double c
double s
public final void rotZ (double)
double angle
double c
double s
public final void mul (double)
double scalar
public final void mul (double, javax.vecmath.Matrix3d)
double scalar
javax.vecmath.Matrix3d m1
public final void mul (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public final void mul (javax.vecmath.Matrix3d, javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
javax.vecmath.Matrix3d m2
public final void mulNormalize (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public final void mulNormalize (javax.vecmath.Matrix3d, javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
javax.vecmath.Matrix3d m2
public final void mulTransposeBoth (javax.vecmath.Matrix3d, javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
javax.vecmath.Matrix3d m2
public final void mulTransposeRight (javax.vecmath.Matrix3d, javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
javax.vecmath.Matrix3d m2
public final void mulTransposeLeft (javax.vecmath.Matrix3d, javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
javax.vecmath.Matrix3d m2
public final void normalize ()
public final void normalize (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public final void normalizeCP ()
double s
public final void normalizeCP (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public boolean equals (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public boolean equals (java.lang.Object)
Object o1
public boolean epsilonEquals (javax.vecmath.Matrix3d, double)
javax.vecmath.Matrix3d m1
double epsilon
public int hashCode ()
long bits
int hash
public final void setZero ()
public final void negate ()
public final void negate (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public final void transform (javax.vecmath.Tuple3d)
javax.vecmath.Tuple3d t
public final void transform (javax.vecmath.Tuple3d, javax.vecmath.Tuple3d)
javax.vecmath.Tuple3d t
javax.vecmath.Tuple3d result
private void set (double, double, double, double, double, double, double, double, double)
double m00
double m01
double m02
double m10
double m11
double m12
double m20
double m21
double m22
private double SVD (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d rot
double s
double n
private void setFromQuat (double, double, double, double)
double x
double y
double z
double w
double n
double s
double xs
double ys
double zs
double wx
double wy
double wz
double xx
double xy
double xz
double yy
double yz
double zz
private void setFromAxisAngle (double, double, double, double)
double x
double y
double z
double angle
double n
double c
double s
double omc
double tmp1
double tmp2
}
javax/vecmath/Matrix3f.class
Matrix3f.java
package javax.vecmath
public javax.vecmath.Matrix3f extends java.lang.Object implements java.io.Serializable {
public float m00
public float m01
public float m02
public float m10
public float m11
public float m12
public float m20
public float m21
public float m22
public void <init> (float, float, float, float, float, float, float, float, float)
float m00
float m01
float m02
float m10
float m11
float m12
float m20
float m21
float m22
public void <init> (float[])
float[] v
public void <init> (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public void <init> (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public void <init> ()
public java.lang.String toString ()
String nl
public final void setIdentity ()
public final void setScale (float)
float scale
public final void setElement (int, int, float)
int row
int column
float value
public final float getElement (int, int)
int row
int column
public final void setRow (int, float, float, float)
int row
float x
float y
float z
public final void setRow (int, javax.vecmath.Vector3f)
int row
javax.vecmath.Vector3f v
public final void getRow (int, float[])
int row
float[] v
public final void getRow (int, javax.vecmath.Vector3f)
int row
javax.vecmath.Vector3f v
public final void setRow (int, float[])
int row
float[] v
public final void setColumn (int, float, float, float)
int column
float x
float y
float z
public final void setColumn (int, javax.vecmath.Vector3f)
int column
javax.vecmath.Vector3f v
public final void setColumn (int, float[])
int column
float[] v
public final void getColumn (int, javax.vecmath.Vector3f)
int column
javax.vecmath.Vector3f v
public final void getColumn (int, float[])
int column
float[] v
public final float getScale ()
public final void add (float)
float scalar
public final void add (float, javax.vecmath.Matrix3f)
float scalar
javax.vecmath.Matrix3f m1
public final void add (javax.vecmath.Matrix3f, javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
javax.vecmath.Matrix3f m2
public final void add (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public final void sub (javax.vecmath.Matrix3f, javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
javax.vecmath.Matrix3f m2
public final void sub (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public final void transpose ()
float tmp
public final void transpose (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public final void set (javax.vecmath.Quat4f)
javax.vecmath.Quat4f q1
public final void set (javax.vecmath.AxisAngle4f)
javax.vecmath.AxisAngle4f a1
public final void set (javax.vecmath.AxisAngle4d)
javax.vecmath.AxisAngle4d a1
public final void set (javax.vecmath.Quat4d)
javax.vecmath.Quat4d q1
public final void set (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public final void set (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public final void set (float[])
float[] m
public final void invert (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public final void invert ()
double s
public final float determinant ()
public final void set (float)
float scale
public final void rotX (float)
float angle
double c
double s
public final void rotY (float)
float angle
double c
double s
public final void rotZ (float)
float angle
double c
double s
public final void mul (float)
float scalar
public final void mul (float, javax.vecmath.Matrix3f)
float scalar
javax.vecmath.Matrix3f m1
public final void mul (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public final void mul (javax.vecmath.Matrix3f, javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
javax.vecmath.Matrix3f m2
public final void mulNormalize (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public final void mulNormalize (javax.vecmath.Matrix3f, javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
javax.vecmath.Matrix3f m2
public final void mulTransposeBoth (javax.vecmath.Matrix3f, javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
javax.vecmath.Matrix3f m2
public final void mulTransposeRight (javax.vecmath.Matrix3f, javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
javax.vecmath.Matrix3f m2
public final void mulTransposeLeft (javax.vecmath.Matrix3f, javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
javax.vecmath.Matrix3f m2
public final void normalize ()
public final void normalize (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public final void normalizeCP ()
double s
public final void normalizeCP (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public boolean equals (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public boolean equals (java.lang.Object)
Object o1
public boolean epsilonEquals (javax.vecmath.Matrix3f, double)
javax.vecmath.Matrix3f m1
double epsilon
public int hashCode ()
public final void setZero ()
public final void negate ()
public final void negate (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public final void transform (javax.vecmath.Tuple3f)
javax.vecmath.Tuple3f t
public final void transform (javax.vecmath.Tuple3f, javax.vecmath.Tuple3f)
javax.vecmath.Tuple3f t
javax.vecmath.Tuple3f result
private void set (float, float, float, float, float, float, float, float, float)
float m00
float m01
float m02
float m10
float m11
float m12
float m20
float m21
float m22
private float SVD (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f rot
float s
float t
private void setFromQuat (double, double, double, double)
double x
double y
double z
double w
double n
double s
double xs
double ys
double zs
double wx
double wy
double wz
double xx
double xy
double xz
double yy
double yz
double zz
private void setFromAxisAngle (double, double, double, double)
double x
double y
double z
double angle
double n
double c
double s
double omc
double tmp1
double tmp2
}
javax/vecmath/Matrix4d.class
Matrix4d.java
package javax.vecmath
public javax.vecmath.Matrix4d extends java.lang.Object implements java.io.Serializable {
public double m00
public double m01
public double m02
public double m03
public double m10
public double m11
public double m12
public double m13
public double m20
public double m21
public double m22
public double m23
public double m30
public double m31
public double m32
public double m33
public void <init> (double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double)
double m00
double m01
double m02
double m03
double m10
double m11
double m12
double m13
double m20
double m21
double m22
double m23
double m30
double m31
double m32
double m33
public void <init> (double[])
double[] v
public void <init> (javax.vecmath.Quat4d, javax.vecmath.Vector3d, double)
javax.vecmath.Quat4d q1
javax.vecmath.Vector3d t1
double s
public void <init> (javax.vecmath.Quat4f, javax.vecmath.Vector3d, double)
javax.vecmath.Quat4f q1
javax.vecmath.Vector3d t1
double s
public void <init> (javax.vecmath.Matrix4d)
javax.vecmath.Matrix4d m1
public void <init> (javax.vecmath.Matrix4f)
javax.vecmath.Matrix4f m1
public void <init> (javax.vecmath.Matrix3f, javax.vecmath.Vector3d, double)
javax.vecmath.Matrix3f m1
javax.vecmath.Vector3d t1
double s
public void <init> (javax.vecmath.Matrix3d, javax.vecmath.Vector3d, double)
javax.vecmath.Matrix3d m1
javax.vecmath.Vector3d t1
double s
public void <init> ()
public java.lang.String toString ()
String nl
public final void setIdentity ()
public final void setElement (int, int, double)
int row
int column
double value
public final double getElement (int, int)
int row
int column
public final void get (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public final void get (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public final double get (javax.vecmath.Matrix3d, javax.vecmath.Vector3d)
javax.vecmath.Matrix3d m1
javax.vecmath.Vector3d t1
public final double get (javax.vecmath.Matrix3f, javax.vecmath.Vector3d)
javax.vecmath.Matrix3f m1
javax.vecmath.Vector3d t1
public final void get (javax.vecmath.Quat4f)
javax.vecmath.Quat4f q1
public final void get (javax.vecmath.Quat4d)
javax.vecmath.Quat4d q1
public final void get (javax.vecmath.Vector3d)
javax.vecmath.Vector3d trans
public final void getRotationScale (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public final void getRotationScale (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public final double getScale ()
public final void setRotationScale (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public final void setRotationScale (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public final void setScale (double)
double scale
public final void setRow (int, double, double, double, double)
int row
double x
double y
double z
double w
public final void setRow (int, javax.vecmath.Vector4d)
int row
javax.vecmath.Vector4d v
public final void setRow (int, double[])
int row
double[] v
public final void getRow (int, javax.vecmath.Vector4d)
int row
javax.vecmath.Vector4d v
public final void getRow (int, double[])
int row
double[] v
public final void setColumn (int, double, double, double, double)
int column
double x
double y
double z
double w
public final void setColumn (int, javax.vecmath.Vector4d)
int column
javax.vecmath.Vector4d v
public final void setColumn (int, double[])
int column
double[] v
public final void getColumn (int, javax.vecmath.Vector4d)
int column
javax.vecmath.Vector4d v
public final void getColumn (int, double[])
int column
double[] v
public final void add (double)
double scalar
public final void add (double, javax.vecmath.Matrix4d)
double scalar
javax.vecmath.Matrix4d m1
public final void add (javax.vecmath.Matrix4d, javax.vecmath.Matrix4d)
javax.vecmath.Matrix4d m1
javax.vecmath.Matrix4d m2
public final void add (javax.vecmath.Matrix4d)
javax.vecmath.Matrix4d m1
public final void sub (javax.vecmath.Matrix4d, javax.vecmath.Matrix4d)
javax.vecmath.Matrix4d m1
javax.vecmath.Matrix4d m2
public final void sub (javax.vecmath.Matrix4d)
javax.vecmath.Matrix4d m1
public final void transpose ()
double tmp
public final void transpose (javax.vecmath.Matrix4d)
javax.vecmath.Matrix4d m1
public final void set (double[])
double[] m
public final void set (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public final void set (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public final void set (javax.vecmath.Quat4d)
javax.vecmath.Quat4d q1
public final void set (javax.vecmath.AxisAngle4d)
javax.vecmath.AxisAngle4d a1
public final void set (javax.vecmath.Quat4f)
javax.vecmath.Quat4f q1
public final void set (javax.vecmath.AxisAngle4f)
javax.vecmath.AxisAngle4f a1
public final void set (javax.vecmath.Quat4d, javax.vecmath.Vector3d, double)
javax.vecmath.Quat4d q1
javax.vecmath.Vector3d t1
double s
public final void set (javax.vecmath.Quat4f, javax.vecmath.Vector3d, double)
javax.vecmath.Quat4f q1
javax.vecmath.Vector3d t1
double s
public final void set (javax.vecmath.Quat4f, javax.vecmath.Vector3f, float)
javax.vecmath.Quat4f q1
javax.vecmath.Vector3f t1
float s
public final void set (javax.vecmath.Matrix4d)
javax.vecmath.Matrix4d m1
public final void set (javax.vecmath.Matrix4f)
javax.vecmath.Matrix4f m1
public final void invert (javax.vecmath.Matrix4d)
javax.vecmath.Matrix4d m1
public final void invert ()
double s
public final double determinant ()
public final void set (double)
double scale
public final void set (javax.vecmath.Vector3d)
javax.vecmath.Vector3d v1
public final void set (double, javax.vecmath.Vector3d)
double scale
javax.vecmath.Vector3d v1
public final void set (javax.vecmath.Vector3d, double)
javax.vecmath.Vector3d v1
double scale
public final void set (javax.vecmath.Matrix3f, javax.vecmath.Vector3f, float)
javax.vecmath.Matrix3f m1
javax.vecmath.Vector3f t1
float scale
public final void set (javax.vecmath.Matrix3d, javax.vecmath.Vector3d, double)
javax.vecmath.Matrix3d m1
javax.vecmath.Vector3d t1
double scale
public final void setTranslation (javax.vecmath.Vector3d)
javax.vecmath.Vector3d trans
public final void rotX (double)
double angle
double c
double s
public final void rotY (double)
double angle
double c
double s
public final void rotZ (double)
double angle
double c
double s
public final void mul (double)
double scalar
public final void mul (double, javax.vecmath.Matrix4d)
double scalar
javax.vecmath.Matrix4d m1
public final void mul (javax.vecmath.Matrix4d)
javax.vecmath.Matrix4d m1
public final void mul (javax.vecmath.Matrix4d, javax.vecmath.Matrix4d)
javax.vecmath.Matrix4d m1
javax.vecmath.Matrix4d m2
public final void mulTransposeBoth (javax.vecmath.Matrix4d, javax.vecmath.Matrix4d)
javax.vecmath.Matrix4d m1
javax.vecmath.Matrix4d m2
public final void mulTransposeRight (javax.vecmath.Matrix4d, javax.vecmath.Matrix4d)
javax.vecmath.Matrix4d m1
javax.vecmath.Matrix4d m2
public final void mulTransposeLeft (javax.vecmath.Matrix4d, javax.vecmath.Matrix4d)
javax.vecmath.Matrix4d m1
javax.vecmath.Matrix4d m2
public boolean equals (javax.vecmath.Matrix4d)
javax.vecmath.Matrix4d m1
public boolean equals (java.lang.Object)
Object o1
public boolean epsilonEquals (javax.vecmath.Matrix4d, float)
javax.vecmath.Matrix4d m1
float epsilon
public boolean epsilonEquals (javax.vecmath.Matrix4d, double)
javax.vecmath.Matrix4d m1
double epsilon
public int hashCode ()
long bits
int hash
public final void transform (javax.vecmath.Tuple4d, javax.vecmath.Tuple4d)
javax.vecmath.Tuple4d vec
javax.vecmath.Tuple4d vecOut
public final void transform (javax.vecmath.Tuple4d)
javax.vecmath.Tuple4d vec
public final void transform (javax.vecmath.Tuple4f, javax.vecmath.Tuple4f)
javax.vecmath.Tuple4f vec
javax.vecmath.Tuple4f vecOut
public final void transform (javax.vecmath.Tuple4f)
javax.vecmath.Tuple4f vec
public final void transform (javax.vecmath.Point3d, javax.vecmath.Point3d)
javax.vecmath.Point3d point
javax.vecmath.Point3d pointOut
public final void transform (javax.vecmath.Point3d)
javax.vecmath.Point3d point
public final void transform (javax.vecmath.Point3f, javax.vecmath.Point3f)
javax.vecmath.Point3f point
javax.vecmath.Point3f pointOut
public final void transform (javax.vecmath.Point3f)
javax.vecmath.Point3f point
public final void transform (javax.vecmath.Vector3d, javax.vecmath.Vector3d)
javax.vecmath.Vector3d normal
javax.vecmath.Vector3d normalOut
public final void transform (javax.vecmath.Vector3d)
javax.vecmath.Vector3d normal
public final void transform (javax.vecmath.Vector3f, javax.vecmath.Vector3f)
javax.vecmath.Vector3f normal
javax.vecmath.Vector3f normalOut
public final void transform (javax.vecmath.Vector3f)
javax.vecmath.Vector3f normal
public final void setRotation (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
double scale
public final void setRotation (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
double scale
public final void setRotation (javax.vecmath.Quat4f)
javax.vecmath.Quat4f q1
double scale
double tx
double ty
double tz
double w0
double w1
double w2
double w3
public final void setRotation (javax.vecmath.Quat4d)
javax.vecmath.Quat4d q1
double scale
double tx
double ty
double tz
double w0
double w1
double w2
double w3
public final void setRotation (javax.vecmath.AxisAngle4d)
javax.vecmath.AxisAngle4d a1
double scale
double tx
double ty
double tz
double w0
double w1
double w2
double w3
public final void setZero ()
public final void negate ()
public final void negate (javax.vecmath.Matrix4d)
javax.vecmath.Matrix4d m1
private void set (double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double)
double m00
double m01
double m02
double m03
double m10
double m11
double m12
double m13
double m20
double m21
double m22
double m23
double m30
double m31
double m32
double m33
private double SVD (javax.vecmath.Matrix3d, javax.vecmath.Matrix4d)
javax.vecmath.Matrix3d rot3
javax.vecmath.Matrix4d rot4
double s
double n
double n
private float SVD (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f rot
double s
double t
private void mulRotationScale (double)
double scale
private void setRotationScale (javax.vecmath.Matrix4d)
javax.vecmath.Matrix4d m1
private void setTranslation (javax.vecmath.Vector3f)
javax.vecmath.Vector3f trans
private void setFromQuat (double, double, double, double)
double x
double y
double z
double w
double n
double s
double xs
double ys
double zs
double wx
double wy
double wz
double xx
double xy
double xz
double yy
double yz
double zz
private void setFromAxisAngle (double, double, double, double)
double x
double y
double z
double angle
double n
double c
double s
double omc
double tmp1
double tmp2
}
javax/vecmath/Matrix4f.class
Matrix4f.java
package javax.vecmath
public javax.vecmath.Matrix4f extends java.lang.Object implements java.io.Serializable {
public float m00
public float m01
public float m02
public float m03
public float m10
public float m11
public float m12
public float m13
public float m20
public float m21
public float m22
public float m23
public float m30
public float m31
public float m32
public float m33
public void <init> (float, float, float, float, float, float, float, float, float, float, float, float, float, float, float, float)
float m00
float m01
float m02
float m03
float m10
float m11
float m12
float m13
float m20
float m21
float m22
float m23
float m30
float m31
float m32
float m33
public void <init> (float[])
float[] v
public void <init> (javax.vecmath.Quat4f, javax.vecmath.Vector3f, float)
javax.vecmath.Quat4f q1
javax.vecmath.Vector3f t1
float s
public void <init> (javax.vecmath.Matrix4d)
javax.vecmath.Matrix4d m1
public void <init> (javax.vecmath.Matrix4f)
javax.vecmath.Matrix4f m1
public void <init> (javax.vecmath.Matrix3f, javax.vecmath.Vector3f, float)
javax.vecmath.Matrix3f m1
javax.vecmath.Vector3f t1
float s
public void <init> ()
public java.lang.String toString ()
String nl
public final void setIdentity ()
public final void setElement (int, int, float)
int row
int column
float value
public final float getElement (int, int)
int row
int column
public final void setScale (float)
float scale
public final void get (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public final void get (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public final float get (javax.vecmath.Matrix3f, javax.vecmath.Vector3f)
javax.vecmath.Matrix3f m1
javax.vecmath.Vector3f t1
public final void get (javax.vecmath.Quat4f)
javax.vecmath.Quat4f q1
public final void get (javax.vecmath.Vector3f)
javax.vecmath.Vector3f trans
public final void getRotationScale (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public final float getScale ()
public final void setRotationScale (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public final void setRow (int, float, float, float, float)
int row
float x
float y
float z
float w
public final void setRow (int, javax.vecmath.Vector4f)
int row
javax.vecmath.Vector4f v
public final void setRow (int, float[])
int row
float[] v
public final void getRow (int, javax.vecmath.Vector4f)
int row
javax.vecmath.Vector4f v
public final void getRow (int, float[])
int row
float[] v
public final void setColumn (int, float, float, float, float)
int column
float x
float y
float z
float w
public final void setColumn (int, javax.vecmath.Vector4f)
int column
javax.vecmath.Vector4f v
public final void setColumn (int, float[])
int column
float[] v
public final void getColumn (int, javax.vecmath.Vector4f)
int column
javax.vecmath.Vector4f v
public final void getColumn (int, float[])
int column
float[] v
public final void add (float)
float scalar
public final void add (float, javax.vecmath.Matrix4f)
float scalar
javax.vecmath.Matrix4f m1
public final void add (javax.vecmath.Matrix4f, javax.vecmath.Matrix4f)
javax.vecmath.Matrix4f m1
javax.vecmath.Matrix4f m2
public final void add (javax.vecmath.Matrix4f)
javax.vecmath.Matrix4f m1
public final void sub (javax.vecmath.Matrix4f, javax.vecmath.Matrix4f)
javax.vecmath.Matrix4f m1
javax.vecmath.Matrix4f m2
public final void sub (javax.vecmath.Matrix4f)
javax.vecmath.Matrix4f m1
public final void transpose ()
float tmp
public final void transpose (javax.vecmath.Matrix4f)
javax.vecmath.Matrix4f m1
public final void set (javax.vecmath.Quat4f)
javax.vecmath.Quat4f q1
public final void set (javax.vecmath.AxisAngle4f)
javax.vecmath.AxisAngle4f a1
public final void set (javax.vecmath.Quat4d)
javax.vecmath.Quat4d q1
public final void set (javax.vecmath.AxisAngle4d)
javax.vecmath.AxisAngle4d a1
public final void set (javax.vecmath.Quat4d, javax.vecmath.Vector3d, double)
javax.vecmath.Quat4d q1
javax.vecmath.Vector3d t1
double s
public final void set (javax.vecmath.Quat4f, javax.vecmath.Vector3f, float)
javax.vecmath.Quat4f q1
javax.vecmath.Vector3f t1
float s
public final void set (javax.vecmath.Matrix4d)
javax.vecmath.Matrix4d m1
public final void set (javax.vecmath.Matrix4f)
javax.vecmath.Matrix4f m1
public final void invert (javax.vecmath.Matrix4f)
javax.vecmath.Matrix4f m1
public final void invert ()
float s
public final float determinant ()
public final void set (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public final void set (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public final void set (float)
float scale
public final void set (float[])
float[] m
public final void set (javax.vecmath.Vector3f)
javax.vecmath.Vector3f v1
public final void set (float, javax.vecmath.Vector3f)
float scale
javax.vecmath.Vector3f v1
public final void set (javax.vecmath.Vector3f, float)
javax.vecmath.Vector3f v1
float scale
public final void set (javax.vecmath.Matrix3f, javax.vecmath.Vector3f, float)
javax.vecmath.Matrix3f m1
javax.vecmath.Vector3f t1
float scale
public final void set (javax.vecmath.Matrix3d, javax.vecmath.Vector3d, double)
javax.vecmath.Matrix3d m1
javax.vecmath.Vector3d t1
double scale
public void setTranslation (javax.vecmath.Vector3f)
javax.vecmath.Vector3f trans
public final void rotX (float)
float angle
float c
float s
public final void rotY (float)
float angle
float c
float s
public final void rotZ (float)
float angle
float c
float s
public final void mul (float)
float scalar
public final void mul (float, javax.vecmath.Matrix4f)
float scalar
javax.vecmath.Matrix4f m1
public final void mul (javax.vecmath.Matrix4f)
javax.vecmath.Matrix4f m1
public final void mul (javax.vecmath.Matrix4f, javax.vecmath.Matrix4f)
javax.vecmath.Matrix4f m1
javax.vecmath.Matrix4f m2
public final void mulTransposeBoth (javax.vecmath.Matrix4f, javax.vecmath.Matrix4f)
javax.vecmath.Matrix4f m1
javax.vecmath.Matrix4f m2
public final void mulTransposeRight (javax.vecmath.Matrix4f, javax.vecmath.Matrix4f)
javax.vecmath.Matrix4f m1
javax.vecmath.Matrix4f m2
public final void mulTransposeLeft (javax.vecmath.Matrix4f, javax.vecmath.Matrix4f)
javax.vecmath.Matrix4f m1
javax.vecmath.Matrix4f m2
public boolean equals (javax.vecmath.Matrix4f)
javax.vecmath.Matrix4f m1
public boolean equals (java.lang.Object)
Object o1
public boolean epsilonEquals (javax.vecmath.Matrix4f, float)
javax.vecmath.Matrix4f m1
float epsilon
public int hashCode ()
public final void transform (javax.vecmath.Tuple4f, javax.vecmath.Tuple4f)
javax.vecmath.Tuple4f vec
javax.vecmath.Tuple4f vecOut
public final void transform (javax.vecmath.Tuple4f)
javax.vecmath.Tuple4f vec
public final void transform (javax.vecmath.Point3f, javax.vecmath.Point3f)
javax.vecmath.Point3f point
javax.vecmath.Point3f pointOut
public final void transform (javax.vecmath.Point3f)
javax.vecmath.Point3f point
public final void transform (javax.vecmath.Vector3f, javax.vecmath.Vector3f)
javax.vecmath.Vector3f normal
javax.vecmath.Vector3f normalOut
public final void transform (javax.vecmath.Vector3f)
javax.vecmath.Vector3f normal
public final void setRotation (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
float scale
public final void setRotation (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
float scale
public final void setRotation (javax.vecmath.Quat4f)
javax.vecmath.Quat4f q1
float scale
float tx
float ty
float tz
float w0
float w1
float w2
float w3
public final void setRotation (javax.vecmath.Quat4d)
javax.vecmath.Quat4d q1
float scale
float tx
float ty
float tz
float w0
float w1
float w2
float w3
public final void setRotation (javax.vecmath.AxisAngle4f)
javax.vecmath.AxisAngle4f a1
float scale
float tx
float ty
float tz
float w0
float w1
float w2
float w3
public final void setZero ()
public final void negate ()
public final void negate (javax.vecmath.Matrix4f)
javax.vecmath.Matrix4f m1
private void set (float, float, float, float, float, float, float, float, float, float, float, float, float, float, float, float)
float m00
float m01
float m02
float m03
float m10
float m11
float m12
float m13
float m20
float m21
float m22
float m23
float m30
float m31
float m32
float m33
private float SVD (javax.vecmath.Matrix3f, javax.vecmath.Matrix4f)
javax.vecmath.Matrix3f rot3
javax.vecmath.Matrix4f rot4
float s
float t
private float SVD (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d rot
float s
float t
private void mulRotationScale (float)
float scale
private void setRotationScale (javax.vecmath.Matrix4f)
javax.vecmath.Matrix4f m1
private void setRotationScale (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
private void setTranslation (javax.vecmath.Vector3d)
javax.vecmath.Vector3d trans
private final void getRotationScale (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
private void setFromQuat (double, double, double, double)
double x
double y
double z
double w
double n
double s
double xs
double ys
double zs
double wx
double wy
double wz
double xx
double xy
double xz
double yy
double yz
double zz
private void setFromAxisAngle (double, double, double, double)
double x
double y
double z
double angle
double n
double c
double s
double omc
double tmp1
double tmp2
}
javax/vecmath/Point2d.class
Point2d.java
package javax.vecmath
public javax.vecmath.Point2d extends javax.vecmath.Tuple2d implements java.io.Serializable {
public void <init> (double, double)
double x
double y
public void <init> (double[])
double[] p
public void <init> (javax.vecmath.Point2d)
javax.vecmath.Point2d p1
public void <init> (javax.vecmath.Point2f)
javax.vecmath.Point2f p1
public void <init> (javax.vecmath.Tuple2d)
javax.vecmath.Tuple2d t1
public void <init> (javax.vecmath.Tuple2f)
javax.vecmath.Tuple2f t1
public void <init> ()
public final double distanceSquared (javax.vecmath.Point2d)
javax.vecmath.Point2d p1
double dx
double dy
public final double distance (javax.vecmath.Point2d)
javax.vecmath.Point2d p1
public final double distanceL1 (javax.vecmath.Point2d)
javax.vecmath.Point2d p1
public final double distanceLinf (javax.vecmath.Point2d)
javax.vecmath.Point2d p1
}
javax/vecmath/Point3d.class
Point3d.java
package javax.vecmath
public javax.vecmath.Point3d extends javax.vecmath.Tuple3d implements java.io.Serializable {
public void <init> (double, double, double)
double x
double y
double z
public void <init> (double[])
double[] p
public void <init> (javax.vecmath.Point3d)
javax.vecmath.Point3d p1
public void <init> (javax.vecmath.Point3f)
javax.vecmath.Point3f p1
public void <init> (javax.vecmath.Tuple3d)
javax.vecmath.Tuple3d t1
public void <init> (javax.vecmath.Tuple3f)
javax.vecmath.Tuple3f t1
public void <init> ()
public final double distanceSquared (javax.vecmath.Point3d)
javax.vecmath.Point3d p1
double dx
double dy
double dz
public final double distance (javax.vecmath.Point3d)
javax.vecmath.Point3d p1
public final double distanceL1 (javax.vecmath.Point3d)
javax.vecmath.Point3d p1
public final double distanceLinf (javax.vecmath.Point3d)
javax.vecmath.Point3d p1
public final void project (javax.vecmath.Point4d)
javax.vecmath.Point4d p1
}
javax/vecmath/Point3f.class
Point3f.java
package javax.vecmath
public javax.vecmath.Point3f extends javax.vecmath.Tuple3f implements java.io.Serializable {
public void <init> (float, float, float)
float x
float y
float z
public void <init> (float[])
float[] p
public void <init> (javax.vecmath.Point3f)
javax.vecmath.Point3f p1
public void <init> (javax.vecmath.Point3d)
javax.vecmath.Point3d p1
public void <init> (javax.vecmath.Tuple3f)
javax.vecmath.Tuple3f t1
public void <init> (javax.vecmath.Tuple3d)
javax.vecmath.Tuple3d t1
public void <init> ()
public final float distanceSquared (javax.vecmath.Point3f)
javax.vecmath.Point3f p1
double dx
double dy
double dz
public final float distance (javax.vecmath.Point3f)
javax.vecmath.Point3f p1
public final float distanceL1 (javax.vecmath.Point3f)
javax.vecmath.Point3f p1
public final float distanceLinf (javax.vecmath.Point3f)
javax.vecmath.Point3f p1
public final void project (javax.vecmath.Point4f)
javax.vecmath.Point4f p1
}
javax/vecmath/Point3i.class
Point3i.java
package javax.vecmath
public javax.vecmath.Point3i extends javax.vecmath.Tuple3i implements java.io.Serializable {
public void <init> (int, int, int)
int x
int y
int z
public void <init> (int[])
int[] t
public void <init> (javax.vecmath.Point3i)
javax.vecmath.Point3i t1
public void <init> ()
}
javax/vecmath/Point4d.class
Point4d.java
package javax.vecmath
public javax.vecmath.Point4d extends javax.vecmath.Tuple4d implements java.io.Serializable {
public void <init> (double, double, double, double)
double x
double y
double z
double w
public void <init> (double[])
double[] p
public void <init> (javax.vecmath.Point4f)
javax.vecmath.Point4f p1
public void <init> (javax.vecmath.Point4d)
javax.vecmath.Point4d p1
public void <init> (javax.vecmath.Tuple4d)
javax.vecmath.Tuple4d t1
public void <init> (javax.vecmath.Tuple4f)
javax.vecmath.Tuple4f t1
public void <init> ()
public void <init> (javax.vecmath.Tuple3d)
javax.vecmath.Tuple3d t1
public final void set (javax.vecmath.Tuple3d)
javax.vecmath.Tuple3d t1
public final double distanceSquared (javax.vecmath.Point4d)
javax.vecmath.Point4d p1
double dx
double dy
double dz
double dw
public final double distance (javax.vecmath.Point4d)
javax.vecmath.Point4d p1
public final double distanceL1 (javax.vecmath.Point4d)
javax.vecmath.Point4d p1
public final double distanceLinf (javax.vecmath.Point4d)
javax.vecmath.Point4d p1
public final void project (javax.vecmath.Point4d)
javax.vecmath.Point4d p1
}
javax/vecmath/Point4f.class
Point4f.java
package javax.vecmath
public javax.vecmath.Point4f extends javax.vecmath.Tuple4f implements java.io.Serializable {
public void <init> (float, float, float, float)
float x
float y
float z
float w
public void <init> (float[])
float[] p
public void <init> (javax.vecmath.Point4f)
javax.vecmath.Point4f p1
public void <init> (javax.vecmath.Point4d)
javax.vecmath.Point4d p1
public void <init> (javax.vecmath.Tuple4d)
javax.vecmath.Tuple4d t1
public void <init> (javax.vecmath.Tuple4f)
javax.vecmath.Tuple4f t1
public void <init> ()
public void <init> (javax.vecmath.Tuple3f)
javax.vecmath.Tuple3f t1
public final void set (javax.vecmath.Tuple3f)
javax.vecmath.Tuple3f t1
public final float distanceSquared (javax.vecmath.Point4f)
javax.vecmath.Point4f p1
double dx
double dy
double dz
double dw
public final float distance (javax.vecmath.Point4f)
javax.vecmath.Point4f p1
public final float distanceL1 (javax.vecmath.Point4f)
javax.vecmath.Point4f p1
public final float distanceLinf (javax.vecmath.Point4f)
javax.vecmath.Point4f p1
public final void project (javax.vecmath.Point4f)
javax.vecmath.Point4f p1
}
javax/vecmath/Quat4d.class
Quat4d.java
package javax.vecmath
public javax.vecmath.Quat4d extends javax.vecmath.Tuple4d implements java.io.Serializable {
public void <init> (double, double, double, double)
double x
double y
double z
double w
public void <init> (double[])
double[] q
public void <init> (javax.vecmath.Quat4d)
javax.vecmath.Quat4d q1
public void <init> (javax.vecmath.Quat4f)
javax.vecmath.Quat4f q1
public void <init> (javax.vecmath.Tuple4d)
javax.vecmath.Tuple4d t1
public void <init> (javax.vecmath.Tuple4f)
javax.vecmath.Tuple4f t1
public void <init> ()
public final void conjugate (javax.vecmath.Quat4d)
javax.vecmath.Quat4d q1
public final void conjugate ()
public final void mul (javax.vecmath.Quat4d, javax.vecmath.Quat4d)
javax.vecmath.Quat4d q1
javax.vecmath.Quat4d q2
public final void mul (javax.vecmath.Quat4d)
javax.vecmath.Quat4d q1
public final void mulInverse (javax.vecmath.Quat4d, javax.vecmath.Quat4d)
javax.vecmath.Quat4d q1
javax.vecmath.Quat4d q2
double n
public final void mulInverse (javax.vecmath.Quat4d)
javax.vecmath.Quat4d q1
double n
private final double norm ()
public final void inverse (javax.vecmath.Quat4d)
javax.vecmath.Quat4d q1
double n
public final void inverse ()
double n
public final void normalize (javax.vecmath.Quat4d)
javax.vecmath.Quat4d q1
double n
public final void normalize ()
double n
public final void set (javax.vecmath.Matrix4f)
javax.vecmath.Matrix4f m1
public final void set (javax.vecmath.Matrix4d)
javax.vecmath.Matrix4d m1
public final void set (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public final void set (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public final void set (javax.vecmath.AxisAngle4f)
javax.vecmath.AxisAngle4f a1
double n
double s
public final void set (javax.vecmath.AxisAngle4d)
javax.vecmath.AxisAngle4d a1
double n
double s
public final void interpolate (javax.vecmath.Quat4d, double)
javax.vecmath.Quat4d q1
double alpha
double n1
double x1
double y1
double z1
double w1
double t
double sin_t
double s
public final void interpolate (javax.vecmath.Quat4d, javax.vecmath.Quat4d, double)
javax.vecmath.Quat4d q1
javax.vecmath.Quat4d q2
double alpha
private void setFromMat (double, double, double, double, double, double, double, double, double)
double m00
double m01
double m02
double m10
double m11
double m12
double m20
double m21
double m22
double s
double tr
double max
}
javax/vecmath/Quat4f.class
Quat4f.java
package javax.vecmath
public javax.vecmath.Quat4f extends javax.vecmath.Tuple4f implements java.io.Serializable {
public void <init> (float, float, float, float)
float x
float y
float z
float w
public void <init> (float[])
float[] q
public void <init> (javax.vecmath.Quat4f)
javax.vecmath.Quat4f q1
public void <init> (javax.vecmath.Quat4d)
javax.vecmath.Quat4d q1
public void <init> (javax.vecmath.Tuple4d)
javax.vecmath.Tuple4d t1
public void <init> (javax.vecmath.Tuple4f)
javax.vecmath.Tuple4f t1
public void <init> ()
public final void conjugate (javax.vecmath.Quat4f)
javax.vecmath.Quat4f q1
public final void conjugate ()
public final void mul (javax.vecmath.Quat4f, javax.vecmath.Quat4f)
javax.vecmath.Quat4f q1
javax.vecmath.Quat4f q2
public final void mul (javax.vecmath.Quat4f)
javax.vecmath.Quat4f q1
public final void mulInverse (javax.vecmath.Quat4f, javax.vecmath.Quat4f)
javax.vecmath.Quat4f q1
javax.vecmath.Quat4f q2
double n
public final void mulInverse (javax.vecmath.Quat4f)
javax.vecmath.Quat4f q1
double n
private final double norm ()
public final void inverse (javax.vecmath.Quat4f)
javax.vecmath.Quat4f q1
double n
public final void inverse ()
double n
public final void normalize (javax.vecmath.Quat4f)
javax.vecmath.Quat4f q1
double n
public final void normalize ()
float n
public final void set (javax.vecmath.Matrix4f)
javax.vecmath.Matrix4f m1
public final void set (javax.vecmath.Matrix4d)
javax.vecmath.Matrix4d m1
public final void set (javax.vecmath.Matrix3f)
javax.vecmath.Matrix3f m1
public final void set (javax.vecmath.Matrix3d)
javax.vecmath.Matrix3d m1
public final void set (javax.vecmath.AxisAngle4f)
javax.vecmath.AxisAngle4f a1
double n
float s
public final void set (javax.vecmath.AxisAngle4d)
javax.vecmath.AxisAngle4d a1
double n
float s
public final void interpolate (javax.vecmath.Quat4f, double)
javax.vecmath.Quat4f q1
double alpha
double n1
double x1
double y1
double z1
double w1
double t
double sin_t
double s
public final void interpolate (javax.vecmath.Quat4f, javax.vecmath.Quat4f, double)
javax.vecmath.Quat4f q1
javax.vecmath.Quat4f q2
double alpha
private void setFromMat (double, double, double, double, double, double, double, double, double)
double m00
double m01
double m02
double m10
double m11
double m12
double m20
double m21
double m22
double s
double tr
double max
}
javax/vecmath/SingularMatrixException.class
SingularMatrixException.java
package javax.vecmath
public javax.vecmath.SingularMatrixException extends java.lang.RuntimeException {
public void <init> ()
public void <init> (java.lang.String)
String str
}
javax/vecmath/Tuple2d.class
Tuple2d.java
package javax.vecmath
public abstract javax.vecmath.Tuple2d extends java.lang.Object implements java.io.Serializable {
public double x
public double y
public void <init> (double, double)
double x
double y
public void <init> (double[])
double[] t
public void <init> (javax.vecmath.Tuple2d)
javax.vecmath.Tuple2d t1
public void <init> (javax.vecmath.Tuple2f)
javax.vecmath.Tuple2f t1
public void <init> ()
public final void set (double, double)
double x
double y
public final void set (double[])
double[] t
public final void set (javax.vecmath.Tuple2d)
javax.vecmath.Tuple2d t1
public final void set (javax.vecmath.Tuple2f)
javax.vecmath.Tuple2f t1
public final void get (double[])
double[] t
public final void add (javax.vecmath.Tuple2d, javax.vecmath.Tuple2d)
javax.vecmath.Tuple2d t1
javax.vecmath.Tuple2d t2
public final void add (javax.vecmath.Tuple2d)
javax.vecmath.Tuple2d t1
public final void sub (javax.vecmath.Tuple2d, javax.vecmath.Tuple2d)
javax.vecmath.Tuple2d t1
javax.vecmath.Tuple2d t2
public final void sub (javax.vecmath.Tuple2d)
javax.vecmath.Tuple2d t1
public final void negate (javax.vecmath.Tuple2d)
javax.vecmath.Tuple2d t1
public final void negate ()
public final void scale (double, javax.vecmath.Tuple2d)
double s
javax.vecmath.Tuple2d t1
public final void scale (double)
double s
public final void scaleAdd (double, javax.vecmath.Tuple2d, javax.vecmath.Tuple2d)
double s
javax.vecmath.Tuple2d t1
javax.vecmath.Tuple2d t2
public final void scaleAdd (double, javax.vecmath.Tuple2d)
double s
javax.vecmath.Tuple2d t1
public int hashCode ()
long xbits
long ybits
public boolean equals (javax.vecmath.Tuple2d)
javax.vecmath.Tuple2d t1
public boolean equals (java.lang.Object)
Object o1
public boolean epsilonEquals (javax.vecmath.Tuple2d, double)
javax.vecmath.Tuple2d t1
double epsilon
public java.lang.String toString ()
public final void clamp (double, double, javax.vecmath.Tuple2d)
double min
double max
javax.vecmath.Tuple2d t
public final void clampMin (double, javax.vecmath.Tuple2d)
double min
javax.vecmath.Tuple2d t
public final void clampMax (double, javax.vecmath.Tuple2d)
double max
javax.vecmath.Tuple2d t
public final void absolute (javax.vecmath.Tuple2d)
javax.vecmath.Tuple2d t
public final void clamp (double, double)
double min
double max
public final void clampMin (double)
double min
public final void clampMax (double)
double max
public final void absolute ()
public final void interpolate (javax.vecmath.Tuple2d, javax.vecmath.Tuple2d, double)
javax.vecmath.Tuple2d t1
javax.vecmath.Tuple2d t2
double alpha
public final void interpolate (javax.vecmath.Tuple2d, double)
javax.vecmath.Tuple2d t1
double alpha
double beta
}
javax/vecmath/Tuple3d.class
Tuple3d.java
package javax.vecmath
public abstract javax.vecmath.Tuple3d extends java.lang.Object implements java.io.Serializable {
public double x
public double y
public double z
public void <init> (double, double, double)
double x
double y
double z
public void <init> (double[])
double[] t
public void <init> (javax.vecmath.Tuple3d)
javax.vecmath.Tuple3d t1
public void <init> (javax.vecmath.Tuple3f)
javax.vecmath.Tuple3f t1
public void <init> ()
public final void set (double, double, double)
double x
double y
double z
public final void set (double[])
double[] t
public final void set (javax.vecmath.Tuple3d)
javax.vecmath.Tuple3d t1
public final void set (javax.vecmath.Tuple3f)
javax.vecmath.Tuple3f t1
public final void get (double[])
double[] t
public final void get (javax.vecmath.Tuple3d)
javax.vecmath.Tuple3d t
public final void add (javax.vecmath.Tuple3d, javax.vecmath.Tuple3d)
javax.vecmath.Tuple3d t1
javax.vecmath.Tuple3d t2
public final void add (javax.vecmath.Tuple3d)
javax.vecmath.Tuple3d t1
public final void sub (javax.vecmath.Tuple3d, javax.vecmath.Tuple3d)
javax.vecmath.Tuple3d t1
javax.vecmath.Tuple3d t2
public final void sub (javax.vecmath.Tuple3d)
javax.vecmath.Tuple3d t1
public final void negate (javax.vecmath.Tuple3d)
javax.vecmath.Tuple3d t1
public final void negate ()
public final void scale (double, javax.vecmath.Tuple3d)
double s
javax.vecmath.Tuple3d t1
public final void scale (double)
double s
public final void scaleAdd (double, javax.vecmath.Tuple3d, javax.vecmath.Tuple3d)
double s
javax.vecmath.Tuple3d t1
javax.vecmath.Tuple3d t2
public final void scaleAdd (double, javax.vecmath.Tuple3d)
double s
javax.vecmath.Tuple3d t1
public int hashCode ()
long xbits
long ybits
long zbits
public boolean equals (javax.vecmath.Tuple3d)
javax.vecmath.Tuple3d t1
public boolean epsilonEquals (javax.vecmath.Tuple3d, double)
javax.vecmath.Tuple3d t1
double epsilon
public java.lang.String toString ()
public final void absolute (javax.vecmath.Tuple3d)
javax.vecmath.Tuple3d t
public final void absolute ()
public final void clamp (float, float)
float min
float max
public final void clamp (float, float, javax.vecmath.Tuple3d)
float min
float max
javax.vecmath.Tuple3d t
public final void clampMin (float)
float min
public final void clampMin (float, javax.vecmath.Tuple3d)
float min
javax.vecmath.Tuple3d t
public final void clampMax (float, javax.vecmath.Tuple3d)
float max
javax.vecmath.Tuple3d t
public final void clampMax (float)
float max
public final void clamp (double, double)
double min
double max
public final void clamp (double, double, javax.vecmath.Tuple3d)
double min
double max
javax.vecmath.Tuple3d t
public final void clampMin (double)
double min
public final void clampMin (double, javax.vecmath.Tuple3d)
double min
javax.vecmath.Tuple3d t
public final void clampMax (double, javax.vecmath.Tuple3d)
double max
javax.vecmath.Tuple3d t
public final void clampMax (double)
double max
public final void interpolate (javax.vecmath.Tuple3d, javax.vecmath.Tuple3d, float)
javax.vecmath.Tuple3d t1
javax.vecmath.Tuple3d t2
float alpha
public final void interpolate (javax.vecmath.Tuple3d, float)
javax.vecmath.Tuple3d t1
float alpha
float beta
public final void interpolate (javax.vecmath.Tuple3d, javax.vecmath.Tuple3d, double)
javax.vecmath.Tuple3d t1
javax.vecmath.Tuple3d t2
double alpha
public final void interpolate (javax.vecmath.Tuple3d, double)
javax.vecmath.Tuple3d t1
double alpha
double beta
}
javax/vecmath/Tuple3f.class
Tuple3f.java
package javax.vecmath
public abstract javax.vecmath.Tuple3f extends java.lang.Object implements java.io.Serializable {
public float x
public float y
public float z
public void <init> (float, float, float)
float x
float y
float z
public void <init> (float[])
float[] t
public void <init> (javax.vecmath.Tuple3f)
javax.vecmath.Tuple3f t1
public void <init> (javax.vecmath.Tuple3d)
javax.vecmath.Tuple3d t1
public void <init> ()
public final void set (float, float, float)
float x
float y
float z
public final void set (float[])
float[] t
public final void set (javax.vecmath.Tuple3f)
javax.vecmath.Tuple3f t1
public final void set (javax.vecmath.Tuple3d)
javax.vecmath.Tuple3d t1
public final void get (float[])
float[] t
public final void get (javax.vecmath.Tuple3f)
javax.vecmath.Tuple3f t
public final void add (javax.vecmath.Tuple3f, javax.vecmath.Tuple3f)
javax.vecmath.Tuple3f t1
javax.vecmath.Tuple3f t2
public final void add (javax.vecmath.Tuple3f)
javax.vecmath.Tuple3f t1
public final void sub (javax.vecmath.Tuple3f, javax.vecmath.Tuple3f)
javax.vecmath.Tuple3f t1
javax.vecmath.Tuple3f t2
public final void sub (javax.vecmath.Tuple3f)
javax.vecmath.Tuple3f t1
public final void negate (javax.vecmath.Tuple3f)
javax.vecmath.Tuple3f t1
public final void negate ()
public final void scale (float, javax.vecmath.Tuple3f)
float s
javax.vecmath.Tuple3f t1
public final void scale (float)
float s
public final void scaleAdd (float, javax.vecmath.Tuple3f, javax.vecmath.Tuple3f)
float s
javax.vecmath.Tuple3f t1
javax.vecmath.Tuple3f t2
public final void scaleAdd (float, javax.vecmath.Tuple3f)
float s
javax.vecmath.Tuple3f t1
public int hashCode ()
int xbits
int ybits
int zbits
public boolean equals (javax.vecmath.Tuple3f)
javax.vecmath.Tuple3f t1
public boolean epsilonEquals (javax.vecmath.Tuple3f, float)
javax.vecmath.Tuple3f t1
float epsilon
public java.lang.String toString ()
public final void clamp (float, float, javax.vecmath.Tuple3f)
float min
float max
javax.vecmath.Tuple3f t
public final void clampMin (float, javax.vecmath.Tuple3f)
float min
javax.vecmath.Tuple3f t
public final void clampMax (float, javax.vecmath.Tuple3f)
float max
javax.vecmath.Tuple3f t
public final void absolute (javax.vecmath.Tuple3f)
javax.vecmath.Tuple3f t
public final void clamp (float, float)
float min
float max
public final void clampMin (float)
float min
public final void clampMax (float)
float max
public final void absolute ()
public final void interpolate (javax.vecmath.Tuple3f, javax.vecmath.Tuple3f, float)
javax.vecmath.Tuple3f t1
javax.vecmath.Tuple3f t2
float alpha
public final void interpolate (javax.vecmath.Tuple3f, float)
javax.vecmath.Tuple3f t1
float alpha
float beta
}
javax/vecmath/Tuple3i.class
Tuple3i.java
package javax.vecmath
public abstract javax.vecmath.Tuple3i extends java.lang.Object implements java.io.Serializable {
public int x
public int y
public int z
public void <init> (int, int, int)
int x
int y
int z
public void <init> (int[])
int[] t
public void <init> (javax.vecmath.Tuple3i)
javax.vecmath.Tuple3i t1
public void <init> ()
public final void set (int, int, int)
int x
int y
int z
public final void set (int[])
int[] t
public final void set (javax.vecmath.Tuple3i)
javax.vecmath.Tuple3i t1
public final void get (int[])
int[] t
public final void get (javax.vecmath.Tuple3i)
javax.vecmath.Tuple3i t
public final void add (javax.vecmath.Tuple3i, javax.vecmath.Tuple3i)
javax.vecmath.Tuple3i t1
javax.vecmath.Tuple3i t2
public final void add (javax.vecmath.Tuple3i)
javax.vecmath.Tuple3i t1
public final void sub (javax.vecmath.Tuple3i, javax.vecmath.Tuple3i)
javax.vecmath.Tuple3i t1
javax.vecmath.Tuple3i t2
public final void sub (javax.vecmath.Tuple3i)
javax.vecmath.Tuple3i t1
public final void negate (javax.vecmath.Tuple3i)
javax.vecmath.Tuple3i t1
public final void negate ()
public final void scale (int, javax.vecmath.Tuple3i)
int s
javax.vecmath.Tuple3i t1
public final void scale (int)
int s
public final void scaleAdd (int, javax.vecmath.Tuple3i, javax.vecmath.Tuple3i)
int s
javax.vecmath.Tuple3i t1
javax.vecmath.Tuple3i t2
public final void scaleAdd (int, javax.vecmath.Tuple3i)
int s
javax.vecmath.Tuple3i t1
public int hashCode ()
private boolean equals (javax.vecmath.Tuple3i)
javax.vecmath.Tuple3i t1
public boolean equals (java.lang.Object)
Object o1
public java.lang.String toString ()
public final void clamp (int, int, javax.vecmath.Tuple3i)
int min
int max
javax.vecmath.Tuple3i t
public final void clampMin (int, javax.vecmath.Tuple3i)
int min
javax.vecmath.Tuple3i t
public final void clampMax (int, javax.vecmath.Tuple3i)
int max
javax.vecmath.Tuple3i t
public final void absolute (javax.vecmath.Tuple3i)
javax.vecmath.Tuple3i t
public final void clamp (int, int)
int min
int max
public final void clampMin (int)
int min
public final void clampMax (int)
int max
public final void absolute ()
}
javax/vecmath/Tuple4d.class
Tuple4d.java
package javax.vecmath
public abstract javax.vecmath.Tuple4d extends java.lang.Object implements java.io.Serializable {
public double x
public double y
public double z
public double w
public void <init> (double, double, double, double)
double x
double y
double z
double w
public void <init> (double[])
double[] t
public void <init> (javax.vecmath.Tuple4d)
javax.vecmath.Tuple4d t1
public void <init> (javax.vecmath.Tuple4f)
javax.vecmath.Tuple4f t1
public void <init> ()
public final void set (double, double, double, double)
double x
double y
double z
double w
public final void set (double[])
double[] t
public final void set (javax.vecmath.Tuple4d)
javax.vecmath.Tuple4d t1
public final void set (javax.vecmath.Tuple4f)
javax.vecmath.Tuple4f t1
public final void get (double[])
double[] t
public final void get (javax.vecmath.Tuple4d)
javax.vecmath.Tuple4d t
public final void add (javax.vecmath.Tuple4d, javax.vecmath.Tuple4d)
javax.vecmath.Tuple4d t1
javax.vecmath.Tuple4d t2
public final void add (javax.vecmath.Tuple4d)
javax.vecmath.Tuple4d t1
public final void sub (javax.vecmath.Tuple4d, javax.vecmath.Tuple4d)
javax.vecmath.Tuple4d t1
javax.vecmath.Tuple4d t2
public final void sub (javax.vecmath.Tuple4d)
javax.vecmath.Tuple4d t1
public final void negate (javax.vecmath.Tuple4d)
javax.vecmath.Tuple4d t1
public final void negate ()
public final void scale (double, javax.vecmath.Tuple4d)
double s
javax.vecmath.Tuple4d t1
public final void scale (double)
double s
public final void scaleAdd (double, javax.vecmath.Tuple4d, javax.vecmath.Tuple4d)
double s
javax.vecmath.Tuple4d t1
javax.vecmath.Tuple4d t2
public final void scaleAdd (double, javax.vecmath.Tuple4d)
double s
javax.vecmath.Tuple4d t1
public int hashCode ()
long xbits
long ybits
long zbits
long wbits
public boolean equals (javax.vecmath.Tuple4d)
javax.vecmath.Tuple4d t1
public boolean epsilonEquals (javax.vecmath.Tuple4d, double)
javax.vecmath.Tuple4d t1
double epsilon
public java.lang.String toString ()
public final void clamp (double, double, javax.vecmath.Tuple4d)
double min
double max
javax.vecmath.Tuple4d t
public final void clampMin (double, javax.vecmath.Tuple4d)
double min
javax.vecmath.Tuple4d t
public final void clampMax (double, javax.vecmath.Tuple4d)
double max
javax.vecmath.Tuple4d t
public final void absolute (javax.vecmath.Tuple4d)
javax.vecmath.Tuple4d t
public final void clamp (double, double)
double min
double max
public final void clampMin (double)
double min
public final void clampMax (double)
double max
public final void absolute ()
public final void interpolate (javax.vecmath.Tuple4d, javax.vecmath.Tuple4d, double)
javax.vecmath.Tuple4d t1
javax.vecmath.Tuple4d t2
double alpha
public final void interpolate (javax.vecmath.Tuple4d, double)
javax.vecmath.Tuple4d t1
double alpha
double beta
}
javax/vecmath/Tuple4f.class
Tuple4f.java
package javax.vecmath
public abstract javax.vecmath.Tuple4f extends java.lang.Object implements java.io.Serializable {
public float x
public float y
public float z
public float w
public void <init> (float, float, float, float)
float x
float y
float z
float w
public void <init> (float[])
float[] t
public void <init> (javax.vecmath.Tuple4f)
javax.vecmath.Tuple4f t1
public void <init> (javax.vecmath.Tuple4d)
javax.vecmath.Tuple4d t1
public void <init> ()
public final void set (float, float, float, float)
float x
float y
float z
float w
public final void set (float[])
float[] t
public final void set (javax.vecmath.Tuple4f)
javax.vecmath.Tuple4f t1
public final void set (javax.vecmath.Tuple4d)
javax.vecmath.Tuple4d t1
public final void get (float[])
float[] t
public final void get (javax.vecmath.Tuple4f)
javax.vecmath.Tuple4f t
public final void add (javax.vecmath.Tuple4f, javax.vecmath.Tuple4f)
javax.vecmath.Tuple4f t1
javax.vecmath.Tuple4f t2
public final void add (javax.vecmath.Tuple4f)
javax.vecmath.Tuple4f t1
public final void sub (javax.vecmath.Tuple4f, javax.vecmath.Tuple4f)
javax.vecmath.Tuple4f t1
javax.vecmath.Tuple4f t2
public final void sub (javax.vecmath.Tuple4f)
javax.vecmath.Tuple4f t1
public final void negate (javax.vecmath.Tuple4f)
javax.vecmath.Tuple4f t1
public final void negate ()
public final void scale (float, javax.vecmath.Tuple4f)
float s
javax.vecmath.Tuple4f t1
public final void scale (float)
float s
public final void scaleAdd (float, javax.vecmath.Tuple4f, javax.vecmath.Tuple4f)
float s
javax.vecmath.Tuple4f t1
javax.vecmath.Tuple4f t2
public final void scaleAdd (float, javax.vecmath.Tuple4f)
float s
javax.vecmath.Tuple4f t1
public int hashCode ()
public boolean equals (javax.vecmath.Tuple4f)
javax.vecmath.Tuple4f t1
public boolean epsilonEquals (javax.vecmath.Tuple4f, float)
javax.vecmath.Tuple4f t1
float epsilon
public java.lang.String toString ()
public final void clamp (float, float, javax.vecmath.Tuple4f)
float min
float max
javax.vecmath.Tuple4f t
public final void clampMin (float, javax.vecmath.Tuple4f)
float min
javax.vecmath.Tuple4f t
public final void clampMax (float, javax.vecmath.Tuple4f)
float max
javax.vecmath.Tuple4f t
public final void absolute (javax.vecmath.Tuple4f)
javax.vecmath.Tuple4f t
public final void clamp (float, float)
float min
float max
public final void clampMin (float)
float min
public final void clampMax (float)
float max
public final void absolute ()
public final void interpolate (javax.vecmath.Tuple4f, javax.vecmath.Tuple4f, float)
javax.vecmath.Tuple4f t1
javax.vecmath.Tuple4f t2
float alpha
public final void interpolate (javax.vecmath.Tuple4f, float)
javax.vecmath.Tuple4f t1
float alpha
float beta
}
javax/vecmath/Vector3d.class
Vector3d.java
package javax.vecmath
public javax.vecmath.Vector3d extends javax.vecmath.Tuple3d implements java.io.Serializable {
public void <init> (double, double, double)
double x
double y
double z
public void <init> (double[])
double[] v
public void <init> (javax.vecmath.Vector3f)
javax.vecmath.Vector3f v1
public void <init> (javax.vecmath.Vector3d)
javax.vecmath.Vector3d v1
public void <init> (javax.vecmath.Tuple3d)
javax.vecmath.Tuple3d t1
public void <init> (javax.vecmath.Tuple3f)
javax.vecmath.Tuple3f t1
public void <init> ()
public final void cross (javax.vecmath.Vector3d, javax.vecmath.Vector3d)
javax.vecmath.Vector3d v1
javax.vecmath.Vector3d v2
public final void normalize (javax.vecmath.Vector3d)
javax.vecmath.Vector3d v1
public final void normalize ()
double d
public final double dot (javax.vecmath.Vector3d)
javax.vecmath.Vector3d v1
public final double lengthSquared ()
public final double length ()
public final double angle (javax.vecmath.Vector3d)
javax.vecmath.Vector3d v1
double xx
double yy
double zz
double cross
}
javax/vecmath/Vector3f.class
Vector3f.java
package javax.vecmath
public javax.vecmath.Vector3f extends javax.vecmath.Tuple3f implements java.io.Serializable {
public void <init> (float, float, float)
float x
float y
float z
public void <init> (float[])
float[] v
public void <init> (javax.vecmath.Vector3f)
javax.vecmath.Vector3f v1
public void <init> (javax.vecmath.Vector3d)
javax.vecmath.Vector3d v1
public void <init> (javax.vecmath.Tuple3d)
javax.vecmath.Tuple3d t1
public void <init> (javax.vecmath.Tuple3f)
javax.vecmath.Tuple3f t1
public void <init> ()
public final float lengthSquared ()
public final float length ()
public final void cross (javax.vecmath.Vector3f, javax.vecmath.Vector3f)
javax.vecmath.Vector3f v1
javax.vecmath.Vector3f v2
public final float dot (javax.vecmath.Vector3f)
javax.vecmath.Vector3f v1
public final void normalize (javax.vecmath.Vector3f)
javax.vecmath.Vector3f v1
public final void normalize ()
double d
public final float angle (javax.vecmath.Vector3f)
javax.vecmath.Vector3f v1
double xx
double yy
double zz
double cross
}
javax/vecmath/Vector4f.class
Vector4f.java
package javax.vecmath
public javax.vecmath.Vector4f extends javax.vecmath.Tuple4f implements java.io.Serializable {
public void <init> (float, float, float, float)
float x
float y
float z
float w
public void <init> (float[])
float[] v
public void <init> (javax.vecmath.Vector4f)
javax.vecmath.Vector4f v1
public void <init> (javax.vecmath.Vector4d)
javax.vecmath.Vector4d v1
public void <init> (javax.vecmath.Tuple4d)
javax.vecmath.Tuple4d t1
public void <init> (javax.vecmath.Tuple4f)
javax.vecmath.Tuple4f t1
public void <init> ()
public void <init> (javax.vecmath.Tuple3f)
javax.vecmath.Tuple3f t1
public final void set (javax.vecmath.Tuple3f)
javax.vecmath.Tuple3f t1
public final float lengthSquared ()
public final float length ()
public final float dot (javax.vecmath.Vector4f)
javax.vecmath.Vector4f v1
public final void normalize (javax.vecmath.Vector4d)
javax.vecmath.Vector4d v1
public final void normalize ()
double d
public final float angle (javax.vecmath.Vector4f)
javax.vecmath.Vector4f v1
double d
double v1_length
double v_length
}
META-INF/INDEX.LIST