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