META-INF/
META-INF/MANIFEST.MF
org/
org/jmol/
org/jmol/adapter/
org/jmol/adapter/readers/
org/jmol/adapter/readers/more/
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
}