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 
}