META-INF/MANIFEST.MF
META-INF/SELFSIGN.SF
META-INF/SELFSIGN.RSA
META-INF/
org/
org/jmol/
org/jmol/adapter/
org/jmol/adapter/readers/
org/jmol/adapter/readers/cifpdb/
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 
}