META-INF/
META-INF/MANIFEST.MF
org/
org/jmol/
org/jmol/modelsetbio/
org/jmol/shapebio/
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/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) 
}