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)
}