org.jmol.modelset

Class ModelSet

public abstract class ModelSet extends ModelCollection

Field Summary
protected Atom[]	closest
boolean	echoShapeActive
protected String	modelSetTypeName
SymmetryInterface	pointGroup
boolean	selectionHaloEnabled
protected Shape[]	shapes
static boolean	useRasMolHbondsCalculation

Method Summary
Shape	allocateShape(int shapeID)
protected void	assignAromaticBonds(boolean isUserCalculation)
int	autoHbond(BitSet bsA, BitSet bsB, BitSet bsBonds)
String	calculatePointGroup(BitSet bsAtoms)
Object	calculatePointGroupForFirstModel(BitSet bsAtoms, boolean doAll, boolean asDraw, boolean asInfo, String type, int index, float scale)
void	calculateStructures(BitSet bsAtoms)
Point3f	checkObjectClicked(int x, int y, int modifiers, BitSet bsVisible)
void	checkObjectDragged(int prevX, int prevY, int deltaX, int deltaY, int modifiers, BitSet bsVisible)
boolean	checkObjectHovered(int x, int y, BitSet bsVisible)
void	deleteAllBonds()
BitSet	deleteAtoms(BitSet bsAtoms, boolean fullModels)
void	fillAtomData(AtomData atomData, int mode)
int	findNearestAtomIndex(int x, int y)
boolean	frankClicked(int x, int y)
BitSet	getAtomBits(int tokType, Object specInfo) general lookup for integer type -- from Eval
BitSet	getBitSetTrajectories()
String	getDefinedState(StringBuffer sfunc, boolean isAll)
boolean	getEchoStateActive()
int	getModelNumberIndex(int modelNumber, boolean useModelNumber, boolean doSetTrajectory)
String	getModelSetTypeName()
String	getPointGroupAsString(BitSet bsAtoms, boolean asDraw, String type, int index, float scale)
Hashtable	getPointGroupInfo(BitSet bsAtoms)
boolean	getSelectionHaloEnabled()
Shape	getShape(int i)
int	getShapeIdFromObjectName(String objectName)
Hashtable	getShapeInfo()
Object	getShapeProperty(int shapeID, String propertyName, int index)
BitSet	getSpecModel(int modelNumber)
String	getState(StringBuffer sfunc, boolean isAll)
String	getTrajectoryInfo()
int	getVanderwaalsMar(int i)
void	includeAllRelatedFrames(BitSet bsModels)
Shape	loadShape(int shapeID)
int[]	makeConnections(float minDistance, float maxDistance, short order, int connectOperation, BitSet bsA, BitSet bsB, BitSet bsBonds, boolean isBonds)
BitSet	modelsOf(BitSet bsAtoms, BitSet bsAllAtoms)
protected void	releaseModelSet()
void	setEchoStateActive(boolean TF)
void	setModelVisibility()
void	setPdbConectBonding(int baseAtomIndex, int baseModelIndex, BitSet bsExclude)
void	setSelectionHaloEnabled(boolean selectionHaloEnabled)
void	setShapeProperty(int shapeID, String propertyName, Object value, BitSet bsSelected)
void	setShapeSize(int shapeID, int size, BitSet bsSelected)
void	setTrajectory(BitSet bsModels)
void	setTrajectory(int modelIndex)

Field Detail

closest

protected final Atom[] closest

echoShapeActive

private boolean echoShapeActive

modelSetTypeName

protected String modelSetTypeName

pointGroup

SymmetryInterface pointGroup

selectionHaloEnabled

private boolean selectionHaloEnabled

shapes

protected final Shape[] shapes

useRasMolHbondsCalculation

private static final boolean useRasMolHbondsCalculation

Method Detail

allocateShape

private Shape allocateShape(int shapeID)

assignAromaticBonds

protected void assignAromaticBonds(boolean isUserCalculation)

autoHbond

public int autoHbond(BitSet bsA, BitSet bsB, BitSet bsBonds)

calculatePointGroup

public String calculatePointGroup(BitSet bsAtoms)

calculatePointGroupForFirstModel

private Object calculatePointGroupForFirstModel(BitSet bsAtoms, boolean doAll, boolean asDraw, boolean asInfo, String type, int index, float scale)

calculateStructures

public void calculateStructures(BitSet bsAtoms)

checkObjectClicked

public Point3f checkObjectClicked(int x, int y, int modifiers, BitSet bsVisible)

checkObjectDragged

public void checkObjectDragged(int prevX, int prevY, int deltaX, int deltaY, int modifiers, BitSet bsVisible)

checkObjectHovered

public boolean checkObjectHovered(int x, int y, BitSet bsVisible)

deleteAllBonds

public void deleteAllBonds()

deleteAtoms

public BitSet deleteAtoms(BitSet bsAtoms, boolean fullModels)

fillAtomData

public void fillAtomData(AtomData atomData, int mode)

findNearestAtomIndex

public int findNearestAtomIndex(int x, int y)

frankClicked

public boolean frankClicked(int x, int y)

getAtomBits

public BitSet getAtomBits(int tokType, Object specInfo)

general lookup for integer type -- from Eval

Parameters: tokType specInfo

Returns: bitset; null only if we mess up with name

getBitSetTrajectories

public BitSet getBitSetTrajectories()

getDefinedState

public String getDefinedState(StringBuffer sfunc, boolean isAll)

getEchoStateActive

public boolean getEchoStateActive()

getModelNumberIndex

public int getModelNumberIndex(int modelNumber, boolean useModelNumber, boolean doSetTrajectory)

getModelSetTypeName

public String getModelSetTypeName()

getPointGroupAsString

public String getPointGroupAsString(BitSet bsAtoms, boolean asDraw, String type, int index, float scale)

getPointGroupInfo

public Hashtable getPointGroupInfo(BitSet bsAtoms)

getSelectionHaloEnabled

public boolean getSelectionHaloEnabled()

getShape

public Shape getShape(int i)

getShapeIdFromObjectName

public int getShapeIdFromObjectName(String objectName)

getShapeInfo

public Hashtable getShapeInfo()

getShapeProperty

public Object getShapeProperty(int shapeID, String propertyName, int index)

getSpecModel

private BitSet getSpecModel(int modelNumber)

getState

public String getState(StringBuffer sfunc, boolean isAll)

getTrajectoryInfo

public String getTrajectoryInfo()

getVanderwaalsMar

public int getVanderwaalsMar(int i)

includeAllRelatedFrames

void includeAllRelatedFrames(BitSet bsModels)

loadShape

public Shape loadShape(int shapeID)

makeConnections

public int[] makeConnections(float minDistance, float maxDistance, short order, int connectOperation, BitSet bsA, BitSet bsB, BitSet bsBonds, boolean isBonds)