org.jmol.modelset

Class ModelSet

public abstract class ModelSet extends ModelCollection

Field Summary
protected Atom[]closest
booleanechoShapeActive
protected StringmodelSetTypeName
SymmetryInterfacepointGroup
booleanselectionHaloEnabled
protected Shape[]shapes
static booleanuseRasMolHbondsCalculation
Method Summary
ShapeallocateShape(int shapeID)
protected voidassignAromaticBonds(boolean isUserCalculation)
intautoHbond(BitSet bsA, BitSet bsB, BitSet bsBonds)
StringcalculatePointGroup(BitSet bsAtoms)
ObjectcalculatePointGroupForFirstModel(BitSet bsAtoms, boolean doAll, boolean asDraw, boolean asInfo, String type, int index, float scale)
voidcalculateStructures(BitSet bsAtoms)
Point3fcheckObjectClicked(int x, int y, int modifiers, BitSet bsVisible)
voidcheckObjectDragged(int prevX, int prevY, int deltaX, int deltaY, int modifiers, BitSet bsVisible)
booleancheckObjectHovered(int x, int y, BitSet bsVisible)
voiddeleteAllBonds()
BitSetdeleteAtoms(BitSet bsAtoms, boolean fullModels)
voidfillAtomData(AtomData atomData, int mode)
intfindNearestAtomIndex(int x, int y)
booleanfrankClicked(int x, int y)
BitSetgetAtomBits(int tokType, Object specInfo)
general lookup for integer type -- from Eval
BitSetgetBitSetTrajectories()
StringgetDefinedState(StringBuffer sfunc, boolean isAll)
booleangetEchoStateActive()
intgetModelNumberIndex(int modelNumber, boolean useModelNumber, boolean doSetTrajectory)
StringgetModelSetTypeName()
StringgetPointGroupAsString(BitSet bsAtoms, boolean asDraw, String type, int index, float scale)
HashtablegetPointGroupInfo(BitSet bsAtoms)
booleangetSelectionHaloEnabled()
ShapegetShape(int i)
intgetShapeIdFromObjectName(String objectName)
HashtablegetShapeInfo()
ObjectgetShapeProperty(int shapeID, String propertyName, int index)
BitSetgetSpecModel(int modelNumber)
StringgetState(StringBuffer sfunc, boolean isAll)
StringgetTrajectoryInfo()
intgetVanderwaalsMar(int i)
voidincludeAllRelatedFrames(BitSet bsModels)
ShapeloadShape(int shapeID)
int[]makeConnections(float minDistance, float maxDistance, short order, int connectOperation, BitSet bsA, BitSet bsB, BitSet bsBonds, boolean isBonds)
BitSetmodelsOf(BitSet bsAtoms, BitSet bsAllAtoms)
protected voidreleaseModelSet()
voidsetEchoStateActive(boolean TF)
voidsetModelVisibility()
voidsetPdbConectBonding(int baseAtomIndex, int baseModelIndex, BitSet bsExclude)
voidsetSelectionHaloEnabled(boolean selectionHaloEnabled)
voidsetShapeProperty(int shapeID, String propertyName, Object value, BitSet bsSelected)
voidsetShapeSize(int shapeID, int size, BitSet bsSelected)
voidsetTrajectory(BitSet bsModels)
voidsetTrajectory(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)

modelsOf

private BitSet modelsOf(BitSet bsAtoms, BitSet bsAllAtoms)

releaseModelSet

protected void releaseModelSet()

setEchoStateActive

public void setEchoStateActive(boolean TF)

setModelVisibility

public void setModelVisibility()

setPdbConectBonding

public void setPdbConectBonding(int baseAtomIndex, int baseModelIndex, BitSet bsExclude)

setSelectionHaloEnabled

public void setSelectionHaloEnabled(boolean selectionHaloEnabled)

setShapeProperty

public void setShapeProperty(int shapeID, String propertyName, Object value, BitSet bsSelected)

setShapeSize

public void setShapeSize(int shapeID, int size, BitSet bsSelected)

setTrajectory

public void setTrajectory(BitSet bsModels)

setTrajectory

public void setTrajectory(int modelIndex)