org.jmol.modelset
public abstract class ModelSet extends ModelCollection
Field Summary | |
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protected Atom[] | closest |
boolean | echoShapeActive |
protected String | modelSetTypeName |
SymmetryInterface | pointGroup |
boolean | selectionHaloEnabled |
protected Shape[] | shapes |
static boolean | useRasMolHbondsCalculation |
Method Summary | |
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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) |
Parameters: tokType specInfo
Returns: bitset; null only if we mess up with name