org.jmol.modelset
Class ModelSet
java.lang.Object
org.jmol.modelset.AtomCollection
org.jmol.modelset.BondCollection
org.jmol.modelset.ModelCollection
org.jmol.modelset.ModelSet
- Direct Known Subclasses:
- ModelLoader
public abstract class ModelSet
- extends ModelCollection
Fields inherited from class org.jmol.modelset.ModelCollection |
baseGroupIndex, bsAll, bsSymmetry, elementsPresent, frameTitles, groupCount, groups, haveBioClasses, isPDB, isXYZ, jbr, modelCount, modelFileNumbers, modelNames, modelNumbers, modelNumbersForAtomLabel, models, modelSetAuxiliaryInfo, modelSetName, modelSetProperties, moleculeCount, molecules, pdbRecords, proteinStructureTainted, someModelsHaveAromaticBonds, someModelsHaveFractionalCoordinates, someModelsHaveSymmetry, stateScripts, structuresDefinedInFile, symTemp, trajectories, unitCells |
Fields inherited from class org.jmol.modelset.AtomCollection |
atomCount, atomNames, atoms, atomSerials, bfactor100s, bsEmpty, bsFoundRectangle, bspf, clientAtomReferences, ellipsoids, g3d, maxBondingRadius, occupancies, partialCharges, showRebondTimes, specialAtomIDs, surfaceDistance100s, TAINT_COORD, TAINT_MAX, tainted, vibrationVectors, viewer |
Method Summary |
private Shape |
allocateShape(int shapeID)
|
protected void |
assignAromaticBonds(boolean isUserCalculation)
|
int |
autoHbond(java.util.BitSet bsA,
java.util.BitSet bsB,
java.util.BitSet bsBonds)
|
java.lang.String |
calculatePointGroup(java.util.BitSet bsAtoms)
|
private java.lang.Object |
calculatePointGroupForFirstModel(java.util.BitSet bsAtoms,
boolean doAll,
boolean asDraw,
boolean asInfo,
java.lang.String type,
int index,
float scale)
|
void |
calculateStructures(java.util.BitSet bsAtoms)
|
javax.vecmath.Point3f |
checkObjectClicked(int x,
int y,
int modifiers,
java.util.BitSet bsVisible)
|
void |
checkObjectDragged(int prevX,
int prevY,
int x,
int y,
int modifiers,
java.util.BitSet bsVisible)
|
boolean |
checkObjectHovered(int x,
int y,
java.util.BitSet bsVisible)
|
void |
deleteAllBonds()
|
java.util.BitSet |
deleteAtoms(java.util.BitSet bsAtoms,
boolean fullModels)
|
void |
fillAtomData(AtomData atomData,
int mode)
|
int |
findNearestAtomIndex(int x,
int y)
|
boolean |
frankClicked(int x,
int y)
|
java.util.BitSet |
getAtomBits(int tokType,
java.lang.Object specInfo)
general lookup for integer type -- from Eval |
java.util.BitSet |
getBitSetTrajectories()
|
java.lang.String |
getDefinedState(java.lang.StringBuffer sfunc,
boolean isAll)
|
boolean |
getEchoStateActive()
|
int |
getModelNumberIndex(int modelNumber,
boolean useModelNumber,
boolean doSetTrajectory)
|
java.lang.String |
getModelSetTypeName()
|
java.lang.String |
getPointGroupAsString(java.util.BitSet bsAtoms,
boolean asDraw,
java.lang.String type,
int index,
float scale)
|
java.util.Hashtable |
getPointGroupInfo(java.util.BitSet bsAtoms)
|
boolean |
getSelectionHaloEnabled()
|
Shape |
getShape(int i)
|
int |
getShapeIdFromObjectName(java.lang.String objectName)
|
java.util.Hashtable |
getShapeInfo()
|
java.lang.Object |
getShapeProperty(int shapeID,
java.lang.String propertyName,
int index)
|
private java.util.BitSet |
getSpecModel(int modelNumber)
|
java.lang.String |
getState(java.lang.StringBuffer sfunc,
boolean isAll)
|
java.lang.String |
getTrajectoryInfo()
|
int |
getVanderwaalsMar(int i)
|
(package private) void |
includeAllRelatedFrames(java.util.BitSet bsModels)
|
Shape |
loadShape(int shapeID)
|
int[] |
makeConnections(float minDistance,
float maxDistance,
short order,
int connectOperation,
java.util.BitSet bsA,
java.util.BitSet bsB,
java.util.BitSet bsBonds,
boolean isBonds)
|
private java.util.BitSet |
modelsOf(java.util.BitSet bsAtoms,
java.util.BitSet bsAllAtoms)
|
protected void |
releaseModelSet()
|
void |
setEchoStateActive(boolean TF)
|
void |
setModelVisibility()
|
void |
setPdbConectBonding(int baseAtomIndex,
int baseModelIndex,
java.util.BitSet bsExclude)
|
void |
setSelectionHaloEnabled(boolean selectionHaloEnabled)
|
void |
setShapeProperty(int shapeID,
java.lang.String propertyName,
java.lang.Object value,
java.util.BitSet bsSelected)
|
void |
setShapeSize(int shapeID,
int size,
java.util.BitSet bsSelected)
|
void |
setTrajectory(java.util.BitSet bsModels)
|
void |
setTrajectory(int modelIndex)
|
Methods inherited from class org.jmol.modelset.ModelCollection |
addBioPolymerToModel, addStateScript, autoBond, calcBoundBoxDimensions, calcHydrogenBonds, calcRotationRadius, calcRotationRadius, calcSelectedGroupsCount, calcSelectedMoleculesCount, calcSelectedMonomersCount, calculateMolecularDipole, calculatePolymers, calculateStraightness, calculateStructuresAllExcept, clearCalculatedHydrogenBonds, clearDataFrameReference, defineStructure, deleteAtoms, getAllAtomInfo, getAllBondInfo, getAllChainInfo, getAllPolymerInfo, getAltLocCountInModel, getAltLocIndexInModel, getAltLocListInModel, getAtomCountInModel, getAtomIdentityInfo, getAtomRecordMOL, getAtomsConnected, getAtomSetCenter, getAtomsWithin, getAtomsWithin, getAuxiliaryInfo, getAverageAtomPoint, getBboxVertices, getBioPolymerCount, getBioPolymerCountInModel, getBondCountInModel, getBondRecordMOL, getBoundBoxCenter, getBoundBoxCommand, getBoundBoxCornerVector, getBoundBoxInfo, getBoundBoxModels, getBoxInfo, getBranchBitSet, getCellInfos, getChainCount, getChainCountInModel, getChimeInfo, getElementsPresentBitSet, getFileHeader, getFrameTitle, getGroupCount, getGroupCountInModel, getHeteroList, getInsertionCodeIndexInModel, getInsertionCountInModel, getIterativeModels, getJmolDataFrameIndex, getJmolDataSourceFrame, getJmolFrameType, getModel, getModelAtomBitSet, getModelAuxiliaryInfo, getModelAuxiliaryInfo, getModelAuxiliaryInfoBoolean, getModelAuxiliaryInfoInt, getModelCellRange, getModelCount, getModelDipole, getModelExtract, getModelFileInfo, getModelFileName, getModelFileNumber, getModelFileType, getModelInfo, getModelInfoAsString, getModelName, getModelNumber, getModelNumberDotted, getModelNumberForAtomLabel, getModelOrientation, getModelProperties, getModelProperty, getModels, getModelSetAuxiliaryInfo, getModelSetAuxiliaryInfo, getModelSetAuxiliaryInfoBoolean, getModelSetAuxiliaryInfoInt, getModelSetName, getModelSetProperties, getModelSetProperty, getModelSymmetryCount, getModelSymmetryList, getModelTitle, getMoleculeBitSet, getMoleculeBitSet, getMoleculeCountInModel, getMoleculeIndex, getMoleculeInfo, getNotionalUnitcell, getPdbAtomData, getPdbData, getPDBHeader, getPolymerLeadMidPoints, getPolymerPointsAndVectors, getProteinStructureState, getSequenceBits, getSpaceGroupInfoText, getSymmetryInfoAsString, getSymmetryInfoAsString, getSymTemp, getTrajectoryCount, getTrajectoryIndex, getUnitCell, getUnitCellInfoText, getUnitCellOffset, getWithinAtomSetIterator, getWithinModelIterator, hasCalculatedHBonds, initializeBspf, initializeBspt, invertSelected, isJmolDataFrame, isTrajectory, isTrajectory, merge, modelFileNumberFromFloat, modelHasVibrationVectors, recalculateLeadMidpointsAndWingVectors, rotateAtoms, saveModelOrientation, selectDisplayedTrajectories, setAtomCoord, setAtomCoordRelative, setAtomProperty, setBoundBox, setConformation, setConformation, setCrystallographicDefaults, setFrameTitle, setJmolDataFrame, setModelAuxiliaryInfo, setModelSetAuxiliaryInfo, setModelSetProperties, setProteinType, setRotationRadius, setUnitCellOffset, setUnitCellOffset, toCartesian, toFractional, toUnitCell |
Methods inherited from class org.jmol.modelset.BondCollection |
addHydrogenBond, assignAromaticBonds, assignAromaticBonds, bondAtoms, bondMutually, checkValencesAndBond, deleteBonds, deleteConnections, getBondAt, getBondAtom1, getBondAtom2, getBondColix1, getBondColix2, getBondCount, getBondIterator, getBondIterator, getBondModelIndex, getBondOrder, getBondOrder, getBondRadius, getBonds, getBondsForSelectedAtoms, getBondsForSelectedAtoms, getDefaultMadFromOrder, resetAromatic, setBond |
Methods inherited from class org.jmol.modelset.AtomCollection |
calculateSurface, clearBfactorRange, deleteAtoms, findAtomsInRectangle, findMaxRadii, findNearestAtomIndex, getAdditionalHydrogens, getAtomAt, getAtomChain, getAtomColix, getAtomCount, getAtomicPropertyState, getAtomicPropertyState, getAtomIndexFromAtomNumber, getAtomIndices, getAtomInfo, getAtomInfoXYZ, getAtomModelIndex, getAtomName, getAtomNames, getAtomNumber, getAtomPoint3f, getAtomRadius, getAtoms, getAtomSequenceCode, getAtomsWithin, getAtomVdwRadius, getAtomX, getAtomY, getAtomZ, getBfactor100Hi, getBfactor100Lo, getBFactors, getChainBits, getClickableSet, getElementName, getElementNumber, getElementSymbol, getEllipsoid, getHybridizationAndAxes, getMaxVanderwaalsRadius, getModelBitSet, getPartialCharges, getQuaternion, getRadiusVdwJmol, getSeqcodeBits, getSurfaceDistance100, getSurfaceDistanceMax, getTaintedAtoms, getUserSettableType, getVibrationCoord, getVibrationVector, getVisibleSet, isAtomHidden, isAtomNameMatch, isCursorOnTopOf, isInLatticeCell, loadData, merge, modelSetHasVibrationVectors, setAtomCoord, setAtomCoordRelative, setAtomCoordRelative, setBFactor, setBsHidden, setEllipsoid, setFormalCharges, setOccupancy, setPartialCharge, setTaintedAtoms, setVibrationVector, taint |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
selectionHaloEnabled
private boolean selectionHaloEnabled
echoShapeActive
private boolean echoShapeActive
modelSetTypeName
protected java.lang.String modelSetTypeName
shapes
protected final Shape[] shapes
closest
protected final Atom[] closest
pointGroup
SymmetryInterface pointGroup
useRasMolHbondsCalculation
private static final boolean useRasMolHbondsCalculation
- See Also:
- Constant Field Values
ModelSet
public ModelSet()
releaseModelSet
protected void releaseModelSet()
- Overrides:
releaseModelSet
in class ModelCollection
setSelectionHaloEnabled
public void setSelectionHaloEnabled(boolean selectionHaloEnabled)
getSelectionHaloEnabled
public boolean getSelectionHaloEnabled()
getEchoStateActive
public boolean getEchoStateActive()
setEchoStateActive
public void setEchoStateActive(boolean TF)
getModelSetTypeName
public java.lang.String getModelSetTypeName()
allocateShape
private Shape allocateShape(int shapeID)
getShape
public Shape getShape(int i)
getModelNumberIndex
public int getModelNumberIndex(int modelNumber,
boolean useModelNumber,
boolean doSetTrajectory)
getTrajectoryInfo
public java.lang.String getTrajectoryInfo()
getBitSetTrajectories
public java.util.BitSet getBitSetTrajectories()
setTrajectory
public void setTrajectory(java.util.BitSet bsModels)
setTrajectory
public void setTrajectory(int modelIndex)
getAtomBits
public java.util.BitSet getAtomBits(int tokType,
java.lang.Object specInfo)
- general lookup for integer type -- from Eval
- Overrides:
getAtomBits
in class ModelCollection
- Parameters:
tokType
- specInfo
-
- Returns:
- bitset; null only if we mess up with name
getSpecModel
private java.util.BitSet getSpecModel(int modelNumber)
findNearestAtomIndex
public int findNearestAtomIndex(int x,
int y)
setShapeSize
public void setShapeSize(int shapeID,
int size,
java.util.BitSet bsSelected)
loadShape
public Shape loadShape(int shapeID)
setShapeProperty
public void setShapeProperty(int shapeID,
java.lang.String propertyName,
java.lang.Object value,
java.util.BitSet bsSelected)
getShapeProperty
public java.lang.Object getShapeProperty(int shapeID,
java.lang.String propertyName,
int index)
getShapeIdFromObjectName
public int getShapeIdFromObjectName(java.lang.String objectName)
setModelVisibility
public void setModelVisibility()
fillAtomData
public void fillAtomData(AtomData atomData,
int mode)
- Overrides:
fillAtomData
in class AtomCollection
frankClicked
public boolean frankClicked(int x,
int y)
checkObjectHovered
public boolean checkObjectHovered(int x,
int y,
java.util.BitSet bsVisible)
checkObjectClicked
public javax.vecmath.Point3f checkObjectClicked(int x,
int y,
int modifiers,
java.util.BitSet bsVisible)
checkObjectDragged
public void checkObjectDragged(int prevX,
int prevY,
int x,
int y,
int modifiers,
java.util.BitSet bsVisible)
getShapeInfo
public java.util.Hashtable getShapeInfo()
calculateStructures
public void calculateStructures(java.util.BitSet bsAtoms)
calculatePointGroup
public java.lang.String calculatePointGroup(java.util.BitSet bsAtoms)
getPointGroupInfo
public java.util.Hashtable getPointGroupInfo(java.util.BitSet bsAtoms)
getPointGroupAsString
public java.lang.String getPointGroupAsString(java.util.BitSet bsAtoms,
boolean asDraw,
java.lang.String type,
int index,
float scale)
calculatePointGroupForFirstModel
private java.lang.Object calculatePointGroupForFirstModel(java.util.BitSet bsAtoms,
boolean doAll,
boolean asDraw,
boolean asInfo,
java.lang.String type,
int index,
float scale)
modelsOf
private java.util.BitSet modelsOf(java.util.BitSet bsAtoms,
java.util.BitSet bsAllAtoms)
autoHbond
public int autoHbond(java.util.BitSet bsA,
java.util.BitSet bsB,
java.util.BitSet bsBonds)
- Overrides:
autoHbond
in class BondCollection
assignAromaticBonds
protected void assignAromaticBonds(boolean isUserCalculation)
makeConnections
public int[] makeConnections(float minDistance,
float maxDistance,
short order,
int connectOperation,
java.util.BitSet bsA,
java.util.BitSet bsB,
java.util.BitSet bsBonds,
boolean isBonds)
- Overrides:
makeConnections
in class ModelCollection
setPdbConectBonding
public void setPdbConectBonding(int baseAtomIndex,
int baseModelIndex,
java.util.BitSet bsExclude)
deleteAllBonds
public void deleteAllBonds()
- Overrides:
deleteAllBonds
in class BondCollection
getDefinedState
public java.lang.String getDefinedState(java.lang.StringBuffer sfunc,
boolean isAll)
getState
public java.lang.String getState(java.lang.StringBuffer sfunc,
boolean isAll)
getVanderwaalsMar
public int getVanderwaalsMar(int i)
includeAllRelatedFrames
void includeAllRelatedFrames(java.util.BitSet bsModels)
deleteAtoms
public java.util.BitSet deleteAtoms(java.util.BitSet bsAtoms,
boolean fullModels)