org.jmol.modelset
Class ModelSet

java.lang.Object
  extended by org.jmol.modelset.AtomCollection
      extended by org.jmol.modelset.BondCollection
          extended by org.jmol.modelset.ModelCollection
              extended by org.jmol.modelset.ModelSet
Direct Known Subclasses:
ModelLoader

public abstract class ModelSet
extends ModelCollection


Nested Class Summary
 
Nested classes/interfaces inherited from class org.jmol.modelset.ModelCollection
ModelCollection.StateScript
 
Field Summary
protected  Atom[] closest
           
private  boolean echoShapeActive
           
protected  java.lang.String modelSetTypeName
           
private  SymmetryInterface pointGroup
           
private  boolean selectionHaloEnabled
           
protected  Shape[] shapes
           
private static boolean useRasMolHbondsCalculation
           
 
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, modelSetName, moleculeCount, molecules, proteinStructureTainted, someModelsHaveAromaticBonds, someModelsHaveFractionalCoordinates, someModelsHaveSymmetry, stateScripts, structuresDefinedInFile, trajectorySteps, unitCells
 
Fields inherited from class org.jmol.modelset.BondCollection
bondCount, bonds, bsAromatic, bsPseudoHBonds, defaultCovalentMad, freeBonds, MAX_BONDS_LENGTH_TO_CACHE, MAX_NUM_TO_CACHE, numCached, showRebondTimes
 
Fields inherited from class org.jmol.modelset.AtomCollection
atomCount, atomNames, atoms, atomSerials, atomTypes, bfactor100s, bspf, clientAtomReferences, ellipsoids, g3d, haveStraightness, maxBondingRadius, occupancies, partialCharges, specialAtomIDs, surfaceDistance100s, TAINT_ATOMNAME, TAINT_ATOMTYPE, TAINT_COORD, TAINT_MAX, tainted, vibrationVectors, viewer
 
Constructor Summary
ModelSet()
           
 
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, float maxXYDistance, float minAttachedAngle)
           
 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)
           
 Point3fi 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, int iShape)
           
 boolean checkObjectHovered(int x, int y, java.util.BitSet bsVisible)
           
 void deleteAllBonds()
           
 java.util.BitSet deleteModels(java.util.BitSet bsAtoms)
           
 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.lang.String getAtomLabel(int i)
           
 java.util.BitSet getBitSetTrajectories()
           
 java.lang.String getDefinedState(java.lang.StringBuffer sfunc, boolean isAll)
           
 boolean getEchoStateActive()
           
 java.lang.Object getFileData(int modelIndex)
           
 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)
           
 boolean getShapeProperty(int shapeID, java.lang.String propertyName, java.lang.Object[] data)
           
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)
           
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 releaseShape(int shapeID)
           
 void setAtomLabel(java.lang.String strLabel, int i)
           
 void setEchoStateActive(boolean TF)
           
 void setLabel(java.lang.String strLabel, java.util.BitSet bsSelection)
           
 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, float fsize, 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, deleteModel, getAllAtomInfo, getAllBondInfo, getAllChainInfo, getAllPolymerInfo, getAltLocCountInModel, getAltLocIndexInModel, getAltLocListInModel, getAtomCountInModel, getAtomIdentityInfo, getAtomsConnected, getAtomSetCenter, getAtomsWithin, getAtomsWithin, getAuxiliaryInfo, getAverageAtomPoint, getBboxVertices, getBioPolymerCount, getBioPolymerCountInModel, getBondCountInModel, getBoundBoxCenter, getBoundBoxCommand, getBoundBoxCornerVector, getBoundBoxInfo, getBoundBoxModels, getBoxInfo, getBranchBitSet, getCellInfos, getChainCount, getChainCountInModel, getChimeInfo, getElementsPresentBitSet, getFileHeader, getFrameOffsets, getFrameTitle, getGroupCount, getGroupCountInModel, getHeteroList, getInsertionCodeIndexInModel, getInsertionCountInModel, getIterativeModels, getJmolDataFrameIndex, getJmolDataSourceFrame, getJmolFrameType, getModel, getModelAtomBitSet, getModelAuxiliaryInfo, getModelAuxiliaryInfo, getModelAuxiliaryInfoBoolean, getModelAuxiliaryInfoInt, getModelBitSet, getModelCellRange, getModelCount, getModelDipole, getModelExtract, getModelFileInfo, getModelFileName, getModelFileNumber, getModelFileType, getModelInfo, getModelInfoAsString, getModelName, getModelNumber, getModelNumberDotted, getModelNumberForAtomLabel, getModelOrientation, getModelProperties, getModelProperty, getModels, getModelSetAuxiliaryInfo, getModelSetAuxiliaryInfo, getModelSetAuxiliaryInfoBoolean, getModelSetName, getModelSetProperties, getModelSetProperty, getModelSymmetryCount, getModelTitle, getMoInfo, getMoleculeBitSet, getMoleculeBitSet, getMoleculeCountInModel, getMoleculeIndex, getMoleculeInfo, getNotionalUnitcell, getPdbAtomData, getPdbData, getPDBHeader, getPolymerLeadMidPoints, getPolymerPointsAndVectors, getProteinStructureState, getSequenceBits, getSpaceGroupInfo, getSymmetryInfo, getSymmetryInfoAsString, getTrajectoryCount, getTrajectoryIndex, getUnitCell, getUnitCellInfoText, 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, setStructureIds, setUnitCellOffset, setUnitCellOffset, sextProteinType, 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, getDefaultMadFromOrder, getOrAddBond, hBondMutually, resetAromatic, setBond
 
Methods inherited from class org.jmol.modelset.AtomCollection
calculateSurface, clearBfactorRange, deleteModelAtoms, findAtomsInRectangle, findMaxRadii, findNearestAtomIndex, getAdditionalHydrogens, getAtomAt, getAtomChain, getAtomColix, getAtomCount, getAtomicCharges, getAtomicPropertyState, getAtomicPropertyState, getAtomIndexFromAtomNumber, getAtomIndices, getAtomInfo, getAtomInfoXYZ, getAtomModelIndex, getAtomName, getAtomNames, getAtomNumber, getAtomPoint3f, getAtomRadius, getAtoms, getAtomSequenceCode, getAtomsWithin, getAtomTypes, getAtomVdwRadius, getAtomX, getAtomY, getAtomZ, getBfactor100Hi, getBfactor100Lo, getBFactors, getChainBits, getClickableSet, getElementName, getElementNumber, getElementSymbol, getEllipsoid, getHaveStraightness, getHelixData, getHybridizationAndAxes, getMaxVanderwaalsRadius, getPartialCharges, getQuaternion, getRadiusVdwJmol, getSeqcodeBits, getSurfaceDistance100, getSurfaceDistanceMax, getTaintedAtoms, getUserSettableType, getVibrationCoord, getVibrationVector, getVisibleSet, isAtomHidden, isCursorOnTopOf, isInLatticeCell, merge, modelSetHasVibrationVectors, setAtomCoord, setAtomCoordRelative, setAtomCoordRelative, setAtomData, setAtomName, setAtomType, setBFactor, setBsHidden, setEllipsoid, setFormalCharges, setHaveStraightness, setOccupancy, setPartialCharge, setTaintedAtoms, setVibrationVector, taint
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

selectionHaloEnabled

private boolean selectionHaloEnabled

echoShapeActive

private boolean echoShapeActive

modelSetTypeName

protected java.lang.String modelSetTypeName

shapes

protected Shape[] shapes

closest

protected final Atom[] closest

pointGroup

private SymmetryInterface pointGroup

useRasMolHbondsCalculation

private static final boolean useRasMolHbondsCalculation
See Also:
Constant Field Values
Constructor Detail

ModelSet

public ModelSet()
Method Detail

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

getAtomLabel

public java.lang.String getAtomLabel(int i)

getSpecModel

private java.util.BitSet getSpecModel(int modelNumber)

findNearestAtomIndex

public int findNearestAtomIndex(int x,
                                int y)

setShapeSize

public void setShapeSize(int shapeID,
                         int size,
                         float fsize,
                         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)

releaseShape

public void releaseShape(int shapeID)

getShapeProperty

public java.lang.Object getShapeProperty(int shapeID,
                                         java.lang.String propertyName,
                                         int index)

getShapeProperty

public boolean getShapeProperty(int shapeID,
                                java.lang.String propertyName,
                                java.lang.Object[] data)

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 Point3fi 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,
                               int iShape)

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,
                     float maxXYDistance,
                     float minAttachedAngle)
Overrides:
autoHbond in class ModelCollection

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

private void includeAllRelatedFrames(java.util.BitSet bsModels)

deleteModels

public java.util.BitSet deleteModels(java.util.BitSet bsAtoms)

setLabel

public void setLabel(java.lang.String strLabel,
                     java.util.BitSet bsSelection)

setAtomLabel

public void setAtomLabel(java.lang.String strLabel,
                         int i)

getFileData

public java.lang.Object getFileData(int modelIndex)