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org::jmol::modelset::ModelCollection Class Reference

Inheritance diagram for org::jmol::modelset::ModelCollection:
Inheritance graph
Collaboration diagram for org::jmol::modelset::ModelCollection:
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List of all members.


class  StateScript

Public Member Functions

StateScript addStateScript (String script1, BitSet bsBonds, BitSet bsAtoms1, BitSet bsAtoms2, String script2, boolean addFrameNumber, boolean postDefinitions)
void appendLoadStates (StringBuffer commands)
void assignAromaticBonds ()
void assignAtom (int atomIndex, String type, boolean autoBond)
int autoBond (BitSet bsA, BitSet bsB, BitSet bsExclude, BitSet bsBonds, short mad, boolean preJmol11_9_24)
int autoHbond (BitSet bsA, BitSet bsB)
Bond bondAtoms (Atom atom1, Atom atom2, int order, short mad, BitSet bsBonds, float energy, boolean isNew)
int calcAtomsMinMax (BitSet bs, BoxInfo boxInfo)
void calcBoundBoxDimensions (BitSet bs, float scale)
void calcRasmolHydrogenBonds (BitSet bsA, BitSet bsB, List vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens)
float calcRotationRadius (BitSet bs)
float calcRotationRadius (int modelIndex, Point3f center)
void calcSelectedGroupsCount (BitSet bsSelected)
void calcSelectedMoleculesCount (BitSet bsSelected)
void calcSelectedMonomersCount (BitSet bsSelected)
Point3f[][] calculateHydrogens (BitSet bs, int[] nTotal, boolean doAll, boolean justCarbon, List vConnect)
Vector3f calculateMolecularDipole (int modelIndex)
void calculateStraightness ()
int calculateStruts (BitSet bs1, BitSet bs2)
Point3f[] calculateSurface (BitSet bsSelected, float envelopeRadius)
float calculateVolume (BitSet bs, int iType)
void clearBfactorRange ()
void clearRasmolHydrogenBonds (int baseIndex, BitSet bsAtoms)
void deleteAtoms (BitSet bs)
void deleteBonds (BitSet bsBonds, boolean isFullModel)
BitSet findAtomsInRectangle (Rectangle rect, BitSet bsModels)
List getAllAtomInfo (BitSet bs)
List getAllBondInfo (BitSet bs)
Hashtable getAllChainInfo (BitSet bs)
Hashtable getAllPolymerInfo (BitSet bs)
int getAltLocCountInModel (int modelIndex)
int getAltLocIndexInModel (int modelIndex, char alternateLocationID)
String getAltLocListInModel (int modelIndex)
BitSet getAtomBits (int tokType, Object specInfo)
String getAtomChain (int i)
short getAtomColix (int i)
int getAtomCount ()
int getAtomCountInModel (int modelIndex)
Quaternion[] getAtomGroupQuaternions (BitSet bsAtoms, int nMax, char qtype)
float[] getAtomicCharges ()
String getAtomicPropertyState (int taintWhat, BitSet bsSelected)
void getAtomicPropertyState (StringBuffer commands, byte type, BitSet bs, String label, float[] fData)
void getAtomIdentityInfo (int i, Hashtable info)
int getAtomIndexFromAtomNumber (int atomNumber, BitSet bsVisibleFrames)
int[] getAtomIndices (BitSet bs)
String getAtomInfo (int i, String format)
String getAtomInfoXYZ (int i, boolean useChimeFormat)
int getAtomModelIndex (int i)
String getAtomName (int i)
int getAtomNumber (int i)
Point3f getAtomPoint3f (int i)
List getAtomPointVector (BitSet bs)
float getAtomRadius (int i)
BitSet getAtomsConnected (float min, float max, int intType, BitSet bs)
String getAtomSequenceCode (int i)
Point3f getAtomSetCenter (BitSet bs)
BitSet getAtomsWithin (float distance, Point4f plane)
BitSet getAtomsWithin (float distance, BitSet bs, boolean withinAllModels)
BitSet getAtomsWithin (float distance, Point3f coord, BitSet bsResult, int modelIndex)
String[] getAtomTypes ()
float getAtomVdwRadius (int i, int iType)
Hashtable getAuxiliaryInfo (BitSet bsModels)
Point3f getAverageAtomPoint ()
Point3fi[] getBboxVertices ()
int getBfactor100Hi ()
int getBfactor100Lo ()
short[] getBFactors ()
int getBioPolymerCount ()
int getBioPolymerCountInModel (int modelIndex)
Bond getBondAt (int bondIndex)
Atom getBondAtom1 (int i)
Atom getBondAtom2 (int i)
short getBondColix1 (int i)
short getBondColix2 (int i)
int getBondCount ()
int getBondCountInModel (int modelIndex)
BondIterator getBondIterator (int bondType, BitSet bsSelected)
BondIterator getBondIterator (BitSet bsSelected)
int getBondModelIndex (int i)
int getBondOrder (int i)
float getBondRadius (int i)
Bond[] getBonds ()
BitSet getBondsForSelectedAtoms (BitSet bsAtoms, boolean bondSelectionModeOr)
Point3f getBoundBoxCenter (int modelIndex)
String getBoundBoxCommand (boolean withOptions)
Vector3f getBoundBoxCornerVector ()
Hashtable getBoundBoxInfo ()
BitSet getBoundBoxModels ()
BoxInfo getBoxInfo (BitSet bs, float scale)
SymmetryInterface[] getCellInfos ()
Point3f[][] getCenterAndPoints (List vAtomSets, boolean addCenters)
int getChainCount (boolean addWater)
int getChainCountInModel (int modelIndex, boolean countWater)
String getChimeInfo (int tok, BitSet bs)
BitSet getClickableSet ()
BitSet getConformation (int modelIndex, int conformationIndex, boolean doSet)
int getDefaultVdwType (int modelIndex)
int getElementNumber (int i)
BitSet getElementsPresentBitSet (int modelIndex)
String getElementSymbol (int i)
Object[] getEllipsoid (int i)
String getFileHeader (int modelIndex)
String getFrameTitle (int modelIndex)
int getGroupAtom (Atom atom, int offset, String name)
int getGroupCount ()
int getGroupCountInModel (int modelIndex)
BitSet getGroupsWithin (int nResidues, BitSet bs)
Object getHelixData (BitSet bs, int tokType)
Hashtable getHeteroList (int modelIndex)
String getHybridizationAndAxes (int atomIndex, Vector3f z, Vector3f x, String lcaoTypeRaw, boolean hybridizationCompatible, boolean doAlignZ)
String getInlineData (int modelIndex)
int getInsertionCodeIndexInModel (int modelIndex, char insertionCode)
int getInsertionCountInModel (int modelIndex)
float[] getIonicRadii ()
BitSet getIterativeModels (boolean allowJmolData)
int getJmolDataFrameIndex (int modelIndex, String type)
int getJmolDataSourceFrame (int modelIndex)
String getJmolFrameType (int modelIndex)
float getMaxVanderwaalsRadius ()
BitSet getModelAtomBitSetIncludingDeleted (BitSet bsModels)
BitSet getModelAtomBitSetIncludingDeleted (int modelIndex, boolean asCopy)
Object getModelAuxiliaryInfo (int modelIndex, String key)
Hashtable getModelAuxiliaryInfo (int modelIndex)
BitSet getModelBitSet (BitSet atomList, boolean allTrajectories)
int[] getModelCellRange (int modelIndex)
String getModelCml (BitSet bs, int atomsMax, boolean addBonds)
int getModelCount ()
Vector3f getModelDipole (int modelIndex)
String getModelExtract (BitSet bs, boolean doTransform, boolean isModelKit, boolean asSDF, boolean asV3000)
String getModelFileInfo (BitSet frames)
String getModelFileName (int modelIndex)
int getModelFileNumber (int modelIndex)
String getModelFileType (int modelIndex)
Hashtable getModelInfo (BitSet bsModels)
String getModelInfoAsString ()
BitSet getModelKitStateBitset (BitSet bs, BitSet bsDeleted)
String getModelName (int modelIndex)
int getModelNumber (int modelIndex)
String getModelNumberDotted (int modelIndex)
String getModelNumberForAtomLabel (int modelIndex)
Orientation getModelOrientation (int modelIndex)
Properties getModelProperties (int modelIndex)
String getModelProperty (int modelIndex, String property)
Model[] getModels ()
Object getModelSetAuxiliaryInfo (String keyName)
Hashtable getModelSetAuxiliaryInfo ()
String getModelSetName ()
Properties getModelSetProperties ()
String getModelSetProperty (String propertyName)
int getModelSymmetryCount (int modelIndex)
String getModelTitle (int modelIndex)
String getMoInfo (int modelIndex)
BitSet getMoleculeBitSet (int atomIndex)
BitSet getMoleculeBitSet (BitSet bs)
int getMoleculeCountInModel (int modelIndex)
int getMoleculeIndex (int atomIndex)
List getMoleculeInfo (BitSet bsAtoms)
JmolMolecule[] getMolecules ()
float[] getNotionalUnitcell ()
float[] getPartialCharges ()
String getPdbAtomData (BitSet bs, OutputStringBuffer sb)
String getPdbData (int modelIndex, String type, BitSet bsSelected, Object[] parameters, OutputStringBuffer sb)
String getPDBHeader (int modelIndex)
List getPlaneIntersection (int type, Point4f plane, float scale, int flags, int modelIndex)
Point3f[] getPolymerLeadMidPoints (int iModel, int iPolymer)
void getPolymerPointsAndVectors (BitSet bs, List vList)
String getProteinStructureState (BitSet bsAtoms, boolean taintedOnly, boolean needPhiPsi, boolean pdbFormat)
Quaternion getQuaternion (int i, char qtype)
AtomIndexIterator getSelectedAtomIterator (BitSet bsSelected, boolean isGreaterOnly, boolean modelZeroBased, boolean hemisphereOnly)
BitSet getSequenceBits (String specInfo, BitSet bs)
Hashtable getSpaceGroupInfo (int modelIndex, String spaceGroup, int symOp, Point3f pt1, Point3f pt2, String drawID)
int getSurfaceDistanceMax ()
Object getSymmetryInfo (BitSet bsAtoms, String xyz, int op, Point3f pt, Point3f pt2, String id, int type)
String getSymmetryInfoAsString ()
String getSymmetryOperation (int modelIndex, String spaceGroup, int symOp, Point3f pt1, Point3f pt2, String drawID, boolean labelOnly)
BitSet getTaintedAtoms (byte type)
int getTrajectoryIndex (int modelIndex)
SymmetryInterface getUnitCell (int modelIndex)
String getUnitCellInfoText ()
float getVibrationCoord (int atomIndex, char c)
Vector3f getVibrationVector (int atomIndex, boolean forceNew)
BitSet getVisibleSet ()
boolean hasCalculatedHBonds (BitSet bs)
boolean haveModelKit ()
void invertSelected (Point3f pt, Point4f plane, int iAtom, BitSet invAtoms, BitSet bs)
boolean isAtomAssignable (int i)
boolean isAtomHidden (int iAtom)
boolean isAtomPDB (int i)
boolean isJmolDataFrame (int modelIndex)
boolean isTrajectory (int modelIndex)
boolean isTrajectory (int[] countPlusIndices)
boolean modelHasVibrationVectors (int modelIndex)
boolean modelSetHasVibrationVectors ()
void recalculateLeadMidpointsAndWingVectors (int modelIndex)
void resetAromatic ()
void rotateAtoms (Matrix3f mNew, Matrix3f matrixRotate, BitSet bsAtoms, boolean fullMolecule, Point3f center, boolean isInternal)
void saveModelOrientation (int modelIndex, Orientation orientation)
void selectDisplayedTrajectories (BitSet bs)
void setAtomCoord (int atomIndex, float x, float y, float z)
void setAtomCoord (BitSet bs, int tokType, Object xyzValues)
void setAtomCoordRelative (int atomIndex, float x, float y, float z)
void setAtomData (int type, String name, String dataString, boolean isDefault)
void setAtomNamesAndNumbers (int iFirst, int baseAtomIndex, AtomCollection mergeSet)
void setAtomProperty (BitSet bs, int tok, int iValue, float fValue, String sValue, float[] values, String[] list)
BitSet setBondOrder (int bondIndex, char type)
void setBoundBox (Point3f pt1, Point3f pt2, boolean byCorner, float scale)
void setBsHidden (BitSet bs)
BitSet setConformation (BitSet bsAtoms)
boolean setCrystallographicDefaults ()
void setFormalCharges (BitSet bs, int formalCharge)
void setFrameTitle (BitSet bsFrames, String title)
void setHaveStraightness (boolean TF)
void setIteratorForAtom (AtomIndexIterator iterator, int modelIndex, int atomIndex, float distance)
void setIteratorForPoint (AtomIndexIterator iterator, int modelIndex, Point3f pt, float distance)
void setJmolDataFrame (String type, int modelIndex, int modelDataIndex)
void setModelAuxiliaryInfo (int modelIndex, Object key, Object value)
void setPreserveState (boolean TF)
void setProteinType (BitSet bs, byte iType)
boolean setRotationRadius (int modelIndex, float angstroms)
void setTaintedAtoms (BitSet bs, byte type)
void taint (BitSet bsAtoms, byte type)
void unTaintAtoms (BitSet bs, byte type)

Static Public Member Functions

static int getUserSettableType (String dataType)
static int modelFileNumberFromFloat (float fDotM)

Public Attributes

Atom[] atoms
Vector3f[] vibrationVectors
Viewer viewer

Static Public Attributes

final static byte TAINT_ATOMNAME = 0
final static byte TAINT_ATOMNO = 12
final static byte TAINT_ATOMTYPE = 1
final static byte TAINT_COORD = 2
final static byte TAINT_ELEMENT = 3
static final byte TAINT_FORMALCHARGE = 4
final static byte TAINT_MAX = 13

Protected Member Functions

Atom addAtom (int modelIndex, Group group, short atomicAndIsotopeNumber, String atomName, int atomSerial, int atomSite, float x, float y, float z)
Atom addAtom (int modelIndex, Group group, short atomicAndIsotopeNumber, String atomName, int atomSerial, int atomSite, float x, float y, float z, float radius, float vectorX, float vectorY, float vectorZ, int formalCharge, float partialCharge, int occupancy, float bfactor, Object[] ellipsoid, boolean isHetero, char alternateLocationID, byte specialAtomID, BitSet atomSymmetry)
void addBioPolymerToModel (Polymer polymer, Model model)
int addHBond (Atom atom1, Atom atom2, int order, float energy)
void assignAromaticBonds (boolean isUserCalculation, BitSet bsBonds)
Bond bondMutually (Atom atom, Atom atomOther, int order, short mad, float energy)
void calculatePolymers (int baseGroupIndex, BitSet alreadyDefined)
String calculateStructuresAllExcept (BitSet alreadyDefined, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha)
boolean checkValencesAndBond (Atom atomA, Atom atomB, int order, short mad, BitSet bsBonds)
void clearDataFrameReference (int modelIndex)
void deleteAllBonds ()
int[] deleteConnections (float minDistance, float maxDistance, int order, BitSet bsA, BitSet bsB, boolean isBonds, boolean matchNull, float minDistanceSquared, float maxDistanceSquared)
void deleteModel (int modelIndex, int firstAtomIndex, int nAtoms, BitSet bsAtoms, BitSet bsBonds)
void deleteModelAtoms (int firstAtomIndex, int nAtoms, BitSet bs)
void fillAtomData (AtomData atomData, int mode)
void findMaxRadii ()
void findNearestAtomIndex (int x, int y, Atom[] closest, BitSet bsNot)
short getBondOrder (float bondingRadiusA, float bondingRadiusB, float distance2, float minBondDistance2, float bondTolerance)
BitSet getChainBits (char chain)
short getDefaultMadFromOrder (int order)
boolean getHaveStraightness ()
boolean getModelAuxiliaryInfoBoolean (int modelIndex, String keyName)
int getModelAuxiliaryInfoInt (int modelIndex, String keyName)
boolean getModelSetAuxiliaryInfoBoolean (String keyName)
float getRadiusVdwJmol (Atom atom)
BitSet getSeqcodeBits (int seqcode, boolean returnEmpty)
int getTrajectoryCount ()
void growAtomArrays (int newLength)
void initializeBspf ()
void initializeBspt (int modelIndex)
boolean isTrajectorySubFrame (int i)
int[] makeConnections (float minDistance, float maxDistance, int order, int connectOperation, BitSet bsA, BitSet bsB, BitSet bsBonds, boolean isBonds, float energy)
void mergeAtomArrays (AtomCollection mergeModelSet)
void mergeModelArrays (ModelSet mergeModelSet)
void mergeModels (ModelSet mergeModelSet)
void releaseModelSet ()
void removeUnnecessaryBonds (Atom atom, boolean deleteAtom)
void setAtomCoordRelative (BitSet bs, float x, float y, float z)
void setAtomName (int atomIndex, String name)
boolean setAtomNumber (int atomIndex, int atomno)
void setAtomType (int atomIndex, String type)
boolean setBFactor (int atomIndex, float bfactor)
Bond setBond (int index, Bond bond)
void setElement (Atom atom, int atomicNumber)
void setEllipsoid (int atomIndex, Object[] ellipsoid)
boolean setIonicRadius (int atomIndex, float radius)
boolean setOccupancy (int atomIndex, int occupancy)
boolean setPartialCharge (int atomIndex, float partialCharge)
void setVibrationVector (int atomIndex, float x, float y, float z)
void taint (int atomIndex, byte type)

Protected Attributes

int bondCount
Bond[] bonds
BitSet bsAll
BitSet bsAromatic = new BitSet()
BitSet bsHBondsRasmol
Bspf bspf
BitSet bsSymmetry
short defaultCovalentMad
BitSet[] elementsPresent
Object[][] ellipsoids
String[] frameTitles = new String[1]
Bond[][][] freeBonds = new Bond[MAX_BONDS_LENGTH_TO_CACHE][][]
Graphics3D g3d
int groupCount
Group[] groups
boolean haveBioClasses = true
boolean haveStraightness
boolean isPDB
boolean isXYZ
JmolBioResolver jbr = null
float maxBondingRadius = Float.MIN_VALUE
int modelCount
int[] modelFileNumbers = new int[1]
String[] modelNames = new String[1]
int[] modelNumbers = new int[1]
String[] modelNumbersForAtomLabel = new String[1]
Model[] models = new Model[1]
Hashtable modelSetAuxiliaryInfo
String modelSetName
Properties modelSetProperties
int moleculeCount
JmolMolecule[] molecules = new JmolMolecule[4]
int[] numCached = new int[MAX_BONDS_LENGTH_TO_CACHE]
boolean preserveState = true
ShapeManager shapeManager
boolean someModelsHaveAromaticBonds
boolean someModelsHaveFractionalCoordinates
boolean someModelsHaveSymmetry
List stateScripts = new ArrayList()
int[] surfaceDistance100s
BitSet[] tainted
List trajectorySteps

Static Protected Attributes

static final int BOND_GROWTH_INCREMENT = 250
static final int MAX_BONDS_LENGTH_TO_CACHE = 5
static final int MAX_NUM_TO_CACHE = 200

Package Functions

 [instance initializer]
String getElementName (int i)
void getRasmolHydrogenBonds (Model m, BitSet bsA, BitSet bsB, List vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens)
int getSurfaceDistance100 (int atomIndex)
boolean isCursorOnTopOf (Atom contender, int x, int y, int radius, Atom champion)
void setStructureIds ()

Static Package Functions

 [static initializer]

Package Attributes

int atomCount
String[] atomNames
int[] atomSerials
String[] atomTypes
short[] bfactor100s
float[] ionicRadii
byte[] occupancies
float[] partialCharges
boolean proteinStructureTainted = false
SymmetryInterface[] unitCells

Private Member Functions

boolean addMolFile (StringBuffer mol, BitSet bsAtoms, BitSet bsBonds, boolean asV3000, Quaternion q)
int[] autoBond (int order, BitSet bsA, BitSet bsB, BitSet bsBonds, boolean isBonds, boolean matchHbond)
int autoBond_Pre_11_9_24 (BitSet bsA, BitSet bsB, BitSet bsExclude, BitSet bsBonds, short mad)
void calcUnitCellMinMax ()
void freezeModels ()
Hashtable getAtomInfoLong (int i)
void getAtomRecordMOL (StringBuffer sb, int i, Atom a, Quaternion q, Point3f pTemp, boolean asV3000)
BitSet getBasePairBits (String specInfo)
String getBasePairInfo (BitSet bs)
Hashtable getBondInfo (int i)
void getBondRecordMOL (int n, StringBuffer sb, int i, int[] atomMap, boolean asV3000)
List getChainInfo (int modelIndex, BitSet bs)
BitSet getCovalentBondsForAtoms (BitSet bsAtoms)
String getFullPDBHeader (int modelIndex)
String getInsertionListInModel (int modelIndex)
String getSymmetryInfoAsString (int modelIndex)
void getSymTemp (boolean forceNew)
boolean isInLatticeCell (int i, Point3f cell, Point3f pt, boolean isAbsolute)
boolean isJmolDataFrame (Atom atom)

Static Private Member Functions

static Point3f checkMinAttachedAngle (Atom atom1, float minAngle, Vector3f v1, Vector3f v2, boolean haveHAtoms)
static void getAtomResidueInfo (StringBuffer info, Atom atom)

Private Attributes

final Point3f averageAtomPoint = new Point3f()
BitSet bboxAtoms
BitSet bboxModels
final BoxInfo boxInfo = new BoxInfo()
boolean isBbcageDefault
final Matrix3f matInv = new Matrix3f()
final Matrix3f matTemp = new Matrix3f()
final Point3f ptTemp = new Point3f()
int selectedMoleculeCount
BitSet selectedMolecules = new BitSet()
SymmetryInterface symTemp
int thisStateModel = 0

Static Private Attributes

static float hbondMin = 2.5f
static final String[] pdbRecords = { "ATOM ", "MODEL ", "HETATM" }
static final boolean showRebondTimes = true

Detailed Description

Definition at line 70 of file ModelCollection.java.

The documentation for this class was generated from the following file:

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