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org::jmol::modelset::ModelSet Class Reference

Inheritance diagram for org::jmol::modelset::ModelSet:
Inheritance graph
Collaboration diagram for org::jmol::modelset::ModelSet:
Collaboration graph

List of all members.

Public Member Functions

BitSet addHydrogens (List vConnections, Point3f[] pts)
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 (int modelIndex, Point3f center)
float calcRotationRadius (BitSet bs)
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)
String calculatePointGroup (BitSet bsAtoms)
void calculateStraightness ()
String calculateStructures (BitSet bsAtoms, boolean asDSSP, boolean dsspIgnoreHydrogen, boolean setStructure)
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 connect (float[][] connections)
void deleteAllBonds ()
void deleteAtoms (BitSet bs)
void deleteBonds (BitSet bsBonds, boolean isFullModel)
BitSet deleteModels (BitSet bsAtoms)
void fillAtomData (AtomData atomData, int mode)
BitSet findAtomsInRectangle (Rectangle rect, BitSet bsModels)
int findNearestAtomIndex (int x, int y, BitSet bsNot)
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 ()
void getAtomicPropertyState (StringBuffer commands, byte type, BitSet bs, String label, float[] fData)
String getAtomicPropertyState (int taintWhat, BitSet bsSelected)
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)
String getAtomLabel (int i)
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, BitSet bs, boolean withinAllModels)
BitSet getAtomsWithin (float distance, Point3f coord, BitSet bsResult, int modelIndex)
BitSet getAtomsWithin (float distance, Point4f plane)
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)
BitSet getBitSetTrajectories ()
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)
String getDefinedState (StringBuffer sfunc, boolean isAll)
boolean getEchoStateActive ()
int getElementNumber (int i)
BitSet getElementsPresentBitSet (int modelIndex)
String getElementSymbol (int i)
Object[] getEllipsoid (int i)
Object getFileData (int modelIndex)
String getFileHeader (int modelIndex)
Point3f[] getFrameOffsets (BitSet bsAtoms)
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)
Hashtable getModelAuxiliaryInfo (int modelIndex)
Object getModelAuxiliaryInfo (int modelIndex, String key)
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)
int getModelNumberIndex (int modelNumber, boolean useModelNumber, boolean doSetTrajectory)
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)
String getModelSetTypeName ()
int getModelSymmetryCount (int modelIndex)
String getModelTitle (int modelIndex)
String getMoInfo (int modelIndex)
BitSet getMoleculeBitSet (BitSet bs)
BitSet getMoleculeBitSet (int atomIndex)
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)
String getPointGroupAsString (BitSet bsAtoms, boolean asDraw, String type, int index, float scale)
Hashtable getPointGroupInfo (BitSet bsAtoms)
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)
boolean getSelectionHaloEnabled ()
BitSet getSequenceBits (String specInfo, BitSet bs)
Hashtable getSpaceGroupInfo (int modelIndex, String spaceGroup, int symOp, Point3f pt1, Point3f pt2, String drawID)
String getState (StringBuffer sfunc, boolean isAll, boolean withProteinStructure)
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)
String getTrajectoryInfo ()
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[] countPlusIndices)
boolean isTrajectory (int modelIndex)
int[] makeConnections (float minDistance, float maxDistance, int order, int connectOperation, BitSet bsA, BitSet bsB, BitSet bsBonds, boolean isBonds, float energy)
boolean modelHasVibrationVectors (int modelIndex)
boolean modelSetHasVibrationVectors ()
void recalculateLeadMidpointsAndWingVectors (int modelIndex)
void recalculatePositionDependentQuantities (BitSet bs)
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 (Tuple3f offset, BitSet bs)
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 setEchoStateActive (boolean TF)
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 setPdbConectBonding (int baseAtomIndex, int baseModelIndex, BitSet bsExclude)
void setPreserveState (boolean TF)
void setProteinType (BitSet bs, byte iType)
boolean setRotationRadius (int modelIndex, float angstroms)
void setSelectionHaloEnabled (boolean selectionHaloEnabled)
void setTaintedAtoms (BitSet bs, byte type)
void setTrajectory (int modelIndex)
void setTrajectory (BitSet bsModels)
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)
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)
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 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)
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
final Atom[] closest = new Atom[1]
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
String modelSetTypeName
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

Object calculatePointGroupForFirstModel (BitSet bsAtoms, boolean doAll, boolean asDraw, boolean asInfo, String type, int index, float scale)
BitSet getSpecModel (int modelNumber)
void includeAllRelatedFrames (BitSet bsModels)
BitSet modelsOf (BitSet bsAtoms, BitSet bsAllAtoms)

Private Attributes

boolean echoShapeActive = false
SymmetryInterface pointGroup
boolean selectionHaloEnabled = false

Detailed Description

Definition at line 70 of file ModelSet.java.

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

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