Package org.jmol.modelset
Class ModelSet
java.lang.Object
org.jmol.modelset.AtomCollection
org.jmol.modelset.BondCollection
org.jmol.modelset.ModelSet
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Nested Class Summary
Nested classes/interfaces inherited from class org.jmol.modelset.AtomCollection
AtomCollection.AtomSorter
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Field Summary
FieldsModifier and TypeFieldDescriptionModel[]
protected BS
protected BS
protected final Atom[]
protected BS[]
String[]
boolean
boolean
protected boolean
int
model countint[]
String[]
protected int[]
String[]
protected String
boolean
protected boolean
protected boolean
protected boolean
P3[]
Fields inherited from class org.jmol.modelset.BondCollection
bo, BOND_GROWTH_INCREMENT, bondCount, bsAromatic, defaultCovalentMad, freeBonds, haveAtropicBonds, haveHiddenBonds, MAX_BONDS_LENGTH_TO_CACHE, MAX_NUM_TO_CACHE, moleculeCount, molecules, numCached, v1, v2
Fields inherited from class org.jmol.modelset.AtomCollection
ac, at, atomTensorList, atomTensors, bioModelset, bsClickable, bsModulated, bsPartialCharges, bspf, bsVisible, CALC_H_ALLOW_H, CALC_H_DOALL, CALC_H_HAVEH, CALC_H_IGNORE_H, CALC_H_JUSTC, CALC_H_QUICK, canSkipLoad, g3d, haveChirality, haveStraightness, maxBondingRadius, occupancies, pointGroup, preserveState, surfaceDistance100s, TAINT_ATOMNAME, TAINT_ATOMNO, TAINT_ATOMTYPE, TAINT_BONDINGRADIUS, TAINT_CHAIN, TAINT_COORD, TAINT_ELEMENT, TAINT_FORMALCHARGE, TAINT_HYDROPHOBICITY, TAINT_MAX, TAINT_OCCUPANCY, TAINT_PARTIALCHARGE, TAINT_RESNO, TAINT_SEQID, TAINT_SITE, TAINT_TEMPERATURE, TAINT_VALENCE, TAINT_VANDERWAALS, TAINT_VIBRATION, tainted, trajectory, userSettableValues, vibrations, vwr
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionaddAtom
(int modelIndex, Group group, int atomicAndIsotopeNumber, String atomName, String atomType, int atomSerial, int atomSeqID, int atomSite, P3 xyz, float radius, V3 vib, int formalCharge, float partialCharge, float occupancy, float bfactor, Lst<Object> tensors, boolean isHetero, byte specialAtomID, BS atomSymmetry, float bondRadius) addHydrogens
(Lst<Atom> vConnections, P3[] pts) these are hydrogens that are being added due to a load 2D command and are therefore not to be flagged as NEWaddStateScript
(String script1, BS bsBonds, BS bsAtoms1, BS bsAtoms2, String script2, boolean addFrameNumber, boolean postDefinitions) void
adjustAtomArrays
(int[] map, int i0, int ac) int
int
a generalized formation of HBONDS, carried out in relation to calculate HBONDS {atomsFrom} {atomsTo}.int
calcAtomsMinMax
(BS bs, BoxInfo boxInfo) void
calcBoundBoxDimensions
(BS bs, float scale) void
calcRasmolHydrogenBonds
(BS bsA, BS bsB, Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, BS bsHBonds) These are not actual hydrogen bonds.float
calcRotationRadius
(int modelIndex, P3 center, boolean useBoundBox) float
void
void
void
calculateChiralityForAtoms
(BS bsAtoms, boolean withReturn) void
calculateDssrProperty
(String dataType) calculateMolecularDipole
(int modelIndex, BS bsAtoms) calculatePointGroup
(BS bsAtoms) protected void
calculatePolymers
(Group[] groups, int groupCount, int baseGroupIndex, BS modelsExcluded) void
calculateStructures
(BS bsAtoms, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, int version) calculateStructuresAllExcept
(BS alreadyDefined, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha, int version) allows rebuilding of PDB structures; also accessed by ModelManager from Evalint
calculateStruts
(BS bs1, BS bs2) see comments in org.jmol.modelsetbio.AlphaPolymer.java Struts are calculated for atoms in bs1 connecting to atoms in bs2.void
protected void
clearDataFrameReference
(int modelIndex) void
clearDB
(int atomIndex) void
clearUnitCell
(int modelIndex) void
connect
(float[][] connections) void
createModels
(int n) void
void
deleteAtoms
(BS bs) void
deleteBonds
(BS bsBonds, boolean isFullModel) void
deleteModelBonds
(int modelIndex) deleteModels
(BS bsModels) void
fillAtomData
(AtomData atomData, int mode) int
findNearestAtomIndex
(int x, int y, BS bsNot, int min) int
getAltLocCountInModel
(int modelIndex) int
getAltLocIndexInModel
(int modelIndex, char alternateLocationID) getAltLocListInModel
(int modelIndex) protected BS
getAtomBitsMaybeDeleted
(int tokType, Object specInfo) int
getAtomCIPChiralityCode
(Atom atom) Determine the Cahn-Ingold-Prelog R/S chirality of an atomint
getAtomCountInModel
(int modelIndex) Quat[]
getAtomGroupQuaternions
(BS bsAtoms, int nMax, char qtype) float
getAtomicDSSRData
(int i) general lookup for integer type -- from EvalgetAtomSetCenter
(BS bs) getAtomsWithin
(float distance, T3 coord, BS bsResult, int modelIndex) getAtomsWithinRadius
(float distance, BS bs, boolean withinAllModels, RadiusData rd, BS bsSubset) Get atoms within a specific distance of any atom in a specific set of atoms either within all models or within just the model(s) of those atomsgetBasisAtom
(int iatom, boolean doCheck) Point3fi[]
int
getBioPolymerCountInModel
(int modelIndex) int
getBondCountInModel
(int modelIndex) for general usegetBoundBoxCenter
(int modelIndex) getBoundBoxCommand
(boolean withOptions) getBoundBoxOrientation
(int type, BS bsAtoms, P3[] points) getBoxInfo
(BS bs, float scale) BS[]
getBsBranches
(float[] dihedralList) float[]
getCellWeights
(BS bsAtoms) P3[][]
getCenterAndPoints
(Lst<Object[]> vAtomSets, boolean addCenters) int
getChainCountInModelWater
(int modelIndex, boolean countWater) getConformation
(int modelIndex, int conformationIndex, boolean doSet, BS bsSelected) getConnectingAtoms
(BS bsAtoms, BS bsFixed) getDefaultStructure
(BS bsAtoms, BS bsModified) getDefaultVdwType
(int modelIndex) int[][]
getDihedralMap
(int[] alist) boolean
getElementsPresentBitSet
(int modelIndex) getFileData
(int modelIndex) getFileHeader
(int modelIndex) long
getFrameDelayMs
(int i) P3[]
getFrameOffsets
(BS bsAtoms, boolean isFull) getFrameTitle
(int modelIndex) int
getGroupCountInModel
(int modelIndex) Group[]
In versions earlier than 12.1.51, groups[] was a field of ModelCollection.getGroupsWithin
(int nResidues, BS bs) getHeteroList
(int modelIndex) protected boolean
protected int
getInlineData
(int modelIndex) int
getInsertionCodeIndexInModel
(int modelIndex, char insertionCode) int
getInsertionCountInModel
(int modelIndex) getIterativeModels
(boolean allowJmolData) only some models can be iterated through.int
getJmolDataFrameIndex
(int modelIndex, String type) int
getJmolDataSourceFrame
(int modelIndex) getJmolFrameType
(int modelIndex) int
getLastVibrationVector
(int modelIndex, int tok) getModelAtomBitSetIncludingDeleted
(int modelIndex, boolean asCopy) Note that this method returns all atoms, included deleted ones.getModelAtomBitSetIncludingDeletedBs
(BS bsModels) note -- this method returns ALL atoms, including deleted.getModelAuxiliaryInfo
(int modelIndex) getModelBS
(BS atomList, boolean allTrajectories) Get the set of models associated with a set of atoms.int[]
getModelCellRange
(int modelIndex) getModelDataBaseName
(BS bsAtoms) getModelDipole
(int modelIndex) getModelFileName
(int modelIndex) getModelFileType
(int modelIndex) int
getModelName
(int modelIndex) int
getModelNumber
(int modelIndex) getModelNumberDotted
(int modelIndex) getModelNumberForAtomLabel
(int modelIndex) int
getModelNumberIndex
(int modelNumber, boolean useModelNumber, boolean doSetTrajectory) getModelOrientation
(int modelIndex) getModelProperty
(int modelIndex, String property) getModelSetAuxiliaryInfo
(BS bsModels) Retrieve the main modelset info Hashtable (or a new non-null Hashtable) with an up-to-date "models" key.int
getModelSymmetryCount
(int modelIndex) getModelTitle
(int modelIndex) getModulationList
(BS bs, char type, P3 t456) getMoleculeBitSet
(BS bs) return cumulative sum of all atoms in molecules containing these atomsgetMoleculeBitSetForAtom
(int atomIndex) int
getMoleculeCountInModel
(int modelIndex) int
getMoleculeIndex
(int atomIndex, boolean inModel) boolean
getMSInfoB
(String keyName) getPDBHeader
(int modelIndex) getPointGroupAsString
(BS bsAtoms, String type, int index, float scale, P3[] pts, P3 center, String id) getPointGroupInfo
(BS bsAtoms) void
getPointTransf
(int i, Atom a, Quat q, P3 pTemp) pick up the appropriate value for this atomvoid
getPolymerPointsAndVectors
(BS bs, Lst<P3[]> vList, boolean isTraceAlpha, float sheetSmoothing) getProteinStructureState
(BS bsAtoms, int mode) getSelectedAtomIterator
(BS bsSelected, boolean isGreaterOnly, boolean modelZeroBased, boolean hemisphereOnly, boolean isMultiModel) getSequenceBits
(String specInfo, BS bsAtoms, BS bsResult) M4[]
getSymMatrices
(int modelIndex) getSymmetryEquivAtoms
(BS bsAtoms, SymmetryInterface sym, BS bsModelAtoms) Return a bitset of equivalent atomsvoid
getSymmetryEquivAtomsForAtom
(int i, BS bsAtoms, BS bsCheck, BS bsEquiv) Set a bitset of the equivalent atoms of an atom.int[]
getSymmetryInvariant
(int iatom) getTranslation
(int iModel) getUnitCell
(int modelIndex) getUnitCellForAtom
(int index) getUnitCellPointsWithin
(float distance, BS bs, P3 pt, boolean asMap) protected void
growAtomArrays
(int newLength) protected void
protected void
initializeBspt
(int modelIndex) void
invertSelected
(P3 pt, P4 plane, int iAtom, BS bsAtoms) Carries out a stereochemical inversion through a point, across a plane, or at a chirality center.boolean
isAtomPDB
(int i) boolean
isBondable
(float bondingRadiusA, float bondingRadiusB, float distance2, float minBondDistance2, float bondTolerance) boolean
isJmolDataFrameForModel
(int modelIndex) boolean
isTrajectory
(int modelIndex) could be the base model or one of the subframesboolean
isTrajectoryMeasurement
(int[] countPlusIndices) boolean
isTrajectorySubFrame
(int i) int[]
makeConnections
(float minDistance, float maxDistance, int order, int connectOperation, BS bsA, BS bsB, BS bsBonds, boolean isBonds, boolean addGroup, float energy) int[]
makeConnections2
(float minD, float maxD, int order, int connectOperation, BS bsA, BS bsB, BS bsBonds, boolean isBonds, boolean addGroup, float energy, SB state) protected void
mergeModelArrays
(ModelSet mergeModelSet) initial transfer of model data from old to new model set.static int
modelFileNumberFromFloat
(float fDotM) void
morphTrajectories
(int m1, int m2, float f) void
moveAtoms
(M4 m4, M3 mNew, M3 rotation, V3 translation, BS bs, P3 center, boolean isInternal, boolean translationOnly) void
recalculateLeadMidpointsAndWingVectors
(int modelIndex) void
recalculatePolymers
(BS bsModelsExcluded) void
recalculatePositionDependentQuantities
(BS bsAtoms, M4 mat) protected void
void
void
restoreAtomPositions
(P3[] apos0) P3[]
void
saveModelOrientation
(int modelIndex, Orientation orientation) protected void
void
setAtomCoords
(BS bs, int tokType, Object xyzValues) void
setAtomCoordsRelative
(T3 offset, BS bs) void
setAtomNamesAndNumbers
(int iFirst, int baseAtomIndex, AtomCollection mergeSet, boolean isModelKit) void
setAtomProperty
(BS bs, int tok, int iValue, float fValue, String sValue, float[] values, String[] list) void
setBoundBox
(T3 pt1, T3 pt2, boolean byCorner, float scale) void
setCentroid
(BS bs, int[] minmax) deletes molecules based on: CENTROID -- molecular centroid is not in unit cell CENTROID PACKED -- all molecule atoms are not in unit cellsetConformation
(BS bsAtoms) boolean
void
setDihedrals
(float[] dihedralList, BS[] bsBranches, float f) void
setEchoStateActive
(boolean TF) void
setFrameDelayMs
(long millis, BS bsModels) void
setFrameTitle
(BS bsFrames, Object title) void
void
setIteratorForAtom
(AtomIndexIterator iterator, int modelIndex, int atomIndex, float distance, RadiusData rd) void
setIteratorForPoint
(AtomIndexIterator iterator, int modelIndex, T3 pt, float distance) void
setJmolDataFrame
(String type, int modelIndex, int modelDataIndex) setModelCage
(int modelIndex, SymmetryInterface simpleCage) This is the model-specific cage created by a UNITCELL or MODELKIT UNITCELL command.setModelCagePts
(int iModel, T3[] originABC, String name) void
setModulation
(BS bs, boolean isOn, P3 qtOffset, boolean isQ) Sets the modulation for all atoms in bs.void
setPdbConectBonding
(int baseAtomIndex, int baseModelIndex, BS bsExclude) void
setProteinType
(BS bs, STR type) boolean
setRotationRadius
(int modelIndex, float angstroms) void
setSpaceGroup
(int mi, SymmetryInterface sg, BS basis) Set up all the model-related fields in association with a new space group.void
void
setStructureList
(Map<STR, float[]> structureList) void
setTrajectory
(int modelIndex) void
setTrajectoryBs
(BS bsModels) void
translateModel
(int iModel, T3 pt) move atoms by vector pt; used for co-centering with FRAME ALIGN {atoms} TRUEvoid
updateBasisFromSite
(int imodel) Methods inherited from class org.jmol.modelset.BondCollection
addConnectedHAtoms, addHBond, allowAromaticBond, assignAromaticBondsBs, bondAtoms, bondMutually, dBb, deleteAllBonds2, deleteConnections, displayBonds, fixD, getAtomBitsMDb, getAtomsConnected, getBondColix1, getBondColix2, getBondIterator, getBondIteratorForType, getBondsForSelectedAtoms, getDefaultMadFromOrder, getOrAddBond, isInRange, releaseModelSetBC, removeUnnecessaryBonds, resetAromatic, setBond, setupBC
Methods inherited from class org.jmol.modelset.AtomCollection
addTensor, calculateHydrogens, calculateSurface, calculateVolume, chainToUpper, clearBfactorRange, clearVisibleSets, deleteModelAtoms, fillADa, findMaxRadii, findNearest2, fixFormalCharges, generateCrystalClass, getAllAtomTensors, getAtom, getAtomBitsMDa, getAtomicCharges, getAtomIdentityInfo, getAtomIndices, getAtomInfo, getAtomPointVector, getAtomsFromAtomNumberInFrame, getAtomsInFrame, getAtomsNearPlane, getAtomTensor, getAtomTensorList, getAtomTypes, getBfactor100Hi, getBfactor100Lo, getBFactors, getBondingRadii, getChainBits, getClickableSet, getElementName, getFirstAtomIndexFromAtomNumber, getHybridizationAndAxes, getHydrophobicity, getLabeler, getMaxVanderwaalsRadius, getMissingHydrogenCount, getModulation, getOccupancyFloat, getPartialCharges, getQuaternion, getRadiusVdwJmol, getSeqcodeBits, getSpecNameOrNull, getSurfaceDistanceMax, getTaintedAtoms, getUserSettableType, getVibCoord, getVibration, getVisibleSet, isAtomHidden, isDeleted, isModulated, mergeAtomArrays, modelSetHasVibrationVectors, releaseModelSetAC, scaleVectorsToMax, setAPa, setAtomCoord, setAtomCoord2, setAtomCoordRelative, setAtomData, setAtomName, setAtomNumber, setAtomsCoordRelative, setAtomTensors, setBFactor, setBondingRadius, setBsHidden, setElement, setFormalCharges, setOccupancy, setPartialCharge, setPreserveState, setSite, setTaintedAtoms, setupAC, setVibrationVector, taintAtom, taintAtoms, unTaintAtoms, validateBspf
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Field Details
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haveBioModels
public boolean haveBioModels -
bsSymmetry
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modelSetName
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am
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mc
public int mcmodel count -
unitCells
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haveUnitCells
public boolean haveUnitCells -
closest
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modelNumbers
protected int[] modelNumbers -
modelFileNumbers
public int[] modelFileNumbers -
modelNumbersForAtomLabel
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modelNames
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frameTitles
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elementsPresent
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isXYZ
protected boolean isXYZ -
modelSetProperties
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msInfo
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someModelsHaveSymmetry
protected boolean someModelsHaveSymmetry -
someModelsHaveAromaticBonds
protected boolean someModelsHaveAromaticBonds -
someModelsHaveFractionalCoordinates
protected boolean someModelsHaveFractionalCoordinates -
bboxModels
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stateScripts
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vibrationSteps
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bsAll
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sm
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proteinStructureTainted
public boolean proteinStructureTainted -
htPeaks
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modelSetTypeName
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translations
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Constructor Details
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ModelSet
- Parameters:
vwr
-name
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Method Details
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getBoxInfo
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releaseModelSet
protected void releaseModelSet() -
getEchoStateActive
public boolean getEchoStateActive() -
setEchoStateActive
public void setEchoStateActive(boolean TF) -
getModelSetTypeName
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getModelNumberIndex
public int getModelNumberIndex(int modelNumber, boolean useModelNumber, boolean doSetTrajectory) - Parameters:
modelNumber
- can be a PDB MODEL number or a simple index number, or a fffnnnnnn f.n numberuseModelNumber
-doSetTrajectory
-- Returns:
- index
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getModelDataBaseName
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setTrajectory
public void setTrajectory(int modelIndex) -
getBitSetTrajectories
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setTrajectoryBs
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morphTrajectories
public void morphTrajectories(int m1, int m2, float f) -
getTranslation
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translateModel
move atoms by vector pt; used for co-centering with FRAME ALIGN {atoms} TRUE- Parameters:
iModel
-pt
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getFrameOffsets
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getAtoms
general lookup for integer type -- from Eval- Parameters:
tokType
-specInfo
-- Returns:
- bitset; null only if we mess up with name
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findNearestAtomIndex
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calculatePointGroup
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getPointGroupInfo
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getPointGroupAsString
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getDefaultStructure
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deleteModelBonds
public void deleteModelBonds(int modelIndex) -
makeConnections
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setPdbConectBonding
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deleteAllBonds
public void deleteAllBonds() -
deleteModels
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resetMolecules
public void resetMolecules() -
setAtomProperty
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getFileData
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addHydrogens
these are hydrogens that are being added due to a load 2D command and are therefore not to be flagged as NEW- Parameters:
vConnections
-pts
-- Returns:
- BitSet of new atoms
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mergeModelArrays
initial transfer of model data from old to new model set. Note that all new models are added later, AFTER thfe old ones. This is very important, because all of the old atom numbers must map onto the same numbers in the new model set, or the state script will not run properly, among other problems.- Parameters:
mergeModelSet
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getUnitCell
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setModelCagePts
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getModelName
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getModelTitle
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getModelFileName
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getModelFileType
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setFrameTitle
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getFrameTitle
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getModelNumberForAtomLabel
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getGroups
In versions earlier than 12.1.51, groups[] was a field of ModelCollection. But this is not necessary, and it was wasting space. This method is only called when polymers are recreated.- Returns:
- full array of groups in modelSet
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setCrystallographicDefaults
public boolean setCrystallographicDefaults() -
getBoundBoxCenter
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getBoundBoxCornerVector
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getBBoxVertices
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setBoundBox
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getBoundBoxCommand
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findAtomsInRectangle
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getDefaultVdwType
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setRotationRadius
public boolean setRotationRadius(int modelIndex, float angstroms) -
calcRotationRadius
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calcBoundBoxDimensions
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getBoxInfo
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calcAtomsMinMax
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calcRotationRadiusBs
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getCenterAndPoints
- Parameters:
vAtomSets
-addCenters
-- Returns:
- array of two lists of points, centers first if desired
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getAtomSetCenter
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getAverageAtomPoint
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setAPm
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addStateScript
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getStructureList
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getInfoM
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getMSInfoB
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isTrajectory
public boolean isTrajectory(int modelIndex) could be the base model or one of the subframes- Parameters:
modelIndex
-- Returns:
- is any part of a trajectory
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isTrajectorySubFrame
public boolean isTrajectorySubFrame(int i) -
isTrajectoryMeasurement
public boolean isTrajectoryMeasurement(int[] countPlusIndices) -
getModelBS
Get the set of models associated with a set of atoms. This must allow for appended models.- Parameters:
atomList
-allTrajectories
-- Returns:
- bit set of models
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getIterativeModels
only some models can be iterated through. models for which trajectoryBaseIndexes[i] != i are trajectories only- Parameters:
allowJmolData
-- Returns:
- bitset of models
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fillAtomData
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getModelNumberDotted
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getModelNumber
public int getModelNumber(int modelIndex) -
getModelProperty
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getModelAuxiliaryInfo
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setInfo
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getInfo
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getInfoB
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getInfoI
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getInsertionCountInModel
public int getInsertionCountInModel(int modelIndex) -
modelFileNumberFromFloat
public static int modelFileNumberFromFloat(float fDotM) -
getChainCountInModelWater
public int getChainCountInModelWater(int modelIndex, boolean countWater) -
getGroupCountInModel
public int getGroupCountInModel(int modelIndex) -
calcSelectedGroupsCount
public void calcSelectedGroupsCount() -
isJmolDataFrameForModel
public boolean isJmolDataFrameForModel(int modelIndex) -
setJmolDataFrame
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getJmolDataFrameIndex
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clearDataFrameReference
protected void clearDataFrameReference(int modelIndex) -
getJmolFrameType
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getJmolDataSourceFrame
public int getJmolDataSourceFrame(int modelIndex) -
saveModelOrientation
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getModelOrientation
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getPDBHeader
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getFileHeader
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getAltLocCountInModel
public int getAltLocCountInModel(int modelIndex) -
getAltLocIndexInModel
public int getAltLocIndexInModel(int modelIndex, char alternateLocationID) -
getInsertionCodeIndexInModel
public int getInsertionCodeIndexInModel(int modelIndex, char insertionCode) -
getAltLocListInModel
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getModelSymmetryCount
public int getModelSymmetryCount(int modelIndex) -
getModelCellRange
public int[] getModelCellRange(int modelIndex) -
getLastVibrationVector
public int getLastVibrationVector(int modelIndex, int tok) -
getModulationList
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getElementsPresentBitSet
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getMoleculeIndex
public int getMoleculeIndex(int atomIndex, boolean inModel) -
getMoleculeBitSet
return cumulative sum of all atoms in molecules containing these atoms- Parameters:
bs
-- Returns:
- bitset of atoms
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getMoleculeBitSetForAtom
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getModelDipole
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calculateMolecularDipole
- Throws:
JmolAsyncException
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getMoleculeCountInModel
public int getMoleculeCountInModel(int modelIndex) -
calcSelectedMoleculesCount
public void calcSelectedMoleculesCount() -
setCentroid
deletes molecules based on: CENTROID -- molecular centroid is not in unit cell CENTROID PACKED -- all molecule atoms are not in unit cell- Parameters:
bs
-minmax
- fractional [xmin, ymin, zmin, xmax, ymax, zmax, 1=packed]
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getMolecules
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initializeBspf
protected void initializeBspf() -
initializeBspt
protected void initializeBspt(int modelIndex) -
setIteratorForPoint
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setIteratorForAtom
public void setIteratorForAtom(AtomIndexIterator iterator, int modelIndex, int atomIndex, float distance, RadiusData rd) - Parameters:
iterator
-modelIndex
-atomIndex
-distance
- if -1, then this will be set later, and here we are just running a CubeIterator, no atom-atom distances, no atom sets, no "hemisphere".rd
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getSelectedAtomIterator
public AtomIndexIterator getSelectedAtomIterator(BS bsSelected, boolean isGreaterOnly, boolean modelZeroBased, boolean hemisphereOnly, boolean isMultiModel) - Parameters:
bsSelected
-isGreaterOnly
-modelZeroBased
-hemisphereOnly
-isMultiModel
-- Returns:
- an iterator
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getBondCountInModel
public int getBondCountInModel(int modelIndex) Description copied from class:BondCollection
for general use- Overrides:
getBondCountInModel
in classBondCollection
- Parameters:
modelIndex
- the model of interest or -1 for all- Returns:
- the actual number of connections
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getAtomCountInModel
public int getAtomCountInModel(int modelIndex) -
getModelAtomBitSetIncludingDeletedBs
note -- this method returns ALL atoms, including deleted.- Parameters:
bsModels
-- Returns:
- bitset of atoms
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getModelAtomBitSetIncludingDeleted
Note that this method returns all atoms, included deleted ones. If you don't want deleted atoms, then use vwr.getModelAtomBitSetUndeleted(modelIndex, TRUE)- Parameters:
modelIndex
-asCopy
- MUST BE TRUE IF THE BITSET IS GOING TO BE MODIFIED!- Returns:
- either the actual bitset or a copy
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getAtomBitsMaybeDeleted
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getAtomsWithinRadius
public BS getAtomsWithinRadius(float distance, BS bs, boolean withinAllModels, RadiusData rd, BS bsSubset) Get atoms within a specific distance of any atom in a specific set of atoms either within all models or within just the model(s) of those atoms- Parameters:
distance
-bs
-withinAllModels
-rd
-bsSubset
- limit selection to this subset of atoms- Returns:
- the set of atoms
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getAtomsWithin
- Parameters:
distance
- negative to check all unitCell distancescoord
-bsResult
-modelIndex
-- Returns:
- bitset
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deleteBonds
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makeConnections2
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autoBondBs4
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isBondable
public boolean isBondable(float bondingRadiusA, float bondingRadiusB, float distance2, float minBondDistance2, float bondTolerance) -
autoHbond
a generalized formation of HBONDS, carried out in relation to calculate HBONDS {atomsFrom} {atomsTo}. The calculation can create pseudo-H bonds for files that do not contain H atoms.- Parameters:
bsA
- "from" set (must contain H if that is desired)bsB
- "to" setonlyIfHaveCalculated
-- Returns:
- negative number of pseudo-hbonds or number of actual hbonds formed
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setStructureIndexes
public void setStructureIndexes() -
getModelInfoAsString
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getSymmetryInfoAsString
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createModels
public void createModels(int n) -
deleteAtoms
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clearDB
public void clearDB(int atomIndex) -
adjustAtomArrays
public void adjustAtomArrays(int[] map, int i0, int ac) -
growAtomArrays
protected void growAtomArrays(int newLength) -
addAtom
public Atom addAtom(int modelIndex, Group group, int atomicAndIsotopeNumber, String atomName, String atomType, int atomSerial, int atomSeqID, int atomSite, P3 xyz, float radius, V3 vib, int formalCharge, float partialCharge, float occupancy, float bfactor, Lst<Object> tensors, boolean isHetero, byte specialAtomID, BS atomSymmetry, float bondRadius) -
getInlineData
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isAtomPDB
public boolean isAtomPDB(int i) -
setAtomNamesAndNumbers
public void setAtomNamesAndNumbers(int iFirst, int baseAtomIndex, AtomCollection mergeSet, boolean isModelKit) - Parameters:
iFirst
- 0 from ModelLoader.freeze; -1 from Viewer.assignAtombaseAtomIndex
-mergeSet
-isModelKit
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connect
public void connect(float[][] connections) -
setFrameDelayMs
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getFrameDelayMs
public long getFrameDelayMs(int i) -
getModelIndexFromId
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getModelSetAuxiliaryInfo
Retrieve the main modelset info Hashtable (or a new non-null Hashtable) with an up-to-date "models" key.- Parameters:
bsModels
-- Returns:
- Map
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getDihedralMap
public int[][] getDihedralMap(int[] alist) -
setModulation
Sets the modulation for all atoms in bs.- Parameters:
bs
-isOn
-qtOffset
- multiples of q or just t.isQ
- true if multiples of q.
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getBoundBoxOrientation
- Parameters:
type
- volume, best, x, y, z, unitcellbsAtoms
-points
- optionally use points, as from $isosurface1, ignoring bsAtoms- Returns:
- quaternion for best rotation or, for volume, string with volume \t{dx dy dz}
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getUnitCellForAtom
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clearCache
public void clearCache() -
getSymMatrices
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getSymmetryInvariant
public int[] getSymmetryInvariant(int iatom) -
getBsBranches
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recalculatePositionDependentQuantities
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moveAtoms
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setDihedrals
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setAtomCoordsRelative
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setAtomCoords
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invertSelected
Carries out a stereochemical inversion through a point, across a plane, or at a chirality center.- Parameters:
pt
- point to invert around if not nullplane
- plane to invert across if not nulliAtom
- atom to switch two groups on if >= 0bsAtoms
- atoms to switch for the atom option
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getCellWeights
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getAtomGroupQuaternions
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getConformation
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getSequenceBits
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getBioPolymerCountInModel
public int getBioPolymerCountInModel(int modelIndex) -
getPolymerPointsAndVectors
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recalculateLeadMidpointsAndWingVectors
public void recalculateLeadMidpointsAndWingVectors(int modelIndex) -
calcRasmolHydrogenBonds
public void calcRasmolHydrogenBonds(BS bsA, BS bsB, Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, BS bsHBonds) These are not actual hydrogen bonds. They are N-O bonds in proteins and nucleic acids The method is called by AminoPolymer and NucleicPolymer methods, which are indirectly called by ModelCollection.autoHbond- Parameters:
bsA
-bsB
-vHBonds
- vector of bonds to fill; if null, creates the HBondsnucleicOnly
-nMax
-dsspIgnoreHydrogens
-bsHBonds
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calculateStraightnessAll
public void calculateStraightnessAll() -
calculateStruts
see comments in org.jmol.modelsetbio.AlphaPolymer.java Struts are calculated for atoms in bs1 connecting to atoms in bs2. The two bitsets may overlap.- Parameters:
bs1
-bs2
-- Returns:
- number of struts found
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getGroupsWithin
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getProteinStructureState
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calculateStructures
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calculateStructuresAllExcept
public String calculateStructuresAllExcept(BS alreadyDefined, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha, int version) allows rebuilding of PDB structures; also accessed by ModelManager from Eval- Parameters:
alreadyDefined
- set to skip calculationasDSSP
-doReport
-dsspIgnoreHydrogen
-setStructure
-includeAlpha
-version
- TODO- Returns:
- report
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recalculatePolymers
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calculatePolymers
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calcSelectedMonomersCount
public void calcSelectedMonomersCount() -
setProteinType
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setStructureList
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setConformation
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getHeteroList
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getUnitCellPointsWithin
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calculateDssrProperty
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getAtomicDSSRData
public float getAtomicDSSRData(int i) -
getAtomCIPChiralityCode
Determine the Cahn-Ingold-Prelog R/S chirality of an atom- Parameters:
atom
-- Returns:
- [0:none, 1:R, 2:S]
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calculateChiralityForAtoms
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getPointTransf
pick up the appropriate value for this atom- Parameters:
i
-a
-q
-pTemp
-
-
getSymmetryEquivAtoms
Return a bitset of equivalent atoms- Parameters:
bsAtoms
-sym
-bsModelAtoms
-- Returns:
- bitset of equivalent atoms
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getSymmetryEquivAtomsForAtom
Set a bitset of the equivalent atoms of an atom.- Parameters:
i
-bsAtoms
- optional bitset of atoms remaining of original set of atomsbsCheck
- bitset atoms to check; if bsAtoms is not null, also cleared of found atomsbsEquiv
- bitset to return
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setSpaceGroup
Set up all the model-related fields in association with a new space group. The basis may or may not be known. Passing an empty bitset to ths method will fill it with the basis as determined by trying all the operators.- Parameters:
mi
-sg
-basis
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setModelCage
This is the model-specific cage created by a UNITCELL or MODELKIT UNITCELL command. It will be used provided it is different from the symmetry unit cell associated with a particular space group setting, if it exists.- Parameters:
modelIndex
-simpleCage
-- Returns:
- simpleCage
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getBasisAtom
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updateBasisFromSite
public void updateBasisFromSite(int imodel) -
getConnectingAtoms
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saveAtomPositions
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restoreAtomPositions
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clearUnitCell
public void clearUnitCell(int modelIndex)
-