Class ModelSet

Method Details

• getBoxInfo

  public BoxInfo getBoxInfo()

• releaseModelSet

  protected void releaseModelSet()

• getEchoStateActive

  public boolean getEchoStateActive()

• setEchoStateActive

  public void setEchoStateActive(boolean TF)

• getModelSetTypeName

  public String getModelSetTypeName()

• 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 number

  useModelNumber -

  doSetTrajectory -

  Returns:

  index

• getModelDataBaseName

  public String getModelDataBaseName(BS bsAtoms)

• setTrajectory

  public void setTrajectory(int modelIndex)

• getBitSetTrajectories

  public BS getBitSetTrajectories()

• setTrajectoryBs

  public void setTrajectoryBs(BS bsModels)

• morphTrajectories

  public void morphTrajectories(int m1, int m2, float f)

• getTranslation

  public P3 getTranslation(int iModel)

• translateModel

  public void translateModel(int iModel, T3 pt)

  move atoms by vector pt; used for co-centering with FRAME ALIGN {atoms} TRUE

  Parameters:

  iModel -

  pt -

• getFrameOffsets

  public P3[] getFrameOffsets(BS bsAtoms, boolean isFull)

• getAtoms

  public BS getAtoms(int tokType, Object specInfo)

  general lookup for integer type -- from Eval

  Parameters:

  tokType -

  specInfo -

  Returns:

  bitset; null only if we mess up with name

• findNearestAtomIndex

  public int findNearestAtomIndex(int x, int y, BS bsNot, int min)

• calculatePointGroup

  public String calculatePointGroup(BS bsAtoms, P3 center)

  ////// atom and shape selecting /////////

• getPointGroupInfo

  public Map<String,Object> getPointGroupInfo(BS bsAtoms, String type)

• getPointGroupAsString

  public String getPointGroupAsString(BS bsAtoms, String type, int index, float scale, P3[] pts, P3 center, String id)

• getDefaultStructure

  public String getDefaultStructure(BS bsAtoms, BS bsModified)

• deleteModelBonds

  public void deleteModelBonds(int modelIndex)

• makeConnections

  public int[] makeConnections(float minDistance, float maxDistance, int order, int connectOperation, BS bsA, BS bsB, BS bsBonds, boolean isBonds, boolean addGroup, float energy)

  // super-overloaded methods ///////

• setPdbConectBonding

  public void setPdbConectBonding(int baseAtomIndex, int baseModelIndex, BS bsExclude)

• deleteAllBonds

  public void deleteAllBonds()

• includeAllRelatedFrames

  public void includeAllRelatedFrames(BS bsModels, boolean includeOriginatingModels)

• deleteModels

  public BS deleteModels(BS bsModels)

• resetMolecules

  public void resetMolecules()

• setAtomProperty

  public void setAtomProperty(BS bs, int tok, int iValue, float fValue, String sValue, float[] values, String[] list)

• getFileData

  public Object getFileData(int modelIndex)

• addHydrogens

  public BS 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 NEW

  Parameters:

  vConnections -

  pts -

  Returns:

  BitSet of new atoms

• mergeModelArrays

  protected void mergeModelArrays(ModelSet mergeModelSet)

  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 -

• getUnitCell

  public SymmetryInterface getUnitCell(int modelIndex)

  Parameters:

  modelIndex - Integer.MIN_VALUE requests a return of the cage, without symmetry

  Returns:

  Symmetry

• setModelCagePts

  public SymmetryInterface setModelCagePts(int iModel, T3[] originABC, String name)

• getModelName

  public String getModelName(int modelIndex)

• getModelTitle

  public String getModelTitle(int modelIndex)

• getModelFileName

  public String getModelFileName(int modelIndex)

• getModelFileType

  public String getModelFileType(int modelIndex)

• setFrameTitle

  public void setFrameTitle(BS bsFrames, Object title)

• getFrameTitle

  public String getFrameTitle(int modelIndex)

• getModelNumberForAtomLabel

  public String getModelNumberForAtomLabel(int modelIndex)

• getGroups

  public Group[] 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

• setCrystallographicDefaults

  public boolean setCrystallographicDefaults()

• getBoundBoxCenter

  public P3 getBoundBoxCenter(int modelIndex)

• getBoundBoxCornerVector

  public V3 getBoundBoxCornerVector()

• getBBoxVertices

  public Point3fi[] getBBoxVertices()

• setBoundBox

  public void setBoundBox(T3 pt1, T3 pt2, boolean byCorner, float scale)

• getBoundBoxCommand

  public String getBoundBoxCommand(boolean withOptions)

• findAtomsInRectangle

  public BS findAtomsInRectangle(Rectangle rect)

• getDefaultVdwType

  public VDW getDefaultVdwType(int modelIndex)

• setRotationRadius

  public boolean setRotationRadius(int modelIndex, float angstroms)

• calcRotationRadius

  public float calcRotationRadius(int modelIndex, P3 center, boolean useBoundBox)

• calcBoundBoxDimensions

  public void calcBoundBoxDimensions(BS bs, float scale)

• getBoxInfo

  public BoxInfo getBoxInfo(BS bs, float scale)

• calcAtomsMinMax

  public int calcAtomsMinMax(BS bs, BoxInfo boxInfo)

• calcRotationRadiusBs

  public float calcRotationRadiusBs(BS bs)

• getCenterAndPoints

  public P3[][] getCenterAndPoints(Lst<Object[]> vAtomSets, boolean addCenters)

  Parameters:

  vAtomSets -

  addCenters -

  Returns:

  array of two lists of points, centers first if desired

• getAtomSetCenter

  public P3 getAtomSetCenter(BS bs)

• getAverageAtomPoint

  public P3 getAverageAtomPoint()

• setAPm

  protected void setAPm(BS bs, int tok, int iValue, float fValue, String sValue, float[] values, String[] list)

• addStateScript

  public StateScript addStateScript(String script1, BS bsBonds, BS bsAtoms1, BS bsAtoms2, String script2, boolean addFrameNumber, boolean postDefinitions)

• getStructureList

  public Map<STR,float[]> getStructureList()

• getInfoM

  public Object getInfoM(String keyName)

• getMSInfoB

  public boolean getMSInfoB(String keyName)

• 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

• isTrajectorySubFrame

  public boolean isTrajectorySubFrame(int i)

• isTrajectoryMeasurement

  public boolean isTrajectoryMeasurement(int[] countPlusIndices)

• getModelBS

  public BS getModelBS(BS atomList, boolean allTrajectories)

  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

• getIterativeModels

  public BS getIterativeModels(boolean allowJmolData)

  only some models can be iterated through. models for which trajectoryBaseIndexes[i] != i are trajectories only

  Parameters:

  allowJmolData -

  Returns:

  bitset of models

• fillAtomData

  public void fillAtomData(AtomData atomData, int mode)

• getModelNumberDotted

  public String getModelNumberDotted(int modelIndex)

• getModelNumber

  public int getModelNumber(int modelIndex)

• getModelProperty

  public String getModelProperty(int modelIndex, String property)

• getModelAuxiliaryInfo

  public Map<String,Object> getModelAuxiliaryInfo(int modelIndex)

• setInfo

  public void setInfo(int modelIndex, Object key, Object value)

• getInfo

  public Object getInfo(int modelIndex, String key)

• getInfoB

  protected boolean getInfoB(int modelIndex, String keyName)

• getInfoI

  protected int getInfoI(int modelIndex, String keyName)

• 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()

• isJmolDataFrame

  public boolean isJmolDataFrame(int modelIndex)

• getJmolDataFrameIndex

  public int getJmolDataFrameIndex(int modelIndex, String type)

• getJmolDataFrameInt

  public int getJmolDataFrameInt(int modelIndex, int type)

  Parameters:

  modelIndex -

  type - T.spin, T.ramachandran, T.data, what else?

  Returns:

  modelIndex for the frame or -1

• clearDataFrameReference

  protected void clearDataFrameReference(int modelIndex)

• getJmolFrameType

  public String getJmolFrameType(int modelIndex)

• getJmolFrameTypeInt

  public int getJmolFrameTypeInt(int modelIndex)

• getJmolDataSourceFrame

  public int getJmolDataSourceFrame(int modelIndex)

• saveModelOrientation

  public void saveModelOrientation(int modelIndex, Orientation orientation)

• getModelOrientation

  public Orientation getModelOrientation(int modelIndex)

• getPDBHeader

  public String getPDBHeader(int modelIndex)

• getFileHeader

  public String getFileHeader(int modelIndex)

• getAltLocCountInModel

  public int getAltLocCountInModel(int modelIndex)

  /////////// individual models ////////////////

• getAltLocIndexInModel

  public int getAltLocIndexInModel(int modelIndex, char alternateLocationID)

• getInsertionCodeIndexInModel

  public int getInsertionCodeIndexInModel(int modelIndex, char insertionCode)

• getAltLocListInModel

  public String getAltLocListInModel(int modelIndex)

• getModelSymmetryCount

  public int getModelSymmetryCount(int modelIndex)

• getModelCellRange

  public int[] getModelCellRange(int modelIndex)

• getLastVibrationVector

  public int getLastVibrationVector(int modelIndex, int tok)

• getModulationList

  public Lst<Object> getModulationList(BS bs, char type, P3 t456)

• getElementsPresentBitSet

  public BS getElementsPresentBitSet(int modelIndex)

• getMoleculeIndex

  public int getMoleculeIndex(int atomIndex, boolean inModel)

  ////// molecules /////////

• getMoleculeBitSet

  public BS getMoleculeBitSet(BS bs)

  return cumulative sum of all atoms in molecules containing these atoms

  Parameters:

  bs -

  Returns:

  bitset of atoms

• getMoleculeBitSetForAtom

  public BS getMoleculeBitSetForAtom(int atomIndex)

• getModelDipole

  public V3 getModelDipole(int modelIndex)

• calculateMolecularDipole

  public V3 calculateMolecularDipole(int modelIndex, BS bsAtoms) throws JmolAsyncException, RuntimeException

  Throws:

  JmolAsyncException

  RuntimeException

• getMoleculeCountInModel

  public int getMoleculeCountInModel(int modelIndex)

• calcSelectedMoleculesCount

  public void calcSelectedMoleculesCount()

• setCentroid

  public 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 cell called from ScriptEval.finalizeLoad()

  Parameters:

  bs -

  minmax - fractional [xmin, ymin, zmin, xmax, ymax, zmax, 1=packed]

• getMolecules

  public JmolMolecule[] getMolecules()

• initializeBspf

  protected void initializeBspf()

  ///////// iterators //////////

• initializeBspt

  protected void initializeBspt(int modelIndex)

• setIteratorForPoint

  public void setIteratorForPoint(AtomIndexIterator iterator, int modelIndex, T3 pt, float distance)

• 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 -

• getSelectedAtomIterator

  public AtomIndexIterator getSelectedAtomIterator(BS bsSelected, boolean isGreaterOnly, boolean modelZeroBased, boolean hemisphereOnly, boolean isMultiModel)

  Parameters:

  bsSelected -

  isGreaterOnly -

  modelZeroBased -

  hemisphereOnly -

  isMultiModel -

  Returns:

  an iterator

• getBondCountInModel

  public int getBondCountInModel(int modelIndex)

  /////// bonds /////////

  Overrides:

  getBondCountInModel in class BondCollection

  Parameters:

  modelIndex - the model of interest or -1 for all

  Returns:

  the actual number of connections

• getAtomCountInModel

  public int getAtomCountInModel(int modelIndex)

• getModelAtomBitSetIncludingDeletedBs

  public BS getModelAtomBitSetIncludingDeletedBs(BS bsModels)

  note -- this method returns ALL atoms, including deleted.

  Parameters:

  bsModels -

  Returns:

  bitset of atoms

• getModelAtomBitSetIncludingDeleted

  public BS getModelAtomBitSetIncludingDeleted(int modelIndex, boolean asCopy)

  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

• getAtomBitsMaybeDeleted

  protected BS getAtomBitsMaybeDeleted(int tokType, Object specInfo)

• 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

• getAtomsWithin

  public BS getAtomsWithin(float distance, T3 coord, BS bsResult, int modelIndex)

  Parameters:

  distance - negative to check all unitCell distances

  coord -

  bsResult -

  modelIndex -

  Returns:

  bitset

• deleteBonds

  public void deleteBonds(BS bsBonds, boolean isFullModel)

• makeConnections2

  public int[] makeConnections2(float minD, float maxD, int order, int connectOperation, BS bsA, BS bsB, BS bsBonds, boolean isBonds, boolean addGroup, float energy, SB state)

• autoBondBs4

  public int autoBondBs4(BS bsA, BS bsB, BS bsExclude, BS bsBonds, short mad, boolean preJmol11_9_24, SB state)

• isBondable

  public boolean isBondable(float bondingRadiusA, float bondingRadiusB, float distance2, float minBondDistance2, float bondTolerance)

• autoHbond

  public int autoHbond(BS bsA, BS bsB, boolean onlyIfHaveCalculated)

  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" set

  onlyIfHaveCalculated -

  Returns:

  negative number of pseudo-hbonds or number of actual hbonds formed

• setStructureIndexes

  public void setStructureIndexes()

  ///////// state definition ///////////

• getModelInfoAsString

  public String getModelInfoAsString()

• getSymmetryInfoAsString

  public String getSymmetryInfoAsString()

• createModels

  public void createModels(int n)

• deleteAtoms

  public void deleteAtoms(BS bs)

• 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, boolean isNegDisorder, byte specialAtomID, BS atomSymmetry, float bondRadius)

• getInlineData

  public String getInlineData(int modelIndex)

• 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.assignAtom

  baseAtomIndex -

  mergeSet -

  isModelKit -

• connect

  public void connect(float[][] connections)

• setFrameDelayMs

  public void setFrameDelayMs(long millis, BS bsModels)

• getFrameDelayMs

  public long getFrameDelayMs(int i)

• getModelIndexFromId

  public int getModelIndexFromId(String id)

• getModelSetAuxiliaryInfo

  public Map<String,Object> getModelSetAuxiliaryInfo(BS bsModels)

  Retrieve the main modelset info Hashtable (or a new non-null Hashtable) with an up-to-date "models" key.

  Parameters:

  bsModels -

  Returns:

  Map

• getDihedralMap

  public int[][] getDihedralMap(int[] alist)

• setModulation

  public void setModulation(BS bs, boolean isOn, P3 qtOffset, boolean isQ)

  Sets the modulation for all atoms in bs.

  Parameters:

  bs -

  isOn -

  qtOffset - multiples of q or just t.

  isQ - true if multiples of q.

• getBoundBoxOrientation

  public Object getBoundBoxOrientation(int type, BS bsAtoms, P3[] points)

  Parameters:

  type - volume, best, x, y, z, unitcell

  bsAtoms -

  points - optionally use points, as from $isosurface1, ignoring bsAtoms

  Returns:

  quaternion for best rotation or, for volume, string with volume \t{dx dy dz}

• getUnitCellForAtom

  public SymmetryInterface getUnitCellForAtom(int index)

• clearCache

  public void clearCache()

• getSymMatrices

  public M4[] getSymMatrices(int modelIndex)

• getSymmetryInvariant

  public int[] getSymmetryInvariant(int iatom)

• getBsBranches

  public BS[] getBsBranches(float[] dihedralList)

• recalculatePositionDependentQuantities

  public void recalculatePositionDependentQuantities(BS bsAtoms, M4 mat)

• moveAtoms

  public void moveAtoms(M4 m4, M3 mNew, M3 rotation, V3 translation, BS bs, P3 center, boolean isInternal, boolean translationOnly)

• setDihedrals

  public void setDihedrals(float[] dihedralList, BS[] bsBranches, float f)

• setAtomCoordsRelative

  public void setAtomCoordsRelative(T3 offset, BS bs)

• setAtomCoords

  public void setAtomCoords(BS bs, int tokType, Object xyzValues)

• invertSelected

  public 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.

  Parameters:

  pt - point to invert around if not null

  plane - plane to invert across if not null

  iAtom - atom to switch two groups on if >= 0

  bsAtoms - atoms to switch for the atom option

• getCellWeights

  public float[] getCellWeights(BS bsAtoms)

• getAtomGroupQuaternions

  public Quat[] getAtomGroupQuaternions(BS bsAtoms, int nMax, char qtype)

• getConformation

  public BS getConformation(int modelIndex, int conformationIndex, boolean doSet, BS bsSelected)

• getSequenceBits

  public BS getSequenceBits(String specInfo, BS bsAtoms, BS bsResult)

  // bio-only methods /////

• getBioPolymerCountInModel

  public int getBioPolymerCountInModel(int modelIndex)

• getPolymerPointsAndVectors

  public void getPolymerPointsAndVectors(BS bs, Lst<P3[]> vList, boolean isTraceAlpha, float sheetSmoothing)

• 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 HBonds

  nucleicOnly -

  nMax -

  dsspIgnoreHydrogens -

  bsHBonds -

• calculateStraightnessAll

  public void calculateStraightnessAll()

• calculateStruts

  public int 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. The two bitsets may overlap.

  Parameters:

  bs1 -

  bs2 -

  Returns:

  number of struts found

• getGroupsWithin

  public BS getGroupsWithin(int nResidues, BS bs)

• getProteinStructureState

  public String getProteinStructureState(BS bsAtoms, int mode)

• calculateStructures

  public String calculateStructures(BS bsAtoms, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, int version)

• 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 calculation

  asDSSP -

  doReport -

  dsspIgnoreHydrogen -

  setStructure -

  includeAlpha -

  version - TODO

  Returns:

  report

• recalculatePolymers

  public void recalculatePolymers(BS bsModelsExcluded)

• calculatePolymers

  protected void calculatePolymers(Group[] groups, int groupCount, int baseGroupIndex, BS modelsExcluded)

• calcSelectedMonomersCount

  public void calcSelectedMonomersCount()

• setProteinType

  public void setProteinType(BS bs, STR type)

• setStructureList

  public void setStructureList(Map<STR,float[]> structureList)

• setConformation

  public BS setConformation(BS bsAtoms)

• getHeteroList

  public Map<String,String> getHeteroList(int modelIndex)

• getUnitCellPointsWithin

  public Object getUnitCellPointsWithin(float distance, BS bs, P3 pt, boolean asMap)

• calculateDssrProperty

  public void calculateDssrProperty(String dataType)

• getAtomicDSSRData

  public float getAtomicDSSRData(int i)

• getAtomCIPChiralityCode

  public int getAtomCIPChiralityCode(Atom atom)

  Determine the Cahn-Ingold-Prelog R/S chirality of an atom

  Parameters:

  atom -

  Returns:

  [0:none, 1:R, 2:S]

• calculateChiralityForAtoms

  public String calculateChiralityForAtoms(BS bsAtoms, boolean withReturn)

• getPointTransf

  public void getPointTransf(int i, Atom a, Quat q, P3 pTemp)

  pick up the appropriate value for this atom

  Parameters:

  i -

  a -

  q -

  pTemp -

• getSymmetryEquivAtoms

  public BS getSymmetryEquivAtoms(BS bsAtoms, SymmetryInterface sym, BS bsModelAtoms)

  Return a bitset of equivalent atoms

  Parameters:

  bsAtoms -

  sym -

  bsModelAtoms -

  Returns:

  bitset of equivalent atoms

• getSymmetryEquivAtomsForAtom

  public void getSymmetryEquivAtomsForAtom(int i, BS bsAtoms, BS bsCheck, BS bsEquiv)

  Set a bitset of the equivalent atoms of an atom.

  Parameters:

  i -

  bsAtoms - optional bitset of atoms remaining of original set of atoms

  bsCheck - bitset atoms to check; if bsAtoms is not null, also cleared of found atoms

  bsEquiv - bitset to return

• setSpaceGroup

  public void setSpaceGroup(int mi, SymmetryInterface sg, BS basis)

  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 -

• setModelCage

  public SymmetryInterface setModelCage(int modelIndex, SymmetryInterface simpleCage)

  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

• getBasisAtom

  public Atom getBasisAtom(int iatom, boolean doCheck)

• updateBasisFromSite

  public void updateBasisFromSite(int imodel)

• getConnectingAtoms

  public BS getConnectingAtoms(BS bsAtoms, BS bsFixed)

• saveAtomPositions

  public P3[] saveAtomPositions()

• restoreAtomPositions

  public void restoreAtomPositions(P3[] apos0)

• clearUnitCell

  public void clearUnitCell(int modelIndex)

• fixDeletedBonds

  public BS fixDeletedBonds(BS bs)

• getEquivalentAtoms

  public BS getEquivalentAtoms(int iatom)

• morphAtoms

  public void morphAtoms(BS bsAtoms, P3[][] points, int ipt, float f, P3 ptemp)

• getCurrentSpinAtoms

  public BS getCurrentSpinAtoms()

  include this frame and all related frames

  Returns:

  atoms with spin, or at least vibrations

• getSpin

  public int getSpin(int atomIndex)

• refreshDataFramePointGroup

  public void refreshDataFramePointGroup(int dataFrameIndex)