Class AtomSetCollection

Method Details

• setCollectionName

  public void setCollectionName(String collectionName)

• clearGlobalBoolean

  public void clearGlobalBoolean(int globalIndex)

• setGlobalBoolean

  public void setGlobalBoolean(int globalIndex)

• setTrajectory

  public void setTrajectory()

• appendAtomSetCollection

  public void appendAtomSetCollection(int collectionIndex, AtomSetCollection collection)

  Appends an AtomSetCollection

  Parameters:

  collectionIndex - collection index for new model number

  collection - AtomSetCollection to append

• setNoAutoBond

  public void setNoAutoBond()

• discardPreviousAtoms

  public void discardPreviousAtoms()

• removeCurrentAtomSet

  public void removeCurrentAtomSet()

• getHydrogenAtomCount

  public int getHydrogenAtomCount()

• newCloneAtom

  public Atom newCloneAtom(Atom atom)

• cloneFirstAtomSet

  public int cloneFirstAtomSet(int atomCount)

• cloneAtomSetWithBonds

  public void cloneAtomSetWithBonds(boolean isLast)

• cloneLastAtomSet

  public int cloneLastAtomSet()

• cloneLastAtomSetFromPoints

  public int cloneLastAtomSetFromPoints(int ac, P3[] pts)

• getLastAtomSetAtomCount

  public int getLastAtomSetAtomCount()

• getLastAtomSetAtomIndex

  public int getLastAtomSetAtomIndex()

• addNewAtom

  public Atom addNewAtom()

• addAtom

  public Atom addAtom(Atom atom)

• addAtomWithMappedName

  public void addAtomWithMappedName(Atom atom)

• addAtomWithMappedSerialNumber

  public void addAtomWithMappedSerialNumber(Atom atom)

• getAtomFromName

  public Atom getAtomFromName(String atomName)

• setAtomMapAnyCase

  public void setAtomMapAnyCase()

• getAtomIndex

  public int getAtomIndex(String name)

• addNewBondWithOrder

  public Bond addNewBondWithOrder(int atomIndex1, int atomIndex2, int order)

• addNewBondFromNames

  public Bond addNewBondFromNames(String atomName1, String atomName2, int order)

• addNewBondWithOrderA

  public Bond addNewBondWithOrderA(Atom atom1, Atom atom2, int order)

• addBond

  public void addBond(Bond bond)

• addBondNoCheck

  public void addBondNoCheck(Bond bond)

• finalizeStructures

  public void finalizeStructures()

• addStructure

  public void addStructure(Structure structure)

• addVibrationVectorWithSymmetry

  public void addVibrationVectorWithSymmetry(int iatom, float vx, float vy, float vz, boolean withSymmetry)

• addVibrationVector

  public V3 addVibrationVector(int iatom, float x, float y, float z)

• setCoordinatesAreFractional

  public void setCoordinatesAreFractional(boolean tf)

• setAnisoBorU

  public void setAnisoBorU(Atom atom, float[] data, int type)

• setU

  public void setU(Atom atom, int i, float val)

• getXSymmetry

  public XtalSymmetry getXSymmetry()

• getSymmetry

  public XtalSymmetry.FileSymmetry getSymmetry()

• setSymmetryFromAuditBlock

  public XtalSymmetry.FileSymmetry setSymmetryFromAuditBlock(XtalSymmetry.FileSymmetry symmetry)

• newFileSymmetry

  public XtalSymmetry.FileSymmetry newFileSymmetry()

• setTensors

  public void setTensors()

• setInfo

  public void setInfo(String key, Object value)

• setAtomSetCollectionPartialCharges

  public boolean setAtomSetCollectionPartialCharges(String auxKey)

  Sets the partial atomic charges based on asc auxiliary info

  Parameters:

  auxKey - The auxiliary key name that contains the charges

  Returns:

  true if the data exist; false if not

• mapPartialCharge

  public void mapPartialCharge(String atomName, float charge)

• finalizeTrajectoryAs

  public void finalizeTrajectoryAs(Lst<P3[]> trajectorySteps, Lst<V3[]> vibrationSteps)

• newAtomSet

  public void newAtomSet()

  Create a new atoms set, clearing the atom map

• newAtomSetClear

  public void newAtomSetClear(boolean doClearMap)

  Create a new atom set, optionally clearing the atom map.

  Parameters:

  doClearMap - set to false only in CastepReader

• getAtomSetAtomIndex

  public int getAtomSetAtomIndex(int i)

• getAtomSetAtomCount

  public int getAtomSetAtomCount(int i)

• getAtomSetBondCount

  public int getAtomSetBondCount(int i)

• setAtomSetName

  public void setAtomSetName(String atomSetName)

  Sets the name for the current AtomSet

  Parameters:

  atomSetName - The name to be associated with the current AtomSet

• setCurrentAtomSetNumber

  public void setCurrentAtomSetNumber(int atomSetNumber)

  Sets the number for the current AtomSet

  Parameters:

  atomSetNumber - The number for the current AtomSet.

• setAtomSetNumber

  public void setAtomSetNumber(int index, int atomSetNumber)

• setAtomSetModelProperty

  public void setAtomSetModelProperty(String key, String value)

  Sets a property for the current AtomSet used specifically for creating directories and plots of frequencies and molecular energies

  Parameters:

  key - The key for the property

  value - The value to be associated with the key

• setAtomSetModelPropertyForSet

  public void setAtomSetModelPropertyForSet(String key, String value, int atomSetIndex)

  Sets the a property for the an AtomSet

  Parameters:

  key - The key for the property

  value - The value for the property

  atomSetIndex - The index of the AtomSet to get the property

• setAtomProperties

  public void setAtomProperties(String key, Object data, int atomSetIndex, boolean isGroup)

  Parameters:

  key -

  data -

  atomSetIndex -

  isGroup -

• getAtomSetAuxiliaryInfoValue

  public Object getAtomSetAuxiliaryInfoValue(int index, String key)

• setCurrentModelInfo

  public void setCurrentModelInfo(String key, Object value)

  Sets auxiliary information for the AtomSet

  Parameters:

  key - The key for the property

  value - The value to be associated with the key

• setModelInfoForSet

  public void setModelInfoForSet(String key, Object value, int atomSetIndex)

  Sets auxiliary information for an AtomSet

  Parameters:

  key - The key for the property

  value - The value for the property

  atomSetIndex - The index of the AtomSet to get the property

• getAtomSetAuxiliaryInfo

  public Map<String,Object> getAtomSetAuxiliaryInfo(int atomSetIndex)

• setAtomSetEnergy

  public void setAtomSetEnergy(String energyString, float value)

  / for XmlChem3dReader, but could be for CUBE

• setAtomSetFrequency

  public String setAtomSetFrequency(int mode, String pathKey, String label, String freq, String units)

• getBondList

  public String[][] getBondList()

• centralize

  public void centralize()

• removeAtomSet

  public void removeAtomSet(int imodel)

  note that sets must be iterated from LAST to FIRST not a general method -- would mess up if we had unit cells

  Parameters:

  imodel -

• removeLastUnselectedAtoms

  public void removeLastUnselectedAtoms()

• checkNoEmptyModel

  public void checkNoEmptyModel()

• getBSAtoms

  public BS getBSAtoms(int n)

  Create bsAtoms if it is null, and set bits if desired.

  Parameters:

  n - if created only, -1 to set all atoms, 0 for no setting, otherwise, set [0,n)

  Returns:

  bsAtoms

• setBSAtomsForSet

  public void setBSAtomsForSet(int iSet)

  Add a full set of atoms to BSAtoms if they are not already indicated there.

  Parameters:

  iSet -

• fix2Stereo

  public void fix2Stereo()