Field Detail

• reader

  AtomSetCollectionReader reader

• bsAtoms

  public BS bsAtoms

• fileTypeName

  public java.lang.String fileTypeName

• collectionName

  java.lang.String collectionName

• atomSetInfo

  public java.util.Map<java.lang.String,​java.lang.Object> atomSetInfo

• globalBooleans

  private static final java.lang.String[] globalBooleans

• GLOBAL_FRACTCOORD

  public static final int GLOBAL_FRACTCOORD

  See Also:

  Constant Field Values

• GLOBAL_SYMMETRY

  public static final int GLOBAL_SYMMETRY

  See Also:

  Constant Field Values

• GLOBAL_UNITCELLS

  public static final int GLOBAL_UNITCELLS

  See Also:

  Constant Field Values

• GLOBAL_CONECT

  public static final int GLOBAL_CONECT

  See Also:

  Constant Field Values

• GLOBAL_ISPDB

  public static final int GLOBAL_ISPDB

  See Also:

  Constant Field Values

• GLOBAL_DOMAINS

  public static final int GLOBAL_DOMAINS

  See Also:

  Constant Field Values

• GLOBAL_VALIDATIONS

  public static final int GLOBAL_VALIDATIONS

  See Also:

  Constant Field Values

• atoms

  public Atom[] atoms

• ac

  public int ac

• bonds

  public Bond[] bonds

• bondCount

  public int bondCount

• structures

  public Structure[] structures

• structureCount

  public int structureCount

• atomSetCount

  public int atomSetCount

• iSet

  public int iSet

• atomSetNumbers

  public int[] atomSetNumbers

• atomSetAtomIndexes

  public int[] atomSetAtomIndexes

• atomSetAtomCounts

  public int[] atomSetAtomCounts

• atomSetBondCounts

  public int[] atomSetBondCounts

• atomSetAuxiliaryInfo

  public java.util.Map<java.lang.String,​java.lang.Object>[] atomSetAuxiliaryInfo

• errorMessage

  public java.lang.String errorMessage

• coordinatesAreFractional

  public boolean coordinatesAreFractional

• isTrajectory

  boolean isTrajectory

• trajectoryStepCount

  private int trajectoryStepCount

• trajectorySteps

  private javajs.util.Lst<javajs.util.P3[]> trajectorySteps

• vibrationSteps

  private javajs.util.Lst<javajs.util.V3[]> vibrationSteps

• trajectoryNames

  private javajs.util.Lst<java.lang.String> trajectoryNames

• doFixPeriodic

  public boolean doFixPeriodic

• allowMultiple

  public boolean allowMultiple

• readerList

  private javajs.util.Lst<AtomSetCollectionReader> readerList

• bsStructuredModels

  public BS bsStructuredModels

• haveAnisou

  public boolean haveAnisou

• baseSymmetryAtomCount

  public int baseSymmetryAtomCount

• checkLatticeOnly

  public boolean checkLatticeOnly

• xtalSymmetry

  public XtalSymmetry xtalSymmetry

• bondIndex0

  int bondIndex0

• checkSpecial

  public boolean checkSpecial

• atomSymbolicMap

  public java.util.Map<java.lang.String,​Atom> atomSymbolicMap

• haveUnitCell

  public boolean haveUnitCell

• vibScale

  public int vibScale

Constructor Detail

• AtomSetCollection

  public AtomSetCollection​(java.lang.String fileTypeName,
                           AtomSetCollectionReader reader,
                           AtomSetCollection[] array,
                           javajs.util.Lst<?> list)

Method Detail

• setCollectionName

  public void setCollectionName​(java.lang.String collectionName)

• clearGlobalBoolean

  public void clearGlobalBoolean​(int globalIndex)

• setGlobalBoolean

  public void setGlobalBoolean​(int globalIndex)

• getGlobalBoolean

  boolean getGlobalBoolean​(int globalIndex)

• appendAtomSetCollectionList

  private void appendAtomSetCollectionList​(javajs.util.Lst<?> list)

• 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()

• freeze

  void freeze​(boolean reverseModels)

• reverseAtomSets

  private void reverseAtomSets()

• reverseSets

  private void reverseSets​(AtomSetObject[] o,
                           int n)

• reverseObject

  private void reverseObject​(java.lang.Object[] o)

• reverseList

  private static void reverseList​(javajs.util.Lst<?> list)

• reverseArray

  private void reverseArray​(int[] a)

• getList

  private void getList​(boolean isAltLoc)

• finish

  void finish()

• discardPreviousAtoms

  public void discardPreviousAtoms()

• removeCurrentAtomSet

  public void removeCurrentAtomSet()

• getHydrogenAtomCount

  public int getHydrogenAtomCount()

• newCloneAtom

  public Atom newCloneAtom​(Atom atom)
                    throws java.lang.Exception

  Throws:

  java.lang.Exception

• cloneFirstAtomSet

  public int cloneFirstAtomSet​(int atomCount)
                        throws java.lang.Exception

  Throws:

  java.lang.Exception

• cloneAtomSetWithBonds

  public void cloneAtomSetWithBonds​(boolean isLast)
                             throws java.lang.Exception

  Throws:

  java.lang.Exception

• cloneLastAtomSet

  public int cloneLastAtomSet()
                       throws java.lang.Exception

  Throws:

  java.lang.Exception

• cloneLastAtomSetFromPoints

  public int cloneLastAtomSetFromPoints​(int ac,
                                        javajs.util.P3[] pts)
                                 throws java.lang.Exception

  Throws:

  java.lang.Exception

• 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​(java.lang.String atomName)

• getAtomIndex

  public int getAtomIndex​(java.lang.String name)

• addNewBondWithOrder

  public void addNewBondWithOrder​(int atomIndex1,
                                  int atomIndex2,
                                  int order)

• addNewBondFromNames

  public void addNewBondFromNames​(java.lang.String atomName1,
                                  java.lang.String atomName2,
                                  int order)

• addNewBondWithOrderA

  public void addNewBondWithOrderA​(Atom atom1,
                                   Atom atom2,
                                   int order)

• addBond

  public void addBond​(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 javajs.util.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 SymmetryInterface getSymmetry()

• setSymmetry

  public SymmetryInterface setSymmetry​(SymmetryInterface symmetry)

• setTensors

  public void setTensors()

• setInfo

  public void setInfo​(java.lang.String key,
                      java.lang.Object value)

• setAtomSetCollectionPartialCharges

  public boolean setAtomSetCollectionPartialCharges​(java.lang.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​(java.lang.String atomName,
                               float charge)

• fixPeriodic

  private static javajs.util.P3 fixPeriodic​(javajs.util.P3 pt,
                                            javajs.util.P3 pt0)

• fixPoint

  private static float fixPoint​(float x,
                                float x0)

• finalizeTrajectoryAs

  public void finalizeTrajectoryAs​(javajs.util.Lst<javajs.util.P3[]> trajectorySteps,
                                   javajs.util.Lst<javajs.util.V3[]> vibrationSteps)

• finalizeTrajectory

  private void finalizeTrajectory()

• 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​(java.lang.String atomSetName)

  Sets the name for the current AtomSet

  Parameters:

  atomSetName - The name to be associated with the current AtomSet

• setTrajectoryName

  private void setTrajectoryName​(java.lang.String name)

• 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​(java.lang.String key,
                                      java.lang.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​(java.lang.String key,
                                            java.lang.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​(java.lang.String key,
                                java.lang.Object data,
                                int atomSetIndex,
                                boolean isGroup)

  Parameters:

  key -

  data -

  atomSetIndex -

  isGroup -

• setAtomSetPartialCharges

  boolean setAtomSetPartialCharges​(java.lang.String auxKey)

  Sets the partial atomic charges based on atomSet auxiliary info

  Parameters:

  auxKey - The auxiliary key name that contains the charges

  Returns:

  true if the data exist; false if not

• getAtomSetAuxiliaryInfoValue

  public java.lang.Object getAtomSetAuxiliaryInfoValue​(int index,
                                                       java.lang.String key)

• setCurrentModelInfo

  public void setCurrentModelInfo​(java.lang.String key,
                                  java.lang.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​(java.lang.String key,
                                 java.lang.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

• getAtomSetNumber

  int getAtomSetNumber​(int atomSetIndex)

• getAtomSetName

  java.lang.String getAtomSetName​(int atomSetIndex)

• getAtomSetAuxiliaryInfo

  public java.util.Map<java.lang.String,​java.lang.Object> getAtomSetAuxiliaryInfo​(int atomSetIndex)

• setAtomSetEnergy

  public void setAtomSetEnergy​(java.lang.String energyString,
                               float value)

• setAtomSetFrequency

  public java.lang.String setAtomSetFrequency​(java.lang.String pathKey,
                                              java.lang.String label,
                                              java.lang.String freq,
                                              java.lang.String units)

• getBondList

  public java.lang.String[][] getBondList()

• centralize

  public void centralize()

• mergeTrajectories

  void mergeTrajectories​(AtomSetCollection a)