Class AtomSetCollection

java.lang.Object
org.jmol.adapter.smarter.AtomSetCollection

public class AtomSetCollection extends Object
  • Field Details

    • reader

    • bsAtoms

      public javajs.util.BS bsAtoms
    • fileTypeName

      public String fileTypeName
    • collectionName

      String collectionName
    • atomSetInfo

      public Map<String,Object> atomSetInfo
    • 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

      private int[] atomSetNumbers
    • atomSetAtomIndexes

      private int[] atomSetAtomIndexes
    • atomSetAtomCounts

      private int[] atomSetAtomCounts
    • atomSetBondCounts

      private int[] atomSetBondCounts
    • atomSetAuxiliaryInfo

      private Map<String,Object>[] atomSetAuxiliaryInfo
    • errorMessage

      public 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<String> trajectoryNames
    • doFixPeriodic

      public boolean doFixPeriodic
    • allowMultiple

      public boolean allowMultiple
    • readerList

      private javajs.util.Lst<AtomSetCollectionReader> readerList
    • atomMapAnyCase

      public boolean atomMapAnyCase
    • fixedSite

      private int fixedSite
    • bsStructuredModels

      public javajs.util.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 Map<String,Atom> atomSymbolicMap
    • haveUnitCell

      public boolean haveUnitCell
    • vibScale

      public int vibScale
    • firstAtomToBond

      public int firstAtomToBond
  • Constructor Details

  • Method Details

    • setCollectionName

      public void setCollectionName(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(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)
    • cloneFirstAtomSet

      public int cloneFirstAtomSet(int atomCount)
    • cloneAtomSetWithBonds

      public void cloneAtomSetWithBonds(boolean isLast)
    • cloneLastAtomSet

      public int cloneLastAtomSet()
    • cloneLastAtomSetFromPoints

      public int cloneLastAtomSetFromPoints(int ac, javajs.util.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 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(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)
    • 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
    • clearMap

      private void clearMap()
    • 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
    • setTrajectoryName

      private void setTrajectoryName(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(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 -
    • setAtomSetPartialCharges

      boolean setAtomSetPartialCharges(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 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
    • getAtomSetNumber

      int getAtomSetNumber(int atomSetIndex)
    • getAtomSetName

      String getAtomSetName(int atomSetIndex)
    • getAtomSetAuxiliaryInfo

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

      public void setAtomSetEnergy(String energyString, float value)
    • setAtomSetFrequency

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

      public String[][] getBondList()
    • centralize

      public void centralize()
    • mergeTrajectories

      void mergeTrajectories(AtomSetCollection a)
    • 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()