Class AtomSetCollection


  • public class AtomSetCollection
    extends java.lang.Object
    • Field Detail

      • 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
      • atoms

        public Atom[] atoms
      • ac

        public int ac
      • bonds

        public Bond[] bonds
      • bondCount

        public int bondCount
      • 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
      • bsStructuredModels

        public BS bsStructuredModels
      • haveAnisou

        public boolean haveAnisou
      • baseSymmetryAtomCount

        public int baseSymmetryAtomCount
      • checkLatticeOnly

        public boolean checkLatticeOnly
      • 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
    • 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)
      • 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()