Package org.jmol.adapter.smarter
Class AtomSetCollection
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollection
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Field Summary
FieldsModifier and TypeFieldDescriptionint
boolean
boolean
Atom[]
private int[]
private int[]
private int[]
int
private int[]
int
int
(package private) int
Bond[]
javajs.util.BS
javajs.util.BS
boolean
boolean
(package private) String
boolean
boolean
int
private int
boolean
boolean
int
(package private) boolean
(package private) AtomSetCollectionReader
private javajs.util.Lst<AtomSetCollectionReader>
int
private javajs.util.Lst<String>
private int
private javajs.util.Lst<javajs.util.P3[]>
private javajs.util.Lst<javajs.util.V3[]>
int
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Constructor Summary
ConstructorsConstructorDescriptionAtomSetCollection
(String fileTypeName, AtomSetCollectionReader reader, AtomSetCollection[] array, javajs.util.Lst<?> list) -
Method Summary
Modifier and TypeMethodDescriptionvoid
addAtomWithMappedName
(Atom atom) void
void
addNewBondFromNames
(String atomName1, String atomName2, int order) addNewBondWithOrder
(int atomIndex1, int atomIndex2, int order) addNewBondWithOrderA
(Atom atom1, Atom atom2, int order) void
addStructure
(Structure structure) javajs.util.V3
addVibrationVector
(int iatom, float x, float y, float z) void
addVibrationVectorWithSymmetry
(int iatom, float vx, float vy, float vz, boolean withSymmetry) void
appendAtomSetCollection
(int collectionIndex, AtomSetCollection collection) Appends an AtomSetCollectionprivate void
appendAtomSetCollectionList
(javajs.util.Lst<?> list) void
void
void
clearGlobalBoolean
(int globalIndex) private void
clearMap()
void
cloneAtomSetWithBonds
(boolean isLast) int
cloneFirstAtomSet
(int atomCount) int
int
cloneLastAtomSetFromPoints
(int ac, javajs.util.P3[] pts) void
void
private void
void
finalizeTrajectoryAs
(javajs.util.Lst<javajs.util.P3[]> trajectorySteps, javajs.util.Lst<javajs.util.V3[]> vibrationSteps) (package private) void
finish()
private static javajs.util.P3
fixPeriodic
(javajs.util.P3 pt, javajs.util.P3 pt0) private static float
fixPoint
(float x, float x0) (package private) void
freeze
(boolean reverseModels) getAtomFromName
(String atomName) int
getAtomIndex
(String name) int
getAtomSetAtomCount
(int i) int
getAtomSetAtomIndex
(int i) getAtomSetAuxiliaryInfo
(int atomSetIndex) getAtomSetAuxiliaryInfoValue
(int index, String key) int
getAtomSetBondCount
(int i) (package private) String
getAtomSetName
(int atomSetIndex) (package private) int
getAtomSetNumber
(int atomSetIndex) String[][]
(package private) boolean
getGlobalBoolean
(int globalIndex) int
int
int
private void
getList
(boolean isAltLoc) void
mapPartialCharge
(String atomName, float charge) (package private) void
void
Create a new atoms set, clearing the atom mapvoid
newAtomSetClear
(boolean doClearMap) Create a new atom set, optionally clearing the atom map.newCloneAtom
(Atom atom) 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 cellsvoid
void
private void
reverseArray
(int[] a) private void
private static void
reverseList
(javajs.util.Lst<?> list) private void
reverseObject
(Object[] o) private void
reverseSets
(AtomSetObject[] o, int n) void
setAnisoBorU
(Atom atom, float[] data, int type) void
void
setAtomProperties
(String key, Object data, int atomSetIndex, boolean isGroup) boolean
Sets the partial atomic charges based on asc auxiliary infovoid
setAtomSetEnergy
(String energyString, float value) setAtomSetFrequency
(int mode, String pathKey, String label, String freq, String units) void
setAtomSetModelProperty
(String key, String value) Sets a property for the current AtomSet used specifically for creating directories and plots of frequencies and molecular energiesvoid
setAtomSetModelPropertyForSet
(String key, String value, int atomSetIndex) Sets the a property for the an AtomSetvoid
setAtomSetName
(String atomSetName) Sets the name for the current AtomSetvoid
setAtomSetNumber
(int index, int atomSetNumber) (package private) boolean
setAtomSetPartialCharges
(String auxKey) Sets the partial atomic charges based on atomSet auxiliary infovoid
setCollectionName
(String collectionName) void
setCoordinatesAreFractional
(boolean tf) void
setCurrentAtomSetNumber
(int atomSetNumber) Sets the number for the current AtomSetvoid
setCurrentModelInfo
(String key, Object value) Sets auxiliary information for the AtomSetvoid
setGlobalBoolean
(int globalIndex) void
void
setModelInfoForSet
(String key, Object value, int atomSetIndex) Sets auxiliary information for an AtomSetvoid
setSymmetry
(SymmetryInterface symmetry) void
void
private void
setTrajectoryName
(String name) void
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Field Details
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reader
AtomSetCollectionReader reader -
bsAtoms
public javajs.util.BS bsAtoms -
fileTypeName
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collectionName
String collectionName -
atomSetInfo
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atoms
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ac
public int ac -
bonds
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bondCount
public int bondCount -
structures
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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
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errorMessage
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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
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doFixPeriodic
public boolean doFixPeriodic -
allowMultiple
public boolean allowMultiple -
readerList
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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
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bondIndex0
int bondIndex0 -
checkSpecial
public boolean checkSpecial -
atomSymbolicMap
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haveUnitCell
public boolean haveUnitCell -
vibScale
public int vibScale -
firstAtomToBond
public int firstAtomToBond
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Constructor Details
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AtomSetCollection
public AtomSetCollection(String fileTypeName, AtomSetCollectionReader reader, AtomSetCollection[] array, javajs.util.Lst<?> list)
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Method Details
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setCollectionName
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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
Appends an AtomSetCollection- Parameters:
collectionIndex
- collection index for new model numbercollection
- AtomSetCollection to append
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setNoAutoBond
public void setNoAutoBond() -
freeze
void freeze(boolean reverseModels) -
reverseAtomSets
private void reverseAtomSets() -
reverseSets
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reverseObject
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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
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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
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addAtom
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addAtomWithMappedName
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addAtomWithMappedSerialNumber
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getAtomFromName
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setAtomMapAnyCase
public void setAtomMapAnyCase() -
getAtomIndex
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addNewBondWithOrder
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addNewBondFromNames
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addNewBondWithOrderA
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addBond
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finalizeStructures
public void finalizeStructures() -
addStructure
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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
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setU
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getXSymmetry
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getSymmetry
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setSymmetry
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setTensors
public void setTensors() -
setInfo
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setAtomSetCollectionPartialCharges
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
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mapPartialCharge
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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
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clearMap
private void clearMap() -
getAtomSetAtomIndex
public int getAtomSetAtomIndex(int i) -
getAtomSetAtomCount
public int getAtomSetAtomCount(int i) -
getAtomSetBondCount
public int getAtomSetBondCount(int i) -
setAtomSetName
Sets the name for the current AtomSet- Parameters:
atomSetName
- The name to be associated with the current AtomSet
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setTrajectoryName
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setCurrentAtomSetNumber
public void setCurrentAtomSetNumber(int atomSetNumber) Sets the number for the current AtomSet- Parameters:
atomSetNumber
- The number for the current AtomSet.
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setAtomSetNumber
public void setAtomSetNumber(int index, int atomSetNumber) -
setAtomSetModelProperty
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 propertyvalue
- The value to be associated with the key
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setAtomSetModelPropertyForSet
Sets the a property for the an AtomSet- Parameters:
key
- The key for the propertyvalue
- The value for the propertyatomSetIndex
- The index of the AtomSet to get the property
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setAtomProperties
- Parameters:
key
-data
-atomSetIndex
-isGroup
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setAtomSetPartialCharges
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
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getAtomSetAuxiliaryInfoValue
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setCurrentModelInfo
Sets auxiliary information for the AtomSet- Parameters:
key
- The key for the propertyvalue
- The value to be associated with the key
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setModelInfoForSet
Sets auxiliary information for an AtomSet- Parameters:
key
- The key for the propertyvalue
- The value for the propertyatomSetIndex
- The index of the AtomSet to get the property
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getAtomSetNumber
int getAtomSetNumber(int atomSetIndex) -
getAtomSetName
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getAtomSetAuxiliaryInfo
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setAtomSetEnergy
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setAtomSetFrequency
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getBondList
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centralize
public void centralize() -
mergeTrajectories
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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
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removeLastUnselectedAtoms
public void removeLastUnselectedAtoms() -
checkNoEmptyModel
public void checkNoEmptyModel()
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