Package org.jmol.adapter.smarter
Class AtomSetCollection
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollection
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Field Summary
Fields -
Constructor Summary
ConstructorsConstructorDescriptionAtomSetCollection
(String fileTypeName, AtomSetCollectionReader reader, AtomSetCollection[] array, Lst<?> list) -
Method Summary
Modifier and TypeMethodDescriptionvoid
addAtomWithMappedName
(Atom atom) void
void
void
addBondNoCheck
(Bond bond) 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) 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 AtomSetCollectionvoid
void
void
clearGlobalBoolean
(int globalIndex) void
cloneAtomSetWithBonds
(boolean isLast) int
cloneFirstAtomSet
(int atomCount) int
int
cloneLastAtomSetFromPoints
(int ac, P3[] pts) void
void
void
finalizeTrajectoryAs
(Lst<P3[]> trajectorySteps, Lst<V3[]> vibrationSteps) void
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) String[][]
getBSAtoms
(int n) Create bsAtoms if it is null, and set bits if desired.int
int
int
void
mapPartialCharge
(String atomName, float charge) 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
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) void
setBSAtomsForSet
(int iSet) Add a full set of atoms to BSAtoms if they are not already indicated there.void
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
(XtalSymmetry.FileSymmetry symmetry) void
void
void
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Field Details
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bsAtoms
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fileTypeName
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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 -
errorMessage
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coordinatesAreFractional
public boolean coordinatesAreFractional -
doFixPeriodic
public boolean doFixPeriodic -
allowMultiple
public boolean allowMultiple -
atomMapAnyCase
public boolean atomMapAnyCase -
bsStructuredModels
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haveAnisou
public boolean haveAnisou -
baseSymmetryAtomCount
public int baseSymmetryAtomCount -
crystalReaderLatticeOpsOnly
public boolean crystalReaderLatticeOpsOnly -
xtalSymmetry
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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, 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) -
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() -
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
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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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addBondNoCheck
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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
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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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newFileSymmetry
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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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finalizeTrajectoryAs
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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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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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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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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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getAtomSetAuxiliaryInfo
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setAtomSetEnergy
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setAtomSetFrequency
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getBondList
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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
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removeLastUnselectedAtoms
public void removeLastUnselectedAtoms() -
checkNoEmptyModel
public void checkNoEmptyModel() -
getBSAtoms
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
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setBSAtomsForSet
public void setBSAtomsForSet(int iSet) Add a full set of atoms to BSAtoms if they are not already indicated there.- Parameters:
iSet
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fix2Stereo
public void fix2Stereo()
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