public class AtomSetCollection
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
int |
ac |
boolean |
allowMultiple |
(package private) java.util.Map<java.lang.String,java.lang.Object> |
ascAuxiliaryInfo |
Atom[] |
atoms |
private int[] |
atomSetAtomCounts |
private int[] |
atomSetAtomIndexes |
private java.util.Map<java.lang.String,java.lang.Object>[] |
atomSetAuxiliaryInfo |
private int[] |
atomSetBondCounts |
int |
atomSetCount |
private int[] |
atomSetNumbers |
private java.util.Map<java.lang.Object,java.lang.Integer> |
atomSymbolicMap |
int |
baseSymmetryAtomCount |
int |
bondCount |
(package private) int |
bondIndex0 |
Bond[] |
bonds |
BS |
bsAtoms |
BS |
bsStructuredModels |
boolean |
checkLatticeOnly |
(package private) boolean |
checkSpecial |
(package private) java.lang.String |
collectionName |
boolean |
coordinatesAreFractional |
int |
currentAtomSetIndex |
boolean |
doFixPeriodic |
java.lang.String |
errorMessage |
java.lang.String |
fileTypeName |
static int |
GLOBAL_CONECT |
static int |
GLOBAL_FRACTCOORD |
static int |
GLOBAL_ISPDB |
static int |
GLOBAL_SYMMETRY |
static int |
GLOBAL_UNITCELLS |
private static java.lang.String[] |
globalBooleans |
boolean |
haveAnisou |
private boolean |
haveMappedSerials |
boolean |
haveUnitCell |
(package private) boolean |
isTrajectory |
static java.lang.String[] |
notionalUnitcellTags |
(package private) AtomSetCollectionReader |
reader |
private javajs.util.List<AtomSetCollectionReader> |
readerList |
int |
structureCount |
Structure[] |
structures |
private javajs.util.List<java.lang.String> |
trajectoryNames |
private int |
trajectoryStepCount |
private javajs.util.List<javajs.util.P3[]> |
trajectorySteps |
private javajs.util.List<javajs.util.V3[]> |
vibrationSteps |
XtalSymmetry |
xtalSymmetry |
Constructor and Description |
---|
AtomSetCollection(java.lang.String fileTypeName,
AtomSetCollectionReader reader,
AtomSetCollection[] array,
javajs.util.List<?> list) |
Modifier and Type | Method and Description |
---|---|
Atom |
addAtom(Atom atom) |
void |
addAtomWithMappedName(Atom atom) |
void |
addAtomWithMappedSerialNumber(Atom atom) |
void |
addBond(Bond bond) |
Atom |
addNewAtom() |
Bond |
addNewBondFromNames(java.lang.String atomName1,
java.lang.String atomName2,
int order) |
Bond |
addNewBondWithMappedSerialNumbers(int atomSerial1,
int atomSerial2,
int order) |
Bond |
addNewBondWithOrder(int atomIndex1,
int atomIndex2,
int order) |
void |
addStructure(Structure structure) |
private void |
addTrajectoryStep() |
void |
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 AtomSetCollection
|
private void |
appendAtomSetCollectionList(javajs.util.List<?> list) |
void |
centralize() |
void |
clearGlobalBoolean(int globalIndex) |
void |
clearSymbolicMap() |
(package private) void |
cloneAtomSetProperties(int index)
Clones the properties of an atom set and associated it with the current
atom set.
|
void |
cloneFirstAtomSet(int ac) |
void |
cloneFirstAtomSetWithBonds(int nBonds) |
void |
cloneLastAtomSet() |
void |
cloneLastAtomSetFromPoints(int ac,
javajs.util.P3[] pts) |
void |
cloneLastAtomSetProperties()
Clones the properties of the last atom set and associates it with the
current atom set.
|
void |
createAtomSerialMap() |
void |
discardPreviousAtoms() |
void |
finalizeStructures() |
private void |
finalizeTrajectory() |
void |
finalizeTrajectoryAs(javajs.util.List<javajs.util.P3[]> trajectorySteps,
javajs.util.List<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) |
float[] |
getAnisoBorU(Atom atom) |
int |
getAtomIndexFromName(java.lang.String atomName) |
int |
getAtomIndexFromSerial(int serialNumber) |
int |
getAtomSetAtomCount(int i) |
int |
getAtomSetAtomIndex(int i) |
(package private) java.util.Map<java.lang.String,java.lang.Object> |
getAtomSetAuxiliaryInfo(int atomSetIndex) |
java.lang.Object |
getAtomSetAuxiliaryInfoValue(int index,
java.lang.String key) |
int |
getAtomSetBondCount(int i) |
java.lang.Object |
getAtomSetCollectionAuxiliaryInfo(java.lang.String key) |
(package private) java.lang.String |
getAtomSetName(int atomSetIndex) |
(package private) int |
getAtomSetNumber(int atomSetIndex) |
java.lang.String[][] |
getBondList() |
int |
getFirstAtomSetAtomCount() |
(package private) boolean |
getGlobalBoolean(int globalIndex) |
int |
getHydrogenAtomCount() |
int |
getLastAtomSetAtomCount() |
int |
getLastAtomSetAtomIndex() |
private void |
getList(boolean isAltLoc) |
private int |
getMapIndex(java.lang.Object nameOrNum) |
SymmetryInterface |
getSymmetry() |
XtalSymmetry |
getXSymmetry() |
void |
mapPartialCharge(java.lang.String atomName,
float charge) |
(package private) void |
mergeTrajectories(AtomSetCollection a) |
void |
newAtomSet() |
void |
newAtomSetClear(boolean doClearMap) |
(package private) Atom |
newCloneAtom(Atom atom) |
void |
removeAtomSet(int imodel)
note that sets must be iterated from LAST to FIRST
|
void |
removeCurrentAtomSet() |
private void |
reverseArray(int[] a) |
private void |
reverseAtomSets() |
private static void |
reverseList(javajs.util.List<?> list) |
private void |
reverseObject(java.lang.Object[] o) |
private void |
reverseSets(AtomSetObject[] o,
int n) |
void |
setAnisoBorU(Atom atom,
float[] data,
int type) |
java.util.Properties |
setAtomNames(java.util.Properties atomIdNames) |
void |
setAtomSetAtomProperty(java.lang.String key,
java.lang.String data,
int atomSetIndex) |
void |
setAtomSetAuxiliaryInfo(java.lang.String key,
java.lang.Object value)
Sets auxiliary information for the AtomSet
|
void |
setAtomSetAuxiliaryInfoForSet(java.lang.String key,
java.lang.Object value,
int atomSetIndex)
Sets auxiliary information for an AtomSet
|
void |
setAtomSetCollectionAuxiliaryInfo(java.lang.String key,
java.lang.Object value) |
boolean |
setAtomSetCollectionPartialCharges(java.lang.String auxKey)
Sets the partial atomic charges based on asc auxiliary info
|
void |
setAtomSetEnergy(java.lang.String energyString,
float value) |
java.lang.String |
setAtomSetFrequency(java.lang.String pathKey,
java.lang.String label,
java.lang.String freq,
java.lang.String units) |
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
|
void |
setAtomSetModelPropertyForSet(java.lang.String key,
java.lang.String value,
int atomSetIndex)
Sets the a property for the an AtomSet
|
void |
setAtomSetName(java.lang.String atomSetName)
Sets the name for the current AtomSet
|
void |
setAtomSetNames(java.lang.String atomSetName,
int n,
BS namedSets)
Sets the atom set names of the last n atomSets
|
void |
setAtomSetNumber(int index,
int atomSetNumber) |
(package private) boolean |
setAtomSetPartialCharges(java.lang.String auxKey)
Sets the partial atomic charges based on atomSet auxiliary info
|
void |
setAtomSetPropertyForSets(java.lang.String key,
java.lang.String value,
int n)
Sets the same properties for the last n atomSets.
|
(package private) void |
setAtomSetSpaceGroupName(java.lang.String spaceGroupName) |
void |
setCheckSpecial(boolean TF) |
void |
setCollectionName(java.lang.String collectionName) |
void |
setCoordinatesAreFractional(boolean tf) |
void |
setCurrentAtomSetNumber(int atomSetNumber)
Sets the number for the current AtomSet
|
void |
setGlobalBoolean(int globalIndex) |
void |
setNoAutoBond() |
SymmetryInterface |
setSymmetry(SymmetryInterface symmetry) |
void |
setTensors() |
void |
setTrajectory() |
private void |
setTrajectoryName(java.lang.String name) |
(package private) void |
toCartesian(SymmetryInterface symmetry) |
AtomSetCollectionReader reader
public BS bsAtoms
public java.lang.String fileTypeName
java.lang.String collectionName
java.util.Map<java.lang.String,java.lang.Object> ascAuxiliaryInfo
private static final java.lang.String[] globalBooleans
public static final int GLOBAL_FRACTCOORD
public static final int GLOBAL_SYMMETRY
public static final int GLOBAL_UNITCELLS
public static final int GLOBAL_CONECT
public static final int GLOBAL_ISPDB
public static final java.lang.String[] notionalUnitcellTags
public Atom[] atoms
public int ac
public Bond[] bonds
public int bondCount
public Structure[] structures
public int structureCount
public int atomSetCount
public int currentAtomSetIndex
private int[] atomSetNumbers
private int[] atomSetAtomIndexes
private int[] atomSetAtomCounts
private int[] atomSetBondCounts
private java.util.Map<java.lang.String,java.lang.Object>[] atomSetAuxiliaryInfo
public java.lang.String errorMessage
public boolean coordinatesAreFractional
boolean isTrajectory
private int trajectoryStepCount
private javajs.util.List<javajs.util.P3[]> trajectorySteps
private javajs.util.List<javajs.util.V3[]> vibrationSteps
private javajs.util.List<java.lang.String> trajectoryNames
public boolean doFixPeriodic
public boolean allowMultiple
private javajs.util.List<AtomSetCollectionReader> readerList
public BS bsStructuredModels
public boolean haveAnisou
public int baseSymmetryAtomCount
public boolean checkLatticeOnly
public XtalSymmetry xtalSymmetry
int bondIndex0
boolean checkSpecial
private java.util.Map<java.lang.Object,java.lang.Integer> atomSymbolicMap
private boolean haveMappedSerials
public boolean haveUnitCell
public AtomSetCollection(java.lang.String fileTypeName, AtomSetCollectionReader reader, AtomSetCollection[] array, javajs.util.List<?> list)
public void setCollectionName(java.lang.String collectionName)
public void clearGlobalBoolean(int globalIndex)
public void setGlobalBoolean(int globalIndex)
boolean getGlobalBoolean(int globalIndex)
private void appendAtomSetCollectionList(javajs.util.List<?> list)
public void setTrajectory()
public void appendAtomSetCollection(int collectionIndex, AtomSetCollection collection)
collectionIndex
- collection index for new model numbercollection
- AtomSetCollection to appendpublic void setNoAutoBond()
void freeze(boolean reverseModels)
private void reverseAtomSets()
private void reverseSets(AtomSetObject[] o, int n)
private void reverseObject(java.lang.Object[] o)
private static void reverseList(javajs.util.List<?> list)
private void reverseArray(int[] a)
private void getList(boolean isAltLoc)
void finish()
public void discardPreviousAtoms()
public void removeAtomSet(int imodel)
imodel
- public void removeCurrentAtomSet()
public int getHydrogenAtomCount()
public void cloneFirstAtomSet(int ac) throws java.lang.Exception
java.lang.Exception
public void cloneFirstAtomSetWithBonds(int nBonds) throws java.lang.Exception
java.lang.Exception
public void cloneLastAtomSet() throws java.lang.Exception
java.lang.Exception
public void cloneLastAtomSetFromPoints(int ac, javajs.util.P3[] pts) throws java.lang.Exception
java.lang.Exception
public int getFirstAtomSetAtomCount()
public int getLastAtomSetAtomCount()
public int getLastAtomSetAtomIndex()
public Atom addNewAtom()
public void addAtomWithMappedName(Atom atom)
public void addAtomWithMappedSerialNumber(Atom atom)
public Bond addNewBondWithOrder(int atomIndex1, int atomIndex2, int order)
public Bond addNewBondFromNames(java.lang.String atomName1, java.lang.String atomName2, int order)
public Bond addNewBondWithMappedSerialNumbers(int atomSerial1, int atomSerial2, int order)
public void addBond(Bond bond)
public void finalizeStructures()
public void addStructure(Structure structure)
public void addVibrationVectorWithSymmetry(int iatom, float vx, float vy, float vz, boolean withSymmetry)
public void addVibrationVector(int iatom, float x, float y, float z)
void setAtomSetSpaceGroupName(java.lang.String spaceGroupName)
public void setCoordinatesAreFractional(boolean tf)
public void setAnisoBorU(Atom atom, float[] data, int type)
public float[] getAnisoBorU(Atom atom)
public XtalSymmetry getXSymmetry()
public SymmetryInterface getSymmetry()
public SymmetryInterface setSymmetry(SymmetryInterface symmetry)
public void setTensors()
public void setCheckSpecial(boolean TF)
public void clearSymbolicMap()
public void createAtomSerialMap()
public int getAtomIndexFromName(java.lang.String atomName)
public int getAtomIndexFromSerial(int serialNumber)
private int getMapIndex(java.lang.Object nameOrNum)
public void setAtomSetCollectionAuxiliaryInfo(java.lang.String key, java.lang.Object value)
public boolean setAtomSetCollectionPartialCharges(java.lang.String auxKey)
auxKey
- The auxiliary key name that contains the chargespublic void mapPartialCharge(java.lang.String atomName, float charge)
public java.lang.Object getAtomSetCollectionAuxiliaryInfo(java.lang.String key)
private void addTrajectoryStep()
private static javajs.util.P3 fixPeriodic(javajs.util.P3 pt, javajs.util.P3 pt0)
private static float fixPoint(float x, float x0)
public void finalizeTrajectoryAs(javajs.util.List<javajs.util.P3[]> trajectorySteps, javajs.util.List<javajs.util.V3[]> vibrationSteps)
private void finalizeTrajectory()
public void newAtomSet()
public void newAtomSetClear(boolean doClearMap)
public int getAtomSetAtomIndex(int i)
public int getAtomSetAtomCount(int i)
public int getAtomSetBondCount(int i)
public void setAtomSetName(java.lang.String atomSetName)
atomSetName
- The name to be associated with the current AtomSetprivate void setTrajectoryName(java.lang.String name)
public void setAtomSetNames(java.lang.String atomSetName, int n, BS namedSets)
atomSetName
- The namen
- The number of last AtomSets that needs these setnamedSets
- public void setCurrentAtomSetNumber(int atomSetNumber)
atomSetNumber
- The number for the current AtomSet.public void setAtomSetNumber(int index, int atomSetNumber)
public void setAtomSetModelProperty(java.lang.String key, java.lang.String value)
key
- The key for the propertyvalue
- The value to be associated with the keypublic void setAtomSetModelPropertyForSet(java.lang.String key, java.lang.String value, int atomSetIndex)
key
- The key for the propertyvalue
- The value for the propertyatomSetIndex
- The index of the AtomSet to get the propertypublic void setAtomSetAtomProperty(java.lang.String key, java.lang.String data, int atomSetIndex)
boolean setAtomSetPartialCharges(java.lang.String auxKey)
auxKey
- The auxiliary key name that contains the chargespublic java.lang.Object getAtomSetAuxiliaryInfoValue(int index, java.lang.String key)
public void setAtomSetAuxiliaryInfo(java.lang.String key, java.lang.Object value)
key
- The key for the propertyvalue
- The value to be associated with the keypublic void setAtomSetAuxiliaryInfoForSet(java.lang.String key, java.lang.Object value, int atomSetIndex)
key
- The key for the propertyvalue
- The value for the propertyatomSetIndex
- The index of the AtomSet to get the propertypublic void setAtomSetPropertyForSets(java.lang.String key, java.lang.String value, int n)
key
- The key for the propertyvalue
- The value of the propertyn
- The number of last AtomSets that needs these setpublic void cloneLastAtomSetProperties()
void cloneAtomSetProperties(int index)
index
- The index of the atom set whose properties are to be cloned.int getAtomSetNumber(int atomSetIndex)
java.lang.String getAtomSetName(int atomSetIndex)
java.util.Map<java.lang.String,java.lang.Object> getAtomSetAuxiliaryInfo(int atomSetIndex)
public java.util.Properties setAtomNames(java.util.Properties atomIdNames)
public void setAtomSetEnergy(java.lang.String energyString, float value)
public java.lang.String setAtomSetFrequency(java.lang.String pathKey, java.lang.String label, java.lang.String freq, java.lang.String units)
void toCartesian(SymmetryInterface symmetry)
public java.lang.String[][] getBondList()
public void centralize()
void mergeTrajectories(AtomSetCollection a)