public class AtomSetCollection
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
private boolean |
allowMultiple |
(package private) boolean |
applySymmetryToBonds |
private int |
atomCount |
private Atom[] |
atoms |
private int[] |
atomSetAtomCounts |
private java.util.Hashtable[] |
atomSetAuxiliaryInfo |
private int[] |
atomSetBondCounts |
private java.util.Hashtable |
atomSetCollectionAuxiliaryInfo |
private int |
atomSetCount |
private int[] |
atomSetNumbers |
(package private) java.util.Hashtable |
atomSymbolicMap |
private int |
bondCount |
(package private) int |
bondCount0 |
(package private) int |
bondIndex0 |
private Bond[] |
bonds |
(package private) javax.vecmath.Point3f[] |
cartesians |
(package private) boolean |
checkSpecial |
private java.lang.String |
collectionName |
(package private) int[] |
connectLast |
(package private) int |
connectNextAtomIndex |
(package private) int |
connectNextAtomSet |
(package private) boolean |
coordinatesAreFractional |
private int |
currentAtomSetIndex |
(package private) boolean |
doFixPeriodic |
(package private) boolean |
doNormalize |
(package private) boolean |
doPackUnitCell |
java.lang.String |
errorMessage |
private java.lang.String |
fileTypeName |
private static int |
GLOBAL_CONECT |
static int |
GLOBAL_FRACTCOORD |
private static int |
GLOBAL_ISPDB |
static int |
GLOBAL_SYMMETRY |
static int |
GLOBAL_UNITCELLS |
private static java.lang.String[] |
globalBooleans |
(package private) boolean |
haveMappedSerials |
(package private) boolean |
haveUnitCell |
private boolean |
isTrajectory |
private int[] |
latticeCells |
private javax.vecmath.Point3i |
maxXYZ |
private javax.vecmath.Point3i |
minXYZ |
private boolean |
needEllipsoids |
(package private) float[] |
notionalUnitCell |
static java.lang.String[] |
notionalUnitcellTags |
private javax.vecmath.Point3f |
ptOffset |
private javax.vecmath.Point3f |
ptTemp |
private javax.vecmath.Point3f |
ptTemp1 |
private javax.vecmath.Point3f |
ptTemp2 |
private float |
rmaxx |
private float |
rmaxy |
private float |
rmaxz |
private float |
rminx |
private float |
rminy |
private float |
rminz |
private int |
structureCount |
private Structure[] |
structures |
(package private) SymmetryInterface |
symmetry |
(package private) float |
symmetryRange |
private javax.vecmath.Point3f[] |
trajectoryStep |
private int |
trajectoryStepCount |
private java.util.List |
trajectorySteps |
private javax.vecmath.Point3f |
unitCellOffset |
(package private) java.util.List |
vConnect |
(package private) VolumeDataInterface |
vd |
Constructor and Description |
---|
AtomSetCollection(AtomSetCollection[] array)
Creates an AtomSetCollection based on an array of AtomSetCollection
|
AtomSetCollection(java.util.List list)
Creates an AtomSetCollection based on a List of
AtomSetCollection or List (from zipped zip files)
|
AtomSetCollection(java.lang.String fileTypeName,
AtomSetCollectionReader atomSetCollectionReader) |
Modifier and Type | Method and Description |
---|---|
void |
addAtom(Atom atom) |
void |
addAtomWithMappedName(Atom atom) |
void |
addAtomWithMappedSerialNumber(Atom atom) |
void |
addBond(Bond bond) |
void |
addConnection(int[] is) |
Atom |
addNewAtom() |
Bond |
addNewBond(int atomIndex1,
int atomIndex2) |
Bond |
addNewBond(int atomIndex1,
int atomIndex2,
int order) |
(package private) Bond |
addNewBond(java.lang.String atomName1,
java.lang.String atomName2) |
Bond |
addNewBond(java.lang.String atomName1,
java.lang.String atomName2,
int order) |
Bond |
addNewBondWithMappedSerialNumbers(int atomSerial1,
int atomSerial2,
int order) |
(package private) boolean |
addSpaceGroupOperation(java.lang.String xyz) |
void |
addStructure(Structure structure) |
private void |
addTrajectoryStep() |
void |
addVibrationVector(int iatom,
float x,
float y,
float z) |
void |
addVibrationVector(int iatom,
float vx,
float vy,
float vz,
boolean withSymmetry) |
private void |
appendAtomProperties(int nTimes) |
protected void |
appendAtomSetCollection(int collectionIndex,
AtomSetCollection collection)
Appends an AtomSetCollection
|
private void |
appendAtomSetCollection(java.util.List list) |
private void |
applyAllSymmetry(int maxX,
int maxY,
int maxZ) |
(package private) void |
applySymmetry() |
private void |
applySymmetry(int maxX,
int maxY,
int maxZ) |
void |
applySymmetry(java.util.List biomts,
float[] notionalUnitCell,
boolean applySymmetryToBonds,
java.lang.String filter) |
(package private) void |
applySymmetry(SymmetryInterface symmetry) |
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() |
void |
cloneFirstAtomSetWithBonds(int nBonds) |
void |
cloneLastAtomSet() |
void |
cloneLastAtomSet(int atomCount) |
void |
cloneLastAtomSetProperties()
Clones the properties of the last atom set and associates it
with the current atom set.
|
void |
connectAll(int maxSerial) |
void |
createAtomSerialMap() |
void |
discardPreviousAtoms() |
private void |
finalizeTrajectory(boolean addStep) |
(package private) void |
finalizeTrajectory(java.util.List trajectorySteps) |
(package private) void |
finish() |
private javax.vecmath.Point3f |
fixPeriodic(javax.vecmath.Point3f pt,
javax.vecmath.Point3f pt0) |
private float |
fixPoint(float x,
float x0) |
(package private) void |
freeze() |
(package private) void |
getAltLocLists() |
float[] |
getAnisoBorU(Atom atom) |
Atom |
getAtom(int i) |
int |
getAtomCount() |
int |
getAtomNameIndex(java.lang.String atomName) |
Atom[] |
getAtoms() |
int |
getAtomSerialNumberIndex(int serialNumber) |
(package private) java.util.Hashtable |
getAtomSetAuxiliaryInfo(int atomSetIndex) |
(package private) java.lang.Object |
getAtomSetAuxiliaryInfo(int index,
java.lang.String key) |
java.util.Hashtable |
getAtomSetCollectionAuxiliaryInfo() |
java.lang.Object |
getAtomSetCollectionAuxiliaryInfo(java.lang.String key) |
int |
getAtomSetCount() |
(package private) java.lang.String |
getAtomSetName(int atomSetIndex) |
(package private) int |
getAtomSetNumber(int atomSetIndex) |
Bond |
getBond(int i) |
int |
getBondCount() |
Bond[] |
getBonds() |
java.lang.String |
getCollectionName() |
int |
getCurrentAtomSetIndex() |
java.lang.String |
getFileTypeName() |
int |
getFirstAtomSetAtomCount() |
(package private) void |
getInsertionLists() |
int |
getLastAtomSetAtomCount() |
int |
getLastAtomSetAtomIndex() |
int |
getStructureCount() |
Structure[] |
getStructures() |
private SymmetryInterface |
getSymmetry() |
java.lang.Object |
getVolumeData() |
(package private) boolean |
hasAlternateLocations() |
(package private) boolean |
hasInsertions() |
private boolean |
isInSymmetryRange(javax.vecmath.Point3f c) |
private static boolean |
isWithinCell(javax.vecmath.Point3f pt,
int minX,
int maxX,
int minY,
int maxY,
int minZ,
int maxZ) |
(package private) void |
mapAtomName(java.lang.String atomName,
int atomIndex) |
(package private) void |
mapMostRecentAtomName() |
(package private) void |
mapMostRecentAtomSerialNumber() |
void |
mapPartialCharge(java.lang.String atomName,
float charge) |
void |
newAtomSet() |
(package private) Atom |
newCloneAtom(Atom atom) |
void |
newVolumeData() |
void |
removeAtomSet() |
void |
setAnisoBorU(Atom atom,
float[] data,
int type) |
java.util.Properties |
setAtomNames(java.util.Properties atomIdNames) |
void |
setAtomSetAuxiliaryInfo(java.lang.String key,
java.lang.Object value)
Sets auxiliary information for the AtomSet
|
(package private) void |
setAtomSetAuxiliaryInfo(java.lang.String key,
java.lang.Object value,
int atomSetIndex)
Sets auxiliary information for an AtomSet
|
void |
setAtomSetAuxiliaryProperty(java.lang.String key,
java.lang.String data) |
void |
setAtomSetCollectionAuxiliaryInfo(java.lang.String key,
java.lang.Object value) |
boolean |
setAtomSetCollectionPartialCharges(java.lang.String auxKey)
Sets the partial atomic charges based on atomSetCollection auxiliary info
|
void |
setAtomSetEnergy(java.lang.String energyString,
float value) |
void |
setAtomSetFrequency(java.lang.String pathKey,
java.lang.String label,
java.lang.String freq,
java.lang.String units) |
void |
setAtomSetName(java.lang.String atomSetName)
Sets the name for the current AtomSet
|
void |
setAtomSetNames(java.lang.String atomSetName,
int n)
Sets the atom set names of the last n atomSets
|
void |
setAtomSetNumber(int atomSetNumber)
Sets the number for the current AtomSet
|
(package private) boolean |
setAtomSetPartialCharges(java.lang.String auxKey)
Sets the partial atomic charges based on atomSet auxiliary info
|
void |
setAtomSetProperties(java.lang.String key,
java.lang.String value,
int n)
Sets the same properties for the last n atomSets.
|
void |
setAtomSetProperty(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
moleular energies
|
void |
setAtomSetProperty(java.lang.String key,
java.lang.String value,
int atomSetIndex)
Sets the a property for the an AtomSet
|
(package private) void |
setAtomSetSpaceGroupName(java.lang.String spaceGroupName) |
void |
setCheckSpecial(boolean TF) |
void |
setCollectionName(java.lang.String collectionName) |
(package private) void |
setCoordinatesAreFractional(boolean coordinatesAreFractional) |
void |
setCurrentAtomSetIndex(int i) |
void |
setDoFixPeriodic() |
(package private) void |
setGlobalBoolean(int globalIndex) |
void |
setIsPDB() |
(package private) void |
setLatticeCells(int[] latticeCells,
boolean applySymmetryToBonds,
boolean doPackUnitCell) |
void |
setLatticeParameter(int latt) |
(package private) void |
setNoAutoBond() |
void |
setNotionalUnitCell(float[] info,
javax.vecmath.Matrix3f matUnitCellOrientation,
javax.vecmath.Point3f unitCellOffset) |
private void |
setSymmetryMinMax(javax.vecmath.Point3f c) |
private void |
setSymmetryOps() |
(package private) void |
setSymmetryRange(float factor) |
void |
setTrajectory() |
void |
setVolumetricOrigin(float x,
float y,
float z) |
void |
setVolumetricVector(int i,
float x,
float y,
float z) |
void |
setVoxelCounts(int nPointsX,
int nPointsY,
int nPointsZ) |
void |
setVoxelData(float[][][] voxelData) |
private int |
symmetryAddAtoms(int iAtomFirst,
int noSymmetryCount,
int transX,
int transY,
int transZ,
int baseCount,
int pt,
int iCellOpPt) |
(package private) void |
toCartesian(SymmetryInterface symmetry) |
private java.lang.String fileTypeName
private java.lang.String collectionName
private java.util.Hashtable atomSetCollectionAuxiliaryInfo
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
private static final int GLOBAL_CONECT
private static final int GLOBAL_ISPDB
public static final java.lang.String[] notionalUnitcellTags
private int atomCount
private Atom[] atoms
private int bondCount
private Bond[] bonds
private int structureCount
private Structure[] structures
private int atomSetCount
private int currentAtomSetIndex
private int[] atomSetNumbers
private int[] atomSetAtomCounts
private int[] atomSetBondCounts
private java.util.Hashtable[] atomSetAuxiliaryInfo
private int[] latticeCells
public java.lang.String errorMessage
boolean coordinatesAreFractional
private boolean isTrajectory
private int trajectoryStepCount
private javax.vecmath.Point3f[] trajectoryStep
private java.util.List trajectorySteps
boolean doFixPeriodic
float[] notionalUnitCell
private boolean allowMultiple
java.util.List vConnect
int connectNextAtomIndex
int connectNextAtomSet
int[] connectLast
float symmetryRange
SymmetryInterface symmetry
boolean haveUnitCell
boolean doNormalize
boolean doPackUnitCell
private float rminx
private float rminy
private float rminz
private float rmaxx
private float rmaxy
private float rmaxz
private final javax.vecmath.Point3f ptOffset
private javax.vecmath.Point3f unitCellOffset
private javax.vecmath.Point3i minXYZ
private javax.vecmath.Point3i maxXYZ
private boolean needEllipsoids
javax.vecmath.Point3f[] cartesians
int bondCount0
int bondIndex0
boolean applySymmetryToBonds
boolean checkSpecial
private final javax.vecmath.Point3f ptTemp
private final javax.vecmath.Point3f ptTemp1
private final javax.vecmath.Point3f ptTemp2
java.util.Hashtable atomSymbolicMap
boolean haveMappedSerials
VolumeDataInterface vd
public AtomSetCollection(java.lang.String fileTypeName, AtomSetCollectionReader atomSetCollectionReader)
public AtomSetCollection(AtomSetCollection[] array)
array
- Array of AtomSetCollectionpublic AtomSetCollection(java.util.List list)
list
- List of AtomSetCollectionpublic java.lang.String getFileTypeName()
public java.lang.String getCollectionName()
public void setCollectionName(java.lang.String collectionName)
public java.util.Hashtable getAtomSetCollectionAuxiliaryInfo()
public void setIsPDB()
public int getAtomCount()
public Atom[] getAtoms()
public Atom getAtom(int i)
public int getBondCount()
public Bond[] getBonds()
public Bond getBond(int i)
public int getStructureCount()
public Structure[] getStructures()
public int getAtomSetCount()
public int getCurrentAtomSetIndex()
public void setCurrentAtomSetIndex(int i)
public void setDoFixPeriodic()
private void appendAtomSetCollection(java.util.List list)
public void setTrajectory()
protected void appendAtomSetCollection(int collectionIndex, AtomSetCollection collection)
collectionIndex
- collection index for new model numbercollection
- AtomSetCollection to appendvoid setNoAutoBond()
void finish()
void freeze()
public void discardPreviousAtoms()
public void removeAtomSet()
public void cloneFirstAtomSet() 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 cloneLastAtomSet(int atomCount) throws java.lang.Exception
java.lang.Exception
public int getFirstAtomSetAtomCount()
public int getLastAtomSetAtomCount()
public int getLastAtomSetAtomIndex()
public Atom addNewAtom()
public void addAtom(Atom atom)
public void addAtomWithMappedName(Atom atom)
public void addAtomWithMappedSerialNumber(Atom atom)
public Bond addNewBond(int atomIndex1, int atomIndex2)
Bond addNewBond(java.lang.String atomName1, java.lang.String atomName2)
public Bond addNewBond(int atomIndex1, int atomIndex2, int order)
public Bond addNewBond(java.lang.String atomName1, java.lang.String atomName2, int order)
public Bond addNewBondWithMappedSerialNumbers(int atomSerial1, int atomSerial2, int order)
public void addConnection(int[] is)
public void connectAll(int maxSerial)
public void addBond(Bond bond)
public void addStructure(Structure structure)
public void addVibrationVector(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)
void setCoordinatesAreFractional(boolean coordinatesAreFractional)
void setSymmetryRange(float factor)
void setLatticeCells(int[] latticeCells, boolean applySymmetryToBonds, boolean doPackUnitCell)
private SymmetryInterface getSymmetry()
public void setNotionalUnitCell(float[] info, javax.vecmath.Matrix3f matUnitCellOrientation, javax.vecmath.Point3f unitCellOffset)
void setGlobalBoolean(int globalIndex)
boolean addSpaceGroupOperation(java.lang.String xyz)
public void setLatticeParameter(int latt)
void applySymmetry() throws java.lang.Exception
java.lang.Exception
void applySymmetry(SymmetryInterface symmetry) throws java.lang.Exception
java.lang.Exception
private void applySymmetry(int maxX, int maxY, int maxZ) throws java.lang.Exception
java.lang.Exception
private void setSymmetryMinMax(javax.vecmath.Point3f c)
private boolean isInSymmetryRange(javax.vecmath.Point3f c)
private static boolean isWithinCell(javax.vecmath.Point3f pt, int minX, int maxX, int minY, int maxY, int minZ, int maxZ)
public void setAnisoBorU(Atom atom, float[] data, int type)
public float[] getAnisoBorU(Atom atom)
private void applyAllSymmetry(int maxX, int maxY, int maxZ) throws java.lang.Exception
java.lang.Exception
private void setSymmetryOps()
public void setCheckSpecial(boolean TF)
private int symmetryAddAtoms(int iAtomFirst, int noSymmetryCount, int transX, int transY, int transZ, int baseCount, int pt, int iCellOpPt) throws java.lang.Exception
java.lang.Exception
public void applySymmetry(java.util.List biomts, float[] notionalUnitCell, boolean applySymmetryToBonds, java.lang.String filter)
void mapMostRecentAtomName()
public void clearSymbolicMap()
void mapMostRecentAtomSerialNumber()
public void createAtomSerialMap()
void mapAtomName(java.lang.String atomName, int atomIndex)
public int getAtomNameIndex(java.lang.String atomName)
public int getAtomSerialNumberIndex(int serialNumber)
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 javax.vecmath.Point3f fixPeriodic(javax.vecmath.Point3f pt, javax.vecmath.Point3f pt0)
private float fixPoint(float x, float x0)
void finalizeTrajectory(java.util.List trajectorySteps)
private void finalizeTrajectory(boolean addStep)
public void newAtomSet()
public void setAtomSetName(java.lang.String atomSetName)
atomSetName
- The name to be associated with the current AtomSetpublic void setAtomSetNames(java.lang.String atomSetName, int n)
atomSetName
- The namen
- The number of last AtomSets that needs these setpublic void setAtomSetNumber(int atomSetNumber)
atomSetNumber
- The number for the current AtomSet.public void setAtomSetProperty(java.lang.String key, java.lang.String value)
key
- The key for the propertyvalue
- The value to be associated with the keypublic void setAtomSetProperty(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 setAtomSetAuxiliaryProperty(java.lang.String key, java.lang.String data)
private void appendAtomProperties(int nTimes)
public void setAtomSetAuxiliaryInfo(java.lang.String key, java.lang.Object value)
key
- The key for the propertyvalue
- The value to be associated with the keyboolean setAtomSetPartialCharges(java.lang.String auxKey)
auxKey
- The auxiliary key name that contains the chargesjava.lang.Object getAtomSetAuxiliaryInfo(int index, java.lang.String key)
void setAtomSetAuxiliaryInfo(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 setAtomSetProperties(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.Hashtable getAtomSetAuxiliaryInfo(int atomSetIndex)
boolean hasAlternateLocations()
void getAltLocLists()
boolean hasInsertions()
void getInsertionLists()
public void newVolumeData()
public void setVoxelCounts(int nPointsX, int nPointsY, int nPointsZ)
public void setVolumetricVector(int i, float x, float y, float z)
public void setVolumetricOrigin(float x, float y, float z)
public void setVoxelData(float[][][] voxelData)
public java.lang.Object getVolumeData()
public java.util.Properties setAtomNames(java.util.Properties atomIdNames)
public void setAtomSetEnergy(java.lang.String energyString, float value)
public void setAtomSetFrequency(java.lang.String pathKey, java.lang.String label, java.lang.String freq, java.lang.String units)
void toCartesian(SymmetryInterface symmetry)