org.jmol.adapter.smarter
public class AtomSetCollection extends Object
Modifier and Type | Field and Description |
---|---|
boolean |
allowMultiple |
(package private) boolean |
applySymmetryToBonds |
private int |
atomCount |
private Atom[] |
atoms |
private int[] |
atomSetAtomCounts |
private Map<String,Object>[] |
atomSetAuxiliaryInfo |
private int[] |
atomSetBondCounts |
private Map<String,Object> |
atomSetCollectionAuxiliaryInfo |
private int |
atomSetCount |
private int[] |
atomSetNumbers |
(package private) Map<Object,Integer> |
atomSymbolicMap |
private int |
baseSymmetryAtomCount |
private int |
bondCount |
(package private) int |
bondCount0 |
(package private) int |
bondIndex0 |
private Bond[] |
bonds |
BitSet |
bsAtoms |
(package private) Point3f[] |
cartesians |
(package private) boolean |
checkSpecial |
private String |
collectionName |
(package private) int[] |
connectLast |
(package private) int |
connectNextAtomIndex |
(package private) int |
connectNextAtomSet |
boolean |
coordinatesAreFractional |
private int |
currentAtomSetIndex |
(package private) boolean |
doFixPeriodic |
(package private) boolean |
doNormalize |
(package private) boolean |
doPackUnitCell |
private int |
dtype |
String |
errorMessage |
private String |
fileTypeName |
float[] |
fmatSuperCell |
private static int |
GLOBAL_CONECT |
static int |
GLOBAL_FRACTCOORD |
(package private) static int |
GLOBAL_ISPDB |
static int |
GLOBAL_SYMMETRY |
static int |
GLOBAL_UNITCELLS |
private static String[] |
globalBooleans |
(package private) boolean |
haveMappedSerials |
(package private) boolean |
haveUnitCell |
private boolean |
isTrajectory |
private int[] |
latticeCells |
private Point3i |
maxXYZ |
private Point3i |
maxXYZ0 |
private Point3i |
minXYZ |
private Point3i |
minXYZ0 |
private boolean |
needEllipsoids |
float[] |
notionalUnitCell |
static String[] |
notionalUnitcellTags |
private Point3f |
ptOffset |
private Point3f |
ptTemp |
private Point3f |
ptTemp1 |
private 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 List<String> |
trajectoryNames |
private int |
trajectoryStepCount |
private List<Point3f[]> |
trajectorySteps |
Point3f |
unitCellOffset |
private Vector3f[] |
unitCellTranslations |
(package private) List<int[]> |
vConnect |
private List<Vector3f[]> |
vibrationSteps |
Constructor and Description |
---|
AtomSetCollection(AtomSetCollection[] array)
Creates an AtomSetCollection based on an array of AtomSetCollection
|
AtomSetCollection(List<?> list)
Creates an AtomSetCollection based on a Vector of
AtomSetCollection or Vector (from zipped zip files)
|
AtomSetCollection(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(String atomName1,
String atomName2) |
Bond |
addNewBond(String atomName1,
String atomName2,
int order) |
Bond |
addNewBondWithMappedSerialNumbers(int atomSerial1,
int atomSerial2,
int order) |
(package private) boolean |
addSpaceGroupOperation(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(List<?> list) |
private void |
applyAllSymmetry() |
(package private) void |
applySymmetry() |
private void |
applySymmetry(int maxX,
int maxY,
int maxZ) |
void |
applySymmetry(List<Matrix4f> biomts,
float[] notionalUnitCell,
boolean applySymmetryToBonds,
String filter) |
(package private) void |
applySymmetry(SymmetryInterface symmetry) |
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 atomCount) |
void |
cloneFirstAtomSetWithBonds(int nBonds) |
void |
cloneLastAtomSet() |
void |
cloneLastAtomSet(int atomCount,
Point3f[] pts) |
void |
cloneLastAtomSetProperties()
Clones the properties of the last atom set and associates it
with the current atom set.
|
void |
connectAll(int maxSerial,
boolean isConnectStateBug) |
private void |
connectAllBad(int maxSerial) |
void |
createAtomSerialMap() |
void |
discardPreviousAtoms() |
private void |
finalizeTrajectory() |
(package private) void |
finalizeTrajectory(List<Point3f[]> trajectorySteps,
List<Vector3f[]> vibrationSteps) |
(package private) void |
finish() |
private static Point3f |
fixPeriodic(Point3f pt,
Point3f pt0) |
private static float |
fixPoint(float x,
float x0) |
(package private) void |
freeze() |
float[] |
getAnisoBorU(Atom atom) |
Atom |
getAtom(int i) |
int |
getAtomCount() |
int |
getAtomNameIndex(String atomName) |
Atom[] |
getAtoms() |
int |
getAtomSerialNumberIndex(int serialNumber) |
(package private) Map<String,Object> |
getAtomSetAuxiliaryInfo(int atomSetIndex) |
private Object |
getAtomSetAuxiliaryInfo(int index,
String key) |
Map<String,Object> |
getAtomSetCollectionAuxiliaryInfo() |
Object |
getAtomSetCollectionAuxiliaryInfo(String key) |
int |
getAtomSetCount() |
(package private) String |
getAtomSetName(int atomSetIndex) |
(package private) int |
getAtomSetNumber(int atomSetIndex) |
Bond |
getBond(int i) |
int |
getBondCount() |
String[][] |
getBondList() |
Bond[] |
getBonds() |
String |
getCollectionName() |
int |
getCurrentAtomSetIndex() |
String |
getFileTypeName() |
int |
getFirstAtomSetAtomCount() |
int |
getHydrogenAtomCount() |
int |
getLastAtomSetAtomCount() |
int |
getLastAtomSetAtomIndex() |
private void |
getList(boolean isAltLoc) |
int |
getStructureCount() |
Structure[] |
getStructures() |
SymmetryInterface |
getSymmetry() |
private boolean |
isInSymmetryRange(Point3f c) |
private static boolean |
isWithinCell(int dtype,
Point3f pt,
int minX,
int maxX,
int minY,
int maxY,
int minZ,
int maxZ) |
(package private) void |
mapAtomName(String atomName,
int atomIndex) |
(package private) void |
mapMostRecentAtomName() |
(package private) void |
mapMostRecentAtomSerialNumber() |
void |
mapPartialCharge(String atomName,
float charge) |
void |
newAtomSet() |
(package private) Atom |
newCloneAtom(Atom atom) |
void |
removeAtomSet() |
void |
setAnisoBorU(Atom atom,
float[] data,
int type) |
Properties |
setAtomNames(Properties atomIdNames) |
void |
setAtomSetAtomProperty(String key,
String data) |
void |
setAtomSetAuxiliaryInfo(String key,
Object value)
Sets auxiliary information for the AtomSet
|
(package private) void |
setAtomSetAuxiliaryInfo(String key,
Object value,
int atomSetIndex)
Sets auxiliary information for an AtomSet
|
void |
setAtomSetCollectionAuxiliaryInfo(String key,
Object value) |
boolean |
setAtomSetCollectionPartialCharges(String auxKey)
Sets the partial atomic charges based on atomSetCollection auxiliary info
|
void |
setAtomSetEnergy(String energyString,
float value) |
void |
setAtomSetFrequency(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
moleular energies
|
void |
setAtomSetName(String atomSetName)
Sets the name for the current AtomSet
|
void |
setAtomSetNames(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(String auxKey)
Sets the partial atomic charges based on atomSet auxiliary info
|
void |
setAtomSetProperties(String key,
String value,
int n)
Sets the same properties for the last n atomSets.
|
void |
setAtomSetProperty(String key,
String value,
int atomSetIndex)
Sets the a property for the an AtomSet
|
(package private) void |
setAtomSetSpaceGroupName(String spaceGroupName) |
void |
setBaseSymmetryAtomCount(int n) |
void |
setCheckSpecial(boolean TF) |
void |
setCollectionName(String collectionName) |
void |
setCoordinatesAreFractional(boolean coordinatesAreFractional) |
void |
setCurrentAtomSetIndex(int i) |
void |
setDoFixPeriodic() |
(package private) void |
setGlobalBoolean(int globalIndex) |
(package private) void |
setLatticeCells(int[] latticeCells,
boolean applySymmetryToBonds,
boolean doPackUnitCell,
String supercell) |
void |
setLatticeParameter(int latt) |
(package private) void |
setNoAutoBond() |
void |
setNotionalUnitCell(float[] info,
Matrix3f matUnitCellOrientation,
Point3f unitCellOffset) |
float[] |
setSuperCell(String supercell,
float[] fmat) |
private Point3f |
setSym(int i,
int j,
int k) |
private void |
setSymmetryMinMax(Point3f c) |
private void |
setSymmetryOps() |
(package private) void |
setSymmetryRange(float factor) |
void |
setTrajectory() |
private void |
setTrajectoryName(String name) |
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 String fileTypeName
private String collectionName
public BitSet bsAtoms
private static final 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
static final int GLOBAL_ISPDB
public static final 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 int[] latticeCells
public String errorMessage
public boolean coordinatesAreFractional
private boolean isTrajectory
private int trajectoryStepCount
boolean doFixPeriodic
public float[] notionalUnitCell
public boolean allowMultiple
List<int[]> vConnect
int connectNextAtomIndex
int connectNextAtomSet
int[] connectLast
float symmetryRange
public float[] fmatSuperCell
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 Point3f ptOffset
public Point3f unitCellOffset
private Point3i minXYZ
private Point3i maxXYZ
private Point3i minXYZ0
private Point3i maxXYZ0
private boolean needEllipsoids
private int dtype
private Vector3f[] unitCellTranslations
private int baseSymmetryAtomCount
Point3f[] cartesians
int bondCount0
int bondIndex0
boolean applySymmetryToBonds
boolean checkSpecial
private final Point3f ptTemp
private final Point3f ptTemp1
private final Point3f ptTemp2
boolean haveMappedSerials
public AtomSetCollection(String fileTypeName, AtomSetCollectionReader atomSetCollectionReader)
public AtomSetCollection(AtomSetCollection[] array)
array
- Array of AtomSetCollectionpublic AtomSetCollection(List<?> list)
list
- Vector of AtomSetCollectionpublic String getFileTypeName()
public String getCollectionName()
public void setCollectionName(String collectionName)
public void clearGlobalBoolean(int globalIndex)
void setGlobalBoolean(int globalIndex)
public int getAtomCount()
public int getHydrogenAtomCount()
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(List<?> list)
public void setTrajectory()
protected void appendAtomSetCollection(int collectionIndex, AtomSetCollection collection)
collectionIndex
- collection index for new model numbercollection
- AtomSetCollection to appendvoid setNoAutoBond()
void freeze()
private void getList(boolean isAltLoc)
void finish()
public void discardPreviousAtoms()
public void removeAtomSet()
public void cloneFirstAtomSetWithBonds(int nBonds) throws Exception
Exception
public void cloneLastAtomSet(int atomCount, Point3f[] pts) throws Exception
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)
public Bond addNewBond(int atomIndex1, int atomIndex2, int order)
public Bond addNewBondWithMappedSerialNumbers(int atomSerial1, int atomSerial2, int order)
public void addConnection(int[] is)
private void connectAllBad(int maxSerial)
public void connectAll(int maxSerial, boolean isConnectStateBug)
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(String spaceGroupName)
public void setCoordinatesAreFractional(boolean coordinatesAreFractional)
void setSymmetryRange(float factor)
void setLatticeCells(int[] latticeCells, boolean applySymmetryToBonds, boolean doPackUnitCell, String supercell)
public float[] setSuperCell(String supercell, float[] fmat)
public SymmetryInterface getSymmetry()
public void setNotionalUnitCell(float[] info, Matrix3f matUnitCellOrientation, Point3f unitCellOffset)
boolean addSpaceGroupOperation(String xyz)
public void setLatticeParameter(int latt)
void applySymmetry(SymmetryInterface symmetry) throws Exception
Exception
private void applySymmetry(int maxX, int maxY, int maxZ) throws Exception
Exception
private Point3f setSym(int i, int j, int k)
private void setSymmetryMinMax(Point3f c)
private boolean isInSymmetryRange(Point3f c)
private static boolean isWithinCell(int dtype, 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)
public void setBaseSymmetryAtomCount(int n)
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 Exception
Exception
public void applySymmetry(List<Matrix4f> biomts, float[] notionalUnitCell, boolean applySymmetryToBonds, String filter)
void mapMostRecentAtomName()
public void clearSymbolicMap()
void mapMostRecentAtomSerialNumber()
public void createAtomSerialMap()
void mapAtomName(String atomName, int atomIndex)
public int getAtomNameIndex(String atomName)
public int getAtomSerialNumberIndex(int serialNumber)
public void setAtomSetCollectionAuxiliaryInfo(String key, Object value)
public boolean setAtomSetCollectionPartialCharges(String auxKey)
auxKey
- The auxiliary key name that contains the chargespublic void mapPartialCharge(String atomName, float charge)
private void addTrajectoryStep()
private static float fixPoint(float x, float x0)
void finalizeTrajectory(List<Point3f[]> trajectorySteps, List<Vector3f[]> vibrationSteps)
private void finalizeTrajectory()
public void newAtomSet()
public void setAtomSetName(String atomSetName)
atomSetName
- The name to be associated with the current AtomSetprivate void setTrajectoryName(String name)
public void setAtomSetNames(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 setAtomSetModelProperty(String key, String value)
key
- The key for the propertyvalue
- The value to be associated with the keypublic void setAtomSetProperty(String key, String value, int atomSetIndex)
key
- The key for the propertyvalue
- The value for the propertyatomSetIndex
- The index of the AtomSet to get the propertyprivate void appendAtomProperties(int nTimes)
public void setAtomSetAuxiliaryInfo(String key, Object value)
key
- The key for the propertyvalue
- The value to be associated with the keyboolean setAtomSetPartialCharges(String auxKey)
auxKey
- The auxiliary key name that contains the chargesvoid setAtomSetAuxiliaryInfo(String key, 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(String key, 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)
String getAtomSetName(int atomSetIndex)
public Properties setAtomNames(Properties atomIdNames)
public void setAtomSetEnergy(String energyString, float value)
public void setAtomSetFrequency(String pathKey, String label, String freq, String units)
void toCartesian(SymmetryInterface symmetry)
public String[][] getBondList()