org.jmol.adapter.smarter
public class AtomSetCollection extends Object
Constructor Summary | |
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AtomSetCollection(String fileTypeName) | |
AtomSetCollection(AtomSetCollection[] array)
Creates an AtomSetCollection based on an array of AtomSetCollection
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AtomSetCollection(Vector list)
Creates an AtomSetCollection based on a Vector of
AtomSetCollection or Vector (from zipped zip files)
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Method Summary | |
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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(String atomName1, String atomName2) |
Bond | addNewBond(int atomIndex1, int atomIndex2, int order) |
Bond | addNewBond(String atomName1, String atomName2, int order) |
Bond | addNewBondWithMappedSerialNumbers(int atomSerial1, int atomSerial2, int order) |
boolean | addSpaceGroupOperation(String xyz) |
void | addStructure(Structure structure) |
void | addTrajectory() |
void | appendAtomSetCollection(Vector list) |
protected void | appendAtomSetCollection(int collectionIndex, AtomSetCollection collection)
Appends an AtomSetCollection
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void | applyAllSymmetry(int maxX, int maxY, int maxZ) |
void | applySymmetry() |
void | applySymmetry(SymmetryInterface symmetry) |
void | applySymmetry(int maxX, int maxY, int maxZ) |
void | applySymmetry(Vector biomts, boolean applySymmetryToBonds, String filter) |
void | clearSymbolicMap() |
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 | 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() |
void | finalizeTrajectories() |
void | finish() |
void | freeze() |
void | getAltLocLists() |
Atom | getAtom(int i) |
int | getAtomCount() |
int | getAtomNameIndex(String atomName) |
Atom[] | getAtoms() |
int | getAtomSerialNumberIndex(int serialNumber) |
Object | getAtomSetAuxiliaryInfo(int index, String key) |
Hashtable | getAtomSetAuxiliaryInfo(int atomSetIndex) |
Object | getAtomSetCollectionAuxiliaryInfo(String key) |
String | getAtomSetCollectionProperty(String key) |
int | getAtomSetCount() |
String | getAtomSetName(int atomSetIndex) |
int | getAtomSetNumber(int atomSetIndex) |
Properties | getAtomSetProperties(int atomSetIndex) |
Bond | getBond(int i) |
int | getBondCount() |
Bond[] | getBonds() |
int | getCurrentAtomSetIndex() |
int | getFirstAtomSetAtomCount() |
void | getInsertionLists() |
int | getLastAtomSetAtomCount() |
int | getLastAtomSetAtomIndex() |
SymmetryInterface | getSymmetry() |
Object | getVolumeData() |
boolean | hasAlternateLocations() |
boolean | hasInsertions() |
boolean | isInSymmetryRange(Point3f c) |
void | mapAtomName(String atomName, int atomIndex) |
void | mapMostRecentAtomName() |
void | mapMostRecentAtomSerialNumber() |
void | mapPartialCharge(String atomName, float charge) |
void | newAtomSet() |
Atom | newCloneAtom(Atom atom) |
void | newVolumeData() |
void | removeAtomSet() |
void | setApplySymmetryToBonds(boolean TF) |
Properties | setAtomNames(Properties atomIdNames) |
void | setAtomSetAuxiliaryInfo(String key, Object value)
Sets auxiliary information for the AtomSet
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void | setAtomSetAuxiliaryInfo(String key, Object value, int atomSetIndex)
Sets auxiliary information for the an AtomSet
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void | setAtomSetCollectionAuxiliaryInfo(String key, Object value) |
boolean | setAtomSetCollectionPartialCharges(String auxKey)
Sets the partial atomic charges based on atomSetCollection auxiliary info
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void | setAtomSetCollectionProperty(String key, String value)
Sets a property for the AtomSetCollection |
void | setAtomSetName(String atomSetName)
Sets the name for the current AtomSet
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void | setAtomSetName(String atomSetName, int atomSetIndex)
Sets the name for an AtomSet
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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
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boolean | setAtomSetPartialCharges(String auxKey)
Sets the partial atomic charges based on atomSet auxiliary info
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void | setAtomSetProperties(String key, String value, int n)
Sets the same properties for the last n atomSets. |
void | setAtomSetProperty(String key, String value)
Sets a property for the AtomSet
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void | setAtomSetProperty(String key, String value, int atomSetIndex)
Sets the a property for the an AtomSet
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void | setAtomSetSpaceGroupName(String spaceGroupName) |
void | setCheckSpecial(boolean TF) |
void | setCollectionName(String collectionName) |
void | setCoordinatesAreFractional(boolean coordinatesAreFractional) |
void | setFileTypeName(String type)
Just sets the overall file type after the fact. |
void | setGlobalBoolean(int globalIndex) |
void | setLatticeCells(int[] latticeCells, boolean applySymmetryToBonds) |
void | setLatticeParameter(int latt) |
boolean | setNotionalUnitCell(float[] info) |
void | setSymmetryMinMax(Point3f c) |
void | setSymmetryRange(float factor) |
boolean | 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) |
int | symmetryAddAtoms(int iAtomFirst, int noSymmetryCount, int transX, int transY, int transZ, int baseCount, int pt, int iCellOpPt) |
Parameters: array Array of AtomSetCollection
Parameters: list Vector of AtomSetCollection
Parameters: collectionIndex collection index for new model number collection AtomSetCollection to append
Parameters: index The index of the atom set whose properties are to be cloned.
Parameters: key The key for the property value The value to be associated with the key
Parameters: key The key for the property value The value for the property atomSetIndex The index of the AtomSet to get the property
Parameters: auxKey The auxiliary key name that contains the charges
Returns: true if the data exist; false if not
Parameters: key The poperty key. value The property value.
Parameters: atomSetName The name to be associated with the current AtomSet
Parameters: atomSetName The number to be associated with the AtomSet atomSetIndex The index of the AtomSet that needs the association
Parameters: atomSetName The name n The number of last AtomSets that need these set
Parameters: atomSetNumber The number for the current AtomSet.
Parameters: auxKey The auxiliary key name that contains the charges
Returns: true if the data exist; false if not
Parameters: key The key for the property value The value of the property n The number of last AtomSets that need these set
Parameters: key The key for the property value The value to be associated with the key
Parameters: key The key for the property value The value for the property atomSetIndex The index of the AtomSet to get the property
Parameters: type