org.jmol.adapter.smarter
public class AtomSetCollection extends Object
| Constructor Summary | |
|---|---|
| AtomSetCollection(String fileTypeName) | |
| AtomSetCollection(AtomSetCollection[] array)
Creates an AtomSetCollection based on an array of AtomSetCollection
| |
| AtomSetCollection(Vector list)
Creates an AtomSetCollection based on a Vector of
AtomSetCollection or Vector (from zipped zip files)
| |
| Method Summary | |
|---|---|
| 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
|
| 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
|
| void | setAtomSetAuxiliaryInfo(String key, Object value, int atomSetIndex)
Sets auxiliary information for the an AtomSet
|
| void | setAtomSetCollectionAuxiliaryInfo(String key, Object value) |
| boolean | setAtomSetCollectionPartialCharges(String auxKey)
Sets the partial atomic charges based on atomSetCollection auxiliary info
|
| void | setAtomSetCollectionProperty(String key, String value)
Sets a property for the AtomSetCollection |
| void | setAtomSetName(String atomSetName)
Sets the name for the current AtomSet
|
| void | setAtomSetName(String atomSetName, int atomSetIndex)
Sets the name for an 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
|
| 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)
Sets a property for the AtomSet
|
| void | setAtomSetProperty(String key, String value, int atomSetIndex)
Sets the a property for the an AtomSet
|
| 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