org.jmol.modelset
public final class Model extends Object
| Field Summary | |
|---|---|
| int | atomCount |
| Hashtable | auxiliaryInfo |
| int | bioPolymerCount |
| Polymer[] | bioPolymers |
| int | biosymmetryCount |
| int | bondCount |
| BitSet | bsAtoms |
| int | chainCount |
| Chain[] | chains |
| Hashtable | dataFrames |
| int | dataSourceFrame |
| float | defaultRotationRadius |
| int | fileIndex |
| int | firstAtomIndex |
| int | firstMolecule |
| int | groupCount |
| boolean | hasCalculatedHBonds |
| boolean | isPDB |
| boolean | isTrajectory |
| String | jmolData |
| String | jmolFrameType |
| int | modelIndex |
| ModelSet | modelSet |
| int | moleculeCount |
| int | nAltLocs |
| int | nInsertions |
| StateManager.Orientation | orientation |
| Properties | properties |
| int | selectedTrajectory |
| boolean | structureTainted |
| int | trajectoryBaseIndex |
| Constructor Summary | |
|---|---|
| Model(ModelSet modelSet, int modelIndex, int trajectoryBaseIndex, String jmolData, Properties properties, Hashtable auxiliaryInfo) | |
| Method Summary | |
|---|---|
| void | addHydrogenBond(Atom atom1, Atom atom2, short order, BitSet bsA, BitSet bsB) |
| void | addSecondaryStructure(byte type, char startChainID, int startSeqcode, char endChainID, int endSeqcode) |
| void | calcHydrogenBonds(BitSet bsA, BitSet bsB) |
| void | calcSelectedGroupsCount(BitSet bsSelected) |
| void | calcSelectedMonomersCount(BitSet bsSelected) |
| void | calculateStructures() |
| void | fixIndices(int modelIndex, int nAtomsDeleted, BitSet bsDeleted) |
| Polymer | getBioPolymer(int polymerIndex) |
| int | getBioPolymerCount() |
| Chain | getChain(char chainID) |
| Chain | getChain(int i) |
| int | getChainCount(boolean countWater) |
| Chain[] | getChains() |
| int | getGroupCount(boolean isHetero) |
| int | getGroupCount() |
| int | getModelIndex() |
| ModelSet | getModelSet()
BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT FINALIZATION
AND CREATE A MEMORY LEAK.
|
| boolean | isAtomHidden(int index) |
| boolean | isStructureTainted() |
| void | selectSeqcodeRange(int seqcodeA, int seqcodeB, char chainID, BitSet bs, boolean caseSensitive) |
| void | setConformation(BitSet bsConformation) |
| void | setNAltLocs(int nAltLocs) |
| void | setNInsertions(int nInsertions) |
Returns: associated ModelSet