org.jmol.modelset
public final class Model extends Object
Field Summary | |
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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 | |
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Model(ModelSet modelSet, int modelIndex, int trajectoryBaseIndex, String jmolData, Properties properties, Hashtable auxiliaryInfo) |
Method Summary | |
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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