org.jmol.modelset
public final class Model extends Object
Modifier and Type | Field and Description |
---|---|
(package private) int |
atomCount |
(package private) Map<String,Object> |
auxiliaryInfo |
(package private) int |
bioPolymerCount |
(package private) Polymer[] |
bioPolymers |
(package private) int |
biosymmetryCount |
private int |
bondCount |
(package private) BitSet |
bsAtoms |
(package private) BitSet |
bsAtomsDeleted |
(package private) int |
chainCount |
(package private) Chain[] |
chains |
(package private) Map<String,Integer> |
dataFrames |
(package private) int |
dataSourceFrame |
(package private) float |
defaultRotationRadius |
(package private) String |
defaultStructure |
(package private) int |
fileIndex |
(package private) int |
firstAtomIndex |
(package private) int |
firstMoleculeIndex |
(package private) int |
groupCount |
(package private) boolean |
hasRasmolHBonds |
int |
hydrogenCount |
(package private) boolean |
isJmolDataFrame |
(package private) boolean |
isModelKit |
boolean |
isPDB |
boolean |
isPdbWithMultipleBonds |
(package private) boolean |
isTrajectory |
(package private) String |
jmolData |
(package private) String |
jmolFrameType |
(package private) StringBuffer |
loadScript |
(package private) String |
loadState |
int |
modelIndex |
(package private) ModelSet |
modelSet |
(package private) int |
moleculeCount |
int |
nAltLocs |
(package private) int |
nInsertions |
(package private) StateManager.Orientation |
orientation |
(package private) Properties |
properties |
(package private) int |
selectedTrajectory |
(package private) boolean |
structureTainted |
(package private) int |
trajectoryBaseIndex |
Constructor and Description |
---|
Model(ModelSet modelSet,
int modelIndex,
int trajectoryBaseIndex,
String jmolData,
Properties properties,
Map<String,Object> auxiliaryInfo) |
Modifier and Type | Method and Description |
---|---|
(package private) void |
addSecondaryStructure(EnumStructure type,
String structureID,
int serialID,
int strandCount,
char startChainID,
int startSeqcode,
char endChainID,
int endSeqcode) |
(package private) void |
calcSelectedGroupsCount(BitSet bsSelected) |
(package private) void |
calcSelectedMonomersCount(BitSet bsSelected) |
(package private) String |
calculateStructures(boolean asDSSP,
boolean doReport,
boolean dsspIgnoreHydrogen,
boolean setStructure,
boolean includeAlpha) |
(package private) void |
fixIndices(int modelIndex,
int nAtomsDeleted,
BitSet bsDeleted) |
Polymer |
getBioPolymer(int polymerIndex) |
int |
getBioPolymerCount() |
(package private) int |
getBondCount() |
(package private) Chain |
getChain(char chainID) |
(package private) Chain |
getChain(int i) |
int |
getChainCount(boolean countWater) |
Chain[] |
getChains() |
(package private) void |
getDefaultLargePDBRendering(StringBuffer sb,
int maxAtoms) |
(package private) int |
getGroupCount() |
int |
getGroupCount(boolean isHetero) |
int |
getModelIndex() |
String |
getModelNumberDotted() |
ModelSet |
getModelSet()
BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT FINALIZATION
AND CREATE A MEMORY LEAK.
|
String |
getModelTitle() |
(package private) boolean |
getPdbConformation(BitSet bsConformation,
int conformationIndex) |
int |
getTrueAtomCount() |
boolean |
isAtomHidden(int index) |
boolean |
isModelkit() |
boolean |
isStructureTainted() |
void |
resetBoundCount() |
(package private) void |
selectSeqcodeRange(int seqcodeA,
int seqcodeB,
char chainID,
BitSet bs,
boolean caseSensitive) |
(package private) void |
setConformation(BitSet bsConformation) |
(package private) void |
setNAltLocs(int nAltLocs) |
(package private) void |
setNInsertions(int nInsertions) |
ModelSet modelSet
public int modelIndex
int fileIndex
public int hydrogenCount
public boolean isPDB
public boolean isPdbWithMultipleBonds
String loadState
StringBuffer loadScript
boolean isModelKit
boolean isTrajectory
int trajectoryBaseIndex
int selectedTrajectory
boolean hasRasmolHBonds
int dataSourceFrame
String jmolData
String jmolFrameType
int firstAtomIndex
int atomCount
final BitSet bsAtoms
final BitSet bsAtomsDeleted
private int bondCount
int firstMoleculeIndex
int moleculeCount
public int nAltLocs
int nInsertions
int groupCount
int chainCount
Chain[] chains
int bioPolymerCount
Polymer[] bioPolymers
int biosymmetryCount
Properties properties
float defaultRotationRadius
String defaultStructure
StateManager.Orientation orientation
boolean structureTainted
boolean isJmolDataFrame
public ModelSet getModelSet()
public boolean isModelkit()
public int getTrueAtomCount()
public void resetBoundCount()
int getBondCount()
void setNAltLocs(int nAltLocs)
void setNInsertions(int nInsertions)
void addSecondaryStructure(EnumStructure type, String structureID, int serialID, int strandCount, char startChainID, int startSeqcode, char endChainID, int endSeqcode)
public String getModelNumberDotted()
public String getModelTitle()
String calculateStructures(boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha)
public boolean isStructureTainted()
void setConformation(BitSet bsConformation)
boolean getPdbConformation(BitSet bsConformation, int conformationIndex)
public Chain[] getChains()
public int getChainCount(boolean countWater)
public int getGroupCount(boolean isHetero)
public int getBioPolymerCount()
void calcSelectedGroupsCount(BitSet bsSelected)
void calcSelectedMonomersCount(BitSet bsSelected)
void selectSeqcodeRange(int seqcodeA, int seqcodeB, char chainID, BitSet bs, boolean caseSensitive)
int getGroupCount()
Chain getChain(char chainID)
Chain getChain(int i)
public Polymer getBioPolymer(int polymerIndex)
void getDefaultLargePDBRendering(StringBuffer sb, int maxAtoms)
public boolean isAtomHidden(int index)
public int getModelIndex()
void fixIndices(int modelIndex, int nAtomsDeleted, BitSet bsDeleted)