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