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.Hashtable auxiliaryInfo)
|
Method Summary |
void |
addHydrogenBond(Atom atom1,
Atom atom2,
short order,
java.util.BitSet bsA,
java.util.BitSet bsB,
float energy)
|
(package private) void |
addSecondaryStructure(byte type,
java.lang.String structureID,
int serialID,
int strandCount,
char startChainID,
int startSeqcode,
char endChainID,
int endSeqcode)
|
(package private) void |
calcHydrogenBonds(java.util.BitSet bsA,
java.util.BitSet bsB)
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(package private) void |
calcSelectedGroupsCount(java.util.BitSet bsSelected)
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(package private) void |
calcSelectedMonomersCount(java.util.BitSet bsSelected)
|
(package private) void |
calculateStructures()
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(package private) void |
fixIndices(int modelIndex,
int nAtomsDeleted,
java.util.BitSet bsDeleted)
|
Polymer |
getBioPolymer(int polymerIndex)
|
int |
getBioPolymerCount()
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(package private) int |
getBondCount()
|
(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) int |
getGroupCount()
|
int |
getGroupCount(boolean isHetero)
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int |
getModelIndex()
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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 |
resetBoundCount()
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(package private) void |
selectSeqcodeRange(int seqcodeA,
int seqcodeB,
char chainID,
java.util.BitSet bs,
boolean caseSensitive)
|
(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
int modelIndex
fileIndex
int fileIndex
isPDB
boolean isPDB
isTrajectory
boolean isTrajectory
trajectoryBaseIndex
int trajectoryBaseIndex
selectedTrajectory
int selectedTrajectory
hasCalculatedHBonds
boolean hasCalculatedHBonds
dataFrames
java.util.Hashtable 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
bondCount
private int bondCount
firstMolecule
int firstMolecule
moleculeCount
int moleculeCount
nAltLocs
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.Hashtable auxiliaryInfo
properties
java.util.Properties properties
defaultRotationRadius
float defaultRotationRadius
orientation
StateManager.Orientation orientation
structureTainted
boolean structureTainted
Model
Model(ModelSet modelSet,
int modelIndex,
int trajectoryBaseIndex,
java.lang.String jmolData,
java.util.Properties properties,
java.util.Hashtable auxiliaryInfo)
getModelSet
public ModelSet getModelSet()
- BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT FINALIZATION
AND CREATE A MEMORY LEAK.
- Returns:
- associated ModelSet
resetBoundCount
public void resetBoundCount()
getBondCount
int getBondCount()
setNAltLocs
void setNAltLocs(int nAltLocs)
setNInsertions
void setNInsertions(int nInsertions)
addSecondaryStructure
void addSecondaryStructure(byte type,
java.lang.String structureID,
int serialID,
int strandCount,
char startChainID,
int startSeqcode,
char endChainID,
int endSeqcode)
calculateStructures
void calculateStructures()
isStructureTainted
public boolean isStructureTainted()
setConformation
void setConformation(java.util.BitSet bsConformation)
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)
calcHydrogenBonds
void calcHydrogenBonds(java.util.BitSet bsA,
java.util.BitSet bsB)
isAtomHidden
public boolean isAtomHidden(int index)
addHydrogenBond
public void addHydrogenBond(Atom atom1,
Atom atom2,
short order,
java.util.BitSet bsA,
java.util.BitSet bsB,
float energy)
getModelIndex
public int getModelIndex()
fixIndices
void fixIndices(int modelIndex,
int nAtomsDeleted,
java.util.BitSet bsDeleted)