public class Model
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
protected int |
atomCount |
protected java.util.Map<java.lang.String,java.lang.Object> |
auxiliaryInfo |
(package private) int |
biosymmetryCount |
private int |
bondCount |
protected java.util.BitSet |
bsAtoms |
(package private) java.util.BitSet |
bsAtomsDeleted |
protected int |
chainCount |
protected Chain[] |
chains |
(package private) java.util.Map<java.lang.String,java.lang.Integer> |
dataFrames |
(package private) int |
dataSourceFrame |
(package private) float |
defaultRotationRadius |
(package private) java.lang.String |
defaultStructure |
(package private) int |
fileIndex |
protected int |
firstAtomIndex |
(package private) int |
firstMoleculeIndex |
long |
frameDelay |
(package private) int |
groupCount |
protected boolean |
hasRasmolHBonds |
int |
hydrogenCount |
boolean |
isBioModel |
(package private) boolean |
isJmolDataFrame |
(package private) boolean |
isModelKit |
boolean |
isPdbWithMultipleBonds |
(package private) boolean |
isTrajectory |
(package private) java.lang.String |
jmolData |
(package private) java.lang.String |
jmolFrameType |
(package private) java.lang.StringBuffer |
loadScript |
(package private) java.lang.String |
loadState |
int |
modelIndex |
ModelSet |
modelSet |
(package private) int |
moleculeCount |
int |
nAltLocs |
(package private) int |
nInsertions |
(package private) StateManager.Orientation |
orientation |
(package private) java.util.Properties |
properties |
(package private) int |
selectedTrajectory |
protected boolean |
structureTainted |
int |
trajectoryBaseIndex |
SymmetryInterface |
unitCell |
Constructor and Description |
---|
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) |
Modifier and Type | Method and Description |
---|---|
void |
addSecondaryStructure(EnumStructure type,
java.lang.String structureID,
int serialID,
int strandCount,
char startChainID,
int startSeqcode,
char endChainID,
int endSeqcode) |
(package private) void |
calcSelectedGroupsCount(java.util.BitSet bsSelected) |
void |
calcSelectedMonomersCount(java.util.BitSet bsSelected) |
void |
calculatePolymers(Group[] groups,
int groupCount,
int baseGroupIndex,
java.util.BitSet modelsExcluded) |
void |
calculateStraightness(Viewer viewer,
char ctype,
char qtype,
int mStep) |
java.lang.String |
calculateStructures(boolean asDSSP,
boolean doReport,
boolean dsspIgnoreHydrogen,
boolean setStructure,
boolean includeAlpha) |
int |
calculateStruts(ModelSet modelSet,
java.util.BitSet bs1,
java.util.BitSet bs2) |
void |
clearBioPolymers() |
void |
clearRasmolHydrogenBonds(java.util.BitSet bsAtoms) |
void |
fixIndices(int modelIndex,
int nAtomsDeleted,
java.util.BitSet bsDeleted) |
void |
freeze() |
void |
getAllPolymerInfo(java.util.BitSet bs,
java.util.Map<java.lang.String,java.util.List<java.util.Map<java.lang.String,java.lang.Object>>> finalInfo,
java.util.List<java.util.Map<java.lang.String,java.lang.Object>> modelVector) |
java.util.List<java.util.BitSet> |
getBioBranches(java.util.List<java.util.BitSet> bioBranches) |
int |
getBioPolymerCount() |
protected int |
getBondCount() |
(package private) Chain |
getChain(char chainID) |
(package private) Chain |
getChain(int i) |
int |
getChainCount(boolean countWater) |
Chain[] |
getChains() |
void |
getChimeInfo(java.lang.StringBuffer sb,
int nHetero) |
void |
getDefaultLargePDBRendering(java.lang.StringBuffer sb,
int maxAtoms) |
java.lang.String |
getFullPDBHeader() |
(package private) int |
getGroupCount() |
int |
getGroupCount(boolean isHetero) |
void |
getGroupsWithin(int nResidues,
java.util.BitSet bs,
java.util.BitSet bsResult) |
java.lang.String |
getModelNumberDotted() |
ModelSet |
getModelSet()
BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT FINALIZATION
AND CREATE A MEMORY LEAK.
|
java.lang.String |
getModelTitle() |
boolean |
getPdbConformation(java.util.BitSet bsConformation,
int conformationIndex) |
void |
getPdbData(Viewer viewer,
java.lang.String type,
char ctype,
boolean isDraw,
java.util.BitSet bsSelected,
OutputStringBuffer sb,
LabelToken[] tokens,
java.lang.StringBuffer pdbCONECT,
java.util.BitSet bsWritten) |
javax.vecmath.Point3f[] |
getPolymerLeadMidPoints(int iPolymer) |
void |
getPolymerPointsAndVectors(java.util.BitSet bs,
java.util.List<javax.vecmath.Point3f[]> vList,
boolean isTraceAlpha,
float sheetSmoothing) |
java.lang.String |
getProteinStructureState(java.util.BitSet bsAtoms,
boolean taintedOnly,
boolean needPhiPsi,
int mode) |
void |
getRasmolHydrogenBonds(java.util.BitSet bsA,
java.util.BitSet bsB,
java.util.List<Bond> vHBonds,
boolean nucleicOnly,
int nMax,
boolean dsspIgnoreHydrogens,
java.util.BitSet bsHBonds) |
void |
getSequenceBits(java.lang.String specInfo,
java.util.BitSet bs,
java.util.BitSet bsResult) |
int |
getTrueAtomCount() |
boolean |
isModelkit() |
boolean |
isStructureTainted() |
void |
recalculateLeadMidpointsAndWingVectors() |
void |
resetBoundCount() |
void |
selectSeqcodeRange(int seqcodeA,
int seqcodeB,
char chainID,
java.util.BitSet bs,
boolean caseSensitive) |
void |
setConformation(java.util.BitSet bsConformation) |
(package private) void |
setNAltLocs(int nAltLocs) |
(package private) void |
setNInsertions(int nInsertions) |
void |
setStructureList(java.util.Map<EnumStructure,float[]> structureList) |
public ModelSet modelSet
public int modelIndex
int fileIndex
public int hydrogenCount
public boolean isBioModel
public boolean isPdbWithMultipleBonds
public int trajectoryBaseIndex
protected boolean hasRasmolHBonds
java.lang.String loadState
java.lang.StringBuffer loadScript
boolean isModelKit
boolean isTrajectory
int selectedTrajectory
java.util.Map<java.lang.String,java.lang.Integer> dataFrames
int dataSourceFrame
java.lang.String jmolData
java.lang.String jmolFrameType
protected int firstAtomIndex
protected int atomCount
protected final java.util.BitSet bsAtoms
final java.util.BitSet bsAtomsDeleted
private int bondCount
int firstMoleculeIndex
int moleculeCount
public int nAltLocs
int nInsertions
int groupCount
protected int chainCount
protected Chain[] chains
int biosymmetryCount
protected java.util.Map<java.lang.String,java.lang.Object> auxiliaryInfo
java.util.Properties properties
float defaultRotationRadius
java.lang.String defaultStructure
StateManager.Orientation orientation
protected boolean structureTainted
boolean isJmolDataFrame
public long frameDelay
public SymmetryInterface unitCell
public 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)
public ModelSet getModelSet()
public boolean isModelkit()
public int getTrueAtomCount()
public void resetBoundCount()
protected int getBondCount()
void setNAltLocs(int nAltLocs)
void setNInsertions(int nInsertions)
public java.lang.String getModelNumberDotted()
public java.lang.String getModelTitle()
public boolean isStructureTainted()
public Chain[] getChains()
public int getChainCount(boolean countWater)
public int getGroupCount(boolean isHetero)
void calcSelectedGroupsCount(java.util.BitSet bsSelected)
int getGroupCount()
Chain getChain(int i)
Chain getChain(char chainID)
public void fixIndices(int modelIndex, int nAtomsDeleted, java.util.BitSet bsDeleted)
public void freeze()
public void getPdbData(Viewer viewer, java.lang.String type, char ctype, boolean isDraw, java.util.BitSet bsSelected, OutputStringBuffer sb, LabelToken[] tokens, java.lang.StringBuffer pdbCONECT, java.util.BitSet bsWritten)
viewer
- type
- ctype
- isDraw
- bsSelected
- sb
- bsWritten
- pdbCONECT
- tokens
- public void getDefaultLargePDBRendering(java.lang.StringBuffer sb, int maxAtoms)
sb
- maxAtoms
- public java.util.List<java.util.BitSet> getBioBranches(java.util.List<java.util.BitSet> bioBranches)
bioBranches
- public void getGroupsWithin(int nResidues, java.util.BitSet bs, java.util.BitSet bsResult)
nResidues
- bs
- bsResult
- public void getSequenceBits(java.lang.String specInfo, java.util.BitSet bs, java.util.BitSet bsResult)
specInfo
- bs
- bsResult
- public void getRasmolHydrogenBonds(java.util.BitSet bsA, java.util.BitSet bsB, java.util.List<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, java.util.BitSet bsHBonds)
bsA
- bsB
- vHBonds
- nucleicOnly
- nMax
- dsspIgnoreHydrogens
- bsHBonds
- public void clearRasmolHydrogenBonds(java.util.BitSet bsAtoms)
bsAtoms
- public void clearBioPolymers()
public void calcSelectedMonomersCount(java.util.BitSet bsSelected)
bsSelected
- public void calculatePolymers(Group[] groups, int groupCount, int baseGroupIndex, java.util.BitSet modelsExcluded)
groups
- groupCount
- baseGroupIndex
- modelsExcluded
- public void getAllPolymerInfo(java.util.BitSet bs, java.util.Map<java.lang.String,java.util.List<java.util.Map<java.lang.String,java.lang.Object>>> finalInfo, java.util.List<java.util.Map<java.lang.String,java.lang.Object>> modelVector)
bs
- finalInfo
- modelVector
- public int getBioPolymerCount()
public void getPolymerPointsAndVectors(java.util.BitSet bs, java.util.List<javax.vecmath.Point3f[]> vList, boolean isTraceAlpha, float sheetSmoothing)
bs
- vList
- isTraceAlpha
- sheetSmoothing
- public javax.vecmath.Point3f[] getPolymerLeadMidPoints(int iPolymer)
iPolymer
- public void recalculateLeadMidpointsAndWingVectors()
public void addSecondaryStructure(EnumStructure type, java.lang.String structureID, int serialID, int strandCount, char startChainID, int startSeqcode, char endChainID, int endSeqcode)
type
- structureID
- serialID
- strandCount
- startChainID
- startSeqcode
- endChainID
- endSeqcode
- public java.lang.String calculateStructures(boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha)
asDSSP
- doReport
- dsspIgnoreHydrogen
- setStructure
- includeAlpha
- public void setStructureList(java.util.Map<EnumStructure,float[]> structureList)
structureList
- public void getChimeInfo(java.lang.StringBuffer sb, int nHetero)
public int calculateStruts(ModelSet modelSet, java.util.BitSet bs1, java.util.BitSet bs2)
modelSet
- bs1
- bs2
- public void calculateStraightness(Viewer viewer, char ctype, char qtype, int mStep)
viewer
- ctype
- qtype
- mStep
- public void selectSeqcodeRange(int seqcodeA, int seqcodeB, char chainID, java.util.BitSet bs, boolean caseSensitive)
seqcodeA
- seqcodeB
- chainID
- bs
- caseSensitive
- public void setConformation(java.util.BitSet bsConformation)
bsConformation
- public boolean getPdbConformation(java.util.BitSet bsConformation, int conformationIndex)
bsConformation
- conformationIndex
- public java.lang.String getProteinStructureState(java.util.BitSet bsAtoms, boolean taintedOnly, boolean needPhiPsi, int mode)
bsAtoms
- taintedOnly
- needPhiPsi
- mode
- public java.lang.String getFullPDBHeader()