public class Model
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
int |
atomCount |
protected java.util.Map<java.lang.String,java.lang.Object> |
auxiliaryInfo |
(package private) int |
biosymmetryCount |
private int |
bondCount |
protected BS |
bsAtoms |
(package private) BS |
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 |
int |
firstAtomIndex |
(package private) int |
firstMoleculeIndex |
long |
frameDelay |
(package private) int |
groupCount |
protected boolean |
hasRasmolHBonds |
int |
hydrogenCount |
boolean |
isBioModel |
boolean |
isJmolDataFrame |
boolean |
isModelKit |
boolean |
isPdbWithMultipleBonds |
boolean |
isTrajectory |
(package private) java.lang.String |
jmolData |
(package private) java.lang.String |
jmolFrameType |
SB |
loadScript |
java.lang.String |
loadState |
int |
modelIndex |
ModelSet |
modelSet |
int |
moleculeCount |
int |
nAltLocs |
(package private) int |
nInsertions |
StateManager.Orientation |
orientation |
java.util.Properties |
properties |
private int |
selectedTrajectory |
SymmetryInterface |
simpleCage |
protected boolean |
structureTainted |
int |
trajectoryBaseIndex |
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 |
---|---|
(package private) void |
calcSelectedGroupsCount(BS bsSelected) |
void |
calcSelectedMonomersCount(BS bsSelected) |
void |
calculatePolymers(Group[] groups,
int groupCount,
int baseGroupIndex,
BS modelsExcluded,
boolean checkConnections) |
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,
BS bs1,
BS bs2) |
void |
clearBioPolymers() |
void |
clearRasmolHydrogenBonds(BS bsAtoms) |
void |
fixIndices(int modelIndex,
int nAtomsDeleted,
BS bsDeleted) |
protected void |
fixIndicesM(int modelIndex,
int nAtomsDeleted,
BS bsDeleted) |
void |
freeze() |
protected void |
freezeM() |
void |
getAllPolymerInfo(BS bs,
java.util.Map<java.lang.String,JmolList<java.util.Map<java.lang.String,java.lang.Object>>> finalInfo,
JmolList<java.util.Map<java.lang.String,java.lang.Object>> modelVector) |
JmolList<BS> |
getBioBranches(JmolList<BS> bioBranches) |
int |
getBioPolymerCount() |
int |
getBondCount() |
(package private) Chain |
getChain(int chainID) |
Chain |
getChainAt(int i) |
int |
getChainCount(boolean countWater) |
Chain[] |
getChains() |
void |
getChimeInfo(SB sb,
int nHetero) |
protected void |
getChimeInfoM(SB sb,
int nHetero) |
void |
getDefaultLargePDBRendering(SB sb,
int maxAtoms) |
java.lang.String |
getFullPDBHeader() |
int |
getGroupCount() |
int |
getGroupCountHetero(boolean isHetero) |
void |
getGroupsWithin(int nResidues,
BS bs,
BS 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(BS bsConformation,
int conformationIndex) |
void |
getPdbData(Viewer viewer,
java.lang.String type,
char ctype,
boolean isDraw,
BS bsSelected,
OutputStringBuilder sb,
LabelToken[] tokens,
SB pdbCONECT,
BS bsWritten) |
P3[] |
getPolymerLeadMidPoints(int iPolymer) |
void |
getPolymerPointsAndVectors(BS bs,
JmolList<P3[]> vList,
boolean isTraceAlpha,
float sheetSmoothing) |
java.lang.String |
getProteinStructureState(BS bsAtoms,
boolean taintedOnly,
boolean needPhiPsi,
int mode) |
void |
getRasmolHydrogenBonds(BS bsA,
BS bsB,
JmolList<Bond> vHBonds,
boolean nucleicOnly,
int nMax,
boolean dsspIgnoreHydrogens,
BS bsHBonds) |
int |
getSelectedTrajectory() |
void |
getSequenceBits(java.lang.String specInfo,
BS bs,
BS bsResult) |
int |
getTrueAtomCount() |
boolean |
isModelkit() |
boolean |
isStructureTainted() |
void |
recalculateLeadMidpointsAndWingVectors() |
void |
resetBoundCount() |
void |
selectSeqcodeRange(int seqcodeA,
int seqcodeB,
int chainID,
BS bs,
boolean caseSensitive) |
void |
setConformation(BS bsConformation) |
(package private) void |
setNAltLocs(int nAltLocs) |
(package private) void |
setNInsertions(int nInsertions) |
(package private) void |
setSelectedTrajectory(int i) |
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
protected boolean hasRasmolHBonds
public java.lang.String loadState
public SB loadScript
public boolean isModelKit
java.util.Map<java.lang.String,java.lang.Integer> dataFrames
int dataSourceFrame
java.lang.String jmolData
java.lang.String jmolFrameType
public int firstAtomIndex
public int atomCount
protected final BS bsAtoms
final BS bsAtomsDeleted
public int trajectoryBaseIndex
public boolean isTrajectory
private int selectedTrajectory
private int bondCount
int firstMoleculeIndex
public 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
public java.util.Properties properties
float defaultRotationRadius
java.lang.String defaultStructure
public StateManager.Orientation orientation
protected boolean structureTainted
public boolean isJmolDataFrame
public long frameDelay
public SymmetryInterface simpleCage
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()
void setSelectedTrajectory(int i)
public int getSelectedTrajectory()
public void resetBoundCount()
public 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 getGroupCountHetero(boolean isHetero)
void calcSelectedGroupsCount(BS bsSelected)
public int getGroupCount()
public Chain getChainAt(int i)
Chain getChain(int chainID)
public void fixIndices(int modelIndex, int nAtomsDeleted, BS bsDeleted)
protected void fixIndicesM(int modelIndex, int nAtomsDeleted, BS bsDeleted)
public void freeze()
protected void freezeM()
public void getPdbData(Viewer viewer, java.lang.String type, char ctype, boolean isDraw, BS bsSelected, OutputStringBuilder sb, LabelToken[] tokens, SB pdbCONECT, BS bsWritten)
viewer
- type
- ctype
- isDraw
- bsSelected
- sb
- bsWritten
- pdbCONECT
- tokens
- public void getDefaultLargePDBRendering(SB sb, int maxAtoms)
sb
- maxAtoms
- public JmolList<BS> getBioBranches(JmolList<BS> bioBranches)
bioBranches
- public void getGroupsWithin(int nResidues, BS bs, BS bsResult)
nResidues
- bs
- bsResult
- public void getSequenceBits(java.lang.String specInfo, BS bs, BS bsResult)
specInfo
- bs
- bsResult
- public void getRasmolHydrogenBonds(BS bsA, BS bsB, JmolList<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, BS bsHBonds)
bsA
- bsB
- vHBonds
- nucleicOnly
- nMax
- dsspIgnoreHydrogens
- bsHBonds
- public void clearRasmolHydrogenBonds(BS bsAtoms)
bsAtoms
- public void clearBioPolymers()
public void calcSelectedMonomersCount(BS bsSelected)
bsSelected
- public void calculatePolymers(Group[] groups, int groupCount, int baseGroupIndex, BS modelsExcluded, boolean checkConnections)
groups
- groupCount
- baseGroupIndex
- modelsExcluded
- checkConnections
- public void getAllPolymerInfo(BS bs, java.util.Map<java.lang.String,JmolList<java.util.Map<java.lang.String,java.lang.Object>>> finalInfo, JmolList<java.util.Map<java.lang.String,java.lang.Object>> modelVector)
bs
- finalInfo
- modelVector
- public int getBioPolymerCount()
public void getPolymerPointsAndVectors(BS bs, JmolList<P3[]> vList, boolean isTraceAlpha, float sheetSmoothing)
bs
- vList
- isTraceAlpha
- sheetSmoothing
- public P3[] getPolymerLeadMidPoints(int iPolymer)
iPolymer
- public void recalculateLeadMidpointsAndWingVectors()
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(SB sb, int nHetero)
protected void getChimeInfoM(SB sb, int nHetero)
public int calculateStruts(ModelSet modelSet, BS bs1, BS 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, int chainID, BS bs, boolean caseSensitive)
seqcodeA
- seqcodeB
- chainID
- bs
- caseSensitive
- public void setConformation(BS bsConformation)
bsConformation
- public boolean getPdbConformation(BS bsConformation, int conformationIndex)
bsConformation
- conformationIndex
- public java.lang.String getProteinStructureState(BS bsAtoms, boolean taintedOnly, boolean needPhiPsi, int mode)
bsAtoms
- taintedOnly
- needPhiPsi
- mode
- public java.lang.String getFullPDBHeader()