public class Model
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
int |
ac |
protected java.util.Map<java.lang.String,java.lang.Object> |
auxiliaryInfo |
SymmetryInterface |
biosymmetry |
(package private) int |
biosymmetryCount |
private int |
bondCount |
BS |
bsAtoms |
BS |
bsAtomsDeleted |
protected int |
chainCount |
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 |
java.util.Map<java.lang.String,java.lang.Object> |
dssrCache |
(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 |
javajs.util.SB |
loadScript |
java.lang.String |
loadState |
int |
modelIndex |
int |
moleculeCount |
ModelSet |
ms |
int |
nAltLocs |
(package private) int |
nInsertions |
Orientation |
orientation |
java.util.Properties |
properties |
int |
selectedTrajectory |
SymmetryInterface |
simpleCage |
boolean |
structureTainted |
int |
trajectoryBaseIndex |
Constructor and Description |
---|
Model() |
Modifier and Type | Method and Description |
---|---|
void |
calcRasmolHydrogenBonds(ModelSet ms,
BS bsA,
BS bsB,
javajs.util.Lst<Bond> vHBonds,
boolean nucleicOnly,
int nMax,
boolean dsspIgnoreHydrogens,
BS bsHBonds) |
(package private) void |
calcSelectedGroupsCount(BS bsSelected) |
void |
calcSelectedMonomersCount(BS bsSelected) |
void |
calculateAllPolymers(ModelSet ms,
Group[] groups,
int groupCount2,
int baseGroupIndex,
BS modelsExcluded) |
void |
calculateStraightnessAll(ModelSet ms) |
java.lang.String |
calculateStructures(boolean asDSSP,
boolean doReport,
boolean dsspIgnoreHydrogen,
boolean setStructure,
boolean includeAlpha) |
int |
calculateStruts(ModelSet ms,
BS bs1,
BS bs2) |
void |
clearBioPolymers() |
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,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>> finalInfo,
javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> modelVector) |
BS |
getBasePairBits(ModelSet ms,
java.lang.String specInfo) |
javajs.util.Lst<BS> |
getBioBranches(javajs.util.Lst<BS> bioBranches) |
int |
getBioPolymerCount() |
int |
getBioPolymerCountInModel(ModelSet ms,
int modelIndex) |
int |
getBondCount() |
(package private) Chain |
getChain(int chainID) |
Chain |
getChainAt(int i) |
int |
getChainCount(boolean countWater) |
void |
getChimeInfo(javajs.util.SB sb,
int nHetero) |
protected void |
getChimeInfoM(javajs.util.SB sb,
int nHetero) |
void |
getDefaultLargePDBRendering(javajs.util.SB sb,
int maxAtoms) |
java.lang.String |
getFullPDBHeader() |
java.lang.String |
getFullProteinStructureState(ModelSet modelSet,
BS bsAtoms2,
boolean taintedOnly,
boolean needPhiPsi,
int mode) |
int |
getGroupCount() |
int |
getGroupCountHetero(boolean isHetero) |
BS |
getGroupsWithinAll(ModelSet ms,
int nResidues,
BS bs) |
ModelSet |
getModelSet()
BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT
FINALIZATION AND CREATE A MEMORY LEAK.
|
boolean |
getPdbConformation(BS bsConformation,
int conformationIndex) |
void |
getPdbData(Viewer vwr,
java.lang.String type,
char ctype,
boolean isDraw,
BS bsSelected,
javajs.util.OC out,
LabelToken[] tokens,
javajs.util.SB pdbCONECT,
BS bsWritten) |
void |
getPolymerPointsAndVectors(BS bs,
javajs.util.Lst<javajs.util.P3[]> vList,
boolean isTraceAlpha,
float sheetSmoothing) |
BS |
getSelectCodeRange(ModelSet ms,
int[] specInfo) |
BS |
getSequenceBits(ModelSet ms,
java.lang.String specInfo,
BS bs) |
int |
getTrueAtomCount() |
boolean |
isModelkit() |
void |
recalculatePoints(ModelSet ms,
int modelIndex) |
void |
resetBoundCount() |
void |
resetRasmolBonds(Model model,
BS bs) |
Model |
set(ModelSet modelSet,
int modelIndex,
int trajectoryBaseIndex,
java.lang.String jmolData,
java.util.Properties properties,
java.util.Map<java.lang.String,java.lang.Object> auxiliaryInfo) |
void |
setConformation(BS bsConformation) |
void |
setStructureList(java.util.Map<STR,float[]> structureList) |
public ModelSet ms
public int modelIndex
int fileIndex
public int hydrogenCount
public boolean isBioModel
public boolean isPdbWithMultipleBonds
protected boolean hasRasmolHBonds
public java.lang.String loadState
public javajs.util.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 ac
public final BS bsAtoms
public final BS bsAtomsDeleted
public int trajectoryBaseIndex
public boolean isTrajectory
public int selectedTrajectory
private int bondCount
int firstMoleculeIndex
public int moleculeCount
public int nAltLocs
int nInsertions
int groupCount
protected int chainCount
public 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 SymmetryInterface biosymmetry
public Orientation orientation
public boolean structureTainted
public boolean isJmolDataFrame
public long frameDelay
public SymmetryInterface simpleCage
public java.util.Map<java.lang.String,java.lang.Object> dssrCache
public ModelSet getModelSet()
public boolean isModelkit()
public int getTrueAtomCount()
public void resetBoundCount()
public int getBondCount()
public Model set(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 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 vwr, java.lang.String type, char ctype, boolean isDraw, BS bsSelected, javajs.util.OC out, LabelToken[] tokens, javajs.util.SB pdbCONECT, BS bsWritten)
vwr
- type
- ctype
- isDraw
- bsSelected
- out
- bsWritten
- pdbCONECT
- tokens
- public javajs.util.Lst<BS> getBioBranches(javajs.util.Lst<BS> bioBranches)
bioBranches
- public void clearBioPolymers()
public void getAllPolymerInfo(BS bs, java.util.Map<java.lang.String,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>> finalInfo, javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> modelVector)
bs
- finalInfo
- modelVector
- public int getBioPolymerCount()
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<STR,float[]> structureList)
structureList
- public void getChimeInfo(javajs.util.SB sb, int nHetero)
protected void getChimeInfoM(javajs.util.SB sb, int nHetero)
public void setConformation(BS bsConformation)
bsConformation
- public boolean getPdbConformation(BS bsConformation, int conformationIndex)
bsConformation
- conformationIndex
- public java.lang.String getFullPDBHeader()
public BS getSequenceBits(ModelSet ms, java.lang.String specInfo, BS bs)
ms
- specInfo
- bs
- public BS getBasePairBits(ModelSet ms, java.lang.String specInfo)
ms
- specInfo
- public void calcRasmolHydrogenBonds(ModelSet ms, BS bsA, BS bsB, javajs.util.Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, BS bsHBonds)
ms
- bsA
- bsB
- vHBonds
- nucleicOnly
- nMax
- dsspIgnoreHydrogens
- bsHBonds
- public java.lang.String getFullProteinStructureState(ModelSet modelSet, BS bsAtoms2, boolean taintedOnly, boolean needPhiPsi, int mode)
modelSet
- bsAtoms2
- taintedOnly
- needPhiPsi
- mode
- public void calculateAllPolymers(ModelSet ms, Group[] groups, int groupCount2, int baseGroupIndex, BS modelsExcluded)
ms
- groups
- groupCount2
- baseGroupIndex
- modelsExcluded
- public BS getGroupsWithinAll(ModelSet ms, int nResidues, BS bs)
ms
- nResidues
- bs
- public BS getSelectCodeRange(ModelSet ms, int[] specInfo)
ms
- specInfo
- public int calculateStruts(ModelSet ms, BS bs1, BS bs2)
ms
- bs1
- bs2
- public void getPolymerPointsAndVectors(BS bs, javajs.util.Lst<javajs.util.P3[]> vList, boolean isTraceAlpha, float sheetSmoothing)
bs
- vList
- isTraceAlpha
- sheetSmoothing
- public void recalculatePoints(ModelSet ms, int modelIndex)
ms
- modelIndex
- public void getDefaultLargePDBRendering(javajs.util.SB sb, int maxAtoms)
sb
- maxAtoms
- public void calcSelectedMonomersCount(BS bsSelected)
bsSelected
- public int getBioPolymerCountInModel(ModelSet ms, int modelIndex)
ms
- modelIndex
- public void calculateStraightnessAll(ModelSet ms)
ms
-