Package org.jmol.modelset
Class Model
- java.lang.Object
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- org.jmol.modelset.Model
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- Direct Known Subclasses:
BioModel
public class Model extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description int
act
atom count; includes deleted atoms only if not being nulled (Jmol 14.31 or below)int
altLocCount
java.util.Map<java.lang.String,java.lang.Object>
auxiliaryInfo
SymmetryInterface
biosymmetry
(package private) int
biosymmetryCount
private int
bondCount
javajs.util.BS
bsAsymmetricUnit
tracks all presymmetry asymmetric unit atoms; atoms added using the ModelKit will add to this.javajs.util.BS
bsAtoms
Note that this bitset may or may not include bsAtomsDeletedjavajs.util.BS
bsAtomsDeleted
private javajs.util.BS
bsCheck
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
java.util.Map<java.lang.String,java.lang.Object>
dssrCache
(package private) int
fileIndex
int
firstAtomIndex
(package private) int
firstMoleculeIndex
long
frameDelay
int
groupCount
(package private) boolean
hasChirality
boolean
hasRasmolHBonds
int
hydrogenCount
(package private) int
insertionCount
boolean
isBioModel
boolean
isJmolDataFrame
boolean
isModelKit
boolean
isOrderly
a flag that, when false, indicates that the model has atoms in different regions of the Atom[] arrayboolean
isPdbWithMultipleBonds
(package private) boolean
isTrajectory
(package private) java.lang.String
jmolData
(package private) java.lang.String
jmolFrameType
javajs.util.SB
loadScript
java.lang.String
loadState
javajs.util.M4
mat4
mat4 tracks the rotation/translation of the full model using rotateSelected or translateSelectedint
modelIndex
int
moleculeCount
ModelSet
ms
BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.Orientation
orientation
java.lang.String
pdbID
java.util.Properties
properties
int
selectedTrajectory
SymmetryInterface
simpleCage
boolean
structureTainted
int
trajectoryBaseIndex
(package private) javajs.util.P3
translation
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Constructor Summary
Constructors Constructor Description Model()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description (package private) void
calcSelectedGroupsCount(javajs.util.BS bsSelected)
void
fixIndices(int modelIndex, int nAtomsDeleted, javajs.util.BS bsDeleted)
protected void
fixIndicesM(int modelIndex, int nAtomsDeleted, javajs.util.BS bsDeleted)
boolean
freeze()
protected void
freezeM()
int
getBondCount()
(package private) Chain
getChain(int chainID)
Chain
getChainAt(int i)
int
getChainCount(boolean countWater)
int
getGroupCount()
int
getTrueAtomCount()
not actually accessed -- just pointing out what it isboolean
isContainedIn(javajs.util.BS bs)
void
resetBoundCount()
void
resetDSSR(boolean totally)
Something has changed; clear the DSSR cache and possibly remove DSSR entirely.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
setSimpleCage(SymmetryInterface ucell)
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Field Detail
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ms
public ModelSet ms
BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.
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mat4
public javajs.util.M4 mat4
mat4 tracks the rotation/translation of the full model using rotateSelected or translateSelected
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modelIndex
public int modelIndex
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fileIndex
int fileIndex
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isBioModel
public boolean isBioModel
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isPdbWithMultipleBonds
public boolean isPdbWithMultipleBonds
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isModelKit
public boolean isModelKit
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chains
public Chain[] chains
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simpleCage
public SymmetryInterface simpleCage
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dssrCache
public java.util.Map<java.lang.String,java.lang.Object> dssrCache
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orientation
public Orientation orientation
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auxiliaryInfo
public java.util.Map<java.lang.String,java.lang.Object> auxiliaryInfo
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properties
public java.util.Properties properties
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biosymmetry
public SymmetryInterface biosymmetry
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dataFrames
java.util.Map<java.lang.String,java.lang.Integer> dataFrames
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translation
javajs.util.P3 translation
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dataSourceFrame
int dataSourceFrame
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loadState
public java.lang.String loadState
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loadScript
public javajs.util.SB loadScript
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hasRasmolHBonds
public boolean hasRasmolHBonds
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structureTainted
public boolean structureTainted
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isJmolDataFrame
public boolean isJmolDataFrame
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isTrajectory
boolean isTrajectory
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trajectoryBaseIndex
public int trajectoryBaseIndex
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altLocCount
public int altLocCount
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insertionCount
int insertionCount
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act
public int act
atom count; includes deleted atoms only if not being nulled (Jmol 14.31 or below)
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bondCount
private int bondCount
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chainCount
protected int chainCount
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groupCount
public int groupCount
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hydrogenCount
public int hydrogenCount
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moleculeCount
public int moleculeCount
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biosymmetryCount
int biosymmetryCount
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firstAtomIndex
public int firstAtomIndex
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firstMoleculeIndex
int firstMoleculeIndex
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bsAtoms
public final javajs.util.BS bsAtoms
Note that this bitset may or may not include bsAtomsDeleted
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bsAtomsDeleted
public final javajs.util.BS bsAtomsDeleted
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defaultRotationRadius
float defaultRotationRadius
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frameDelay
public long frameDelay
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selectedTrajectory
public int selectedTrajectory
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jmolData
java.lang.String jmolData
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jmolFrameType
java.lang.String jmolFrameType
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pdbID
public java.lang.String pdbID
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bsCheck
private javajs.util.BS bsCheck
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hasChirality
boolean hasChirality
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isOrderly
public boolean isOrderly
a flag that, when false, indicates that the model has atoms in different regions of the Atom[] array
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bsAsymmetricUnit
public javajs.util.BS bsAsymmetricUnit
tracks all presymmetry asymmetric unit atoms; atoms added using the ModelKit will add to this.
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Method Detail
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set
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)
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getTrueAtomCount
public int getTrueAtomCount()
not actually accessed -- just pointing out what it is- Returns:
- true atom count
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isContainedIn
public boolean isContainedIn(javajs.util.BS bs)
- Parameters:
bs
-- Returns:
- true if all undeleted atom bits in this model are in bs
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resetBoundCount
public void resetBoundCount()
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getBondCount
public int getBondCount()
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getChainCount
public int getChainCount(boolean countWater)
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calcSelectedGroupsCount
void calcSelectedGroupsCount(javajs.util.BS bsSelected)
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getGroupCount
public int getGroupCount()
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getChainAt
public Chain getChainAt(int i)
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getChain
Chain getChain(int chainID)
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resetDSSR
public void resetDSSR(boolean totally)
Something has changed; clear the DSSR cache and possibly remove DSSR entirely.- Parameters:
totally
- set TRUE if atoms have moved so we force a new DSSR calculation.
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fixIndices
public void fixIndices(int modelIndex, int nAtomsDeleted, javajs.util.BS bsDeleted)
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fixIndicesM
protected void fixIndicesM(int modelIndex, int nAtomsDeleted, javajs.util.BS bsDeleted)
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freeze
public boolean freeze()
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freezeM
protected void freezeM()
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setSimpleCage
public void setSimpleCage(SymmetryInterface ucell)
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