Package org.jmol.modelset
Class Model
java.lang.Object
org.jmol.modelset.Model
- Direct Known Subclasses:
BioModel
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Field Summary
FieldsModifier and TypeFieldDescriptionint
atom count; includes deleted atoms only if not being nulled (Jmol 14.31 or below)int
tracks all presymmetry asymmetric unit atoms; atoms added using the ModelKit will add to this.Note that this bitset may or may not include bsAtomsDeletedprotected int
Chain[]
int
long
int
boolean
int
boolean
boolean
boolean
boolean
a flag that, when false, indicates that the model has atoms in different regions of the Atom[] arrayboolean
mat4 tracks the rotation/translation of the full model using rotateSelected or translateSelectedint
int
BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.int
boolean
int
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
fixIndices
(int modelIndex, int nAtomsDeleted, BS bsDeleted) protected void
fixIndicesM
(int modelIndex, int nAtomsDeleted, BS bsDeleted) boolean
freeze()
protected void
freezeM()
int
getChainAt
(int i) int
getChainCount
(boolean countWater) int
int
not actually accessed -- just pointing out what it isboolean
isContainedIn
(BS bs) void
void
resetDSSR
(boolean totally) Something has changed; clear the DSSR cache and possibly remove DSSR entirely.set
(ModelSet modelSet, int modelIndex, int trajectoryBaseIndex, String jmolData, Properties properties, Map<String, Object> auxiliaryInfo) void
setSimpleCage
(SymmetryInterface ucell) protected void
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Field Details
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ms
BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK. -
mat4
mat4 tracks the rotation/translation of the full model using rotateSelected or translateSelected -
modelIndex
public int modelIndex -
isBioModel
public boolean isBioModel -
isPdbWithMultipleBonds
public boolean isPdbWithMultipleBonds -
isModelKit
public boolean isModelKit -
chains
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simpleCage
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dssrCache
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orientation
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auxiliaryInfo
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properties
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biosymmetry
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loadState
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loadScript
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hasRasmolHBonds
public boolean hasRasmolHBonds -
structureTainted
public boolean structureTainted -
isJmolDataFrame
public boolean isJmolDataFrame -
trajectoryBaseIndex
public int trajectoryBaseIndex -
altLocCount
public int altLocCount -
act
public int actatom count; includes deleted atoms only if not being nulled (Jmol 14.31 or below) -
chainCount
protected int chainCount -
groupCount
public int groupCount -
hydrogenCount
public int hydrogenCount -
moleculeCount
public int moleculeCount -
firstAtomIndex
public int firstAtomIndex -
bsAtoms
Note that this bitset may or may not include bsAtomsDeleted -
bsAtomsDeleted
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frameDelay
public long frameDelay -
selectedTrajectory
public int selectedTrajectory -
pdbID
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isOrderly
public boolean isOrderlya flag that, when false, indicates that the model has atoms in different regions of the Atom[] array -
bsAsymmetricUnit
tracks all presymmetry asymmetric unit atoms; atoms added using the ModelKit will add to this.
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Constructor Details
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Model
public Model()
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Method Details
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setupArrays
protected void setupArrays() -
set
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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
- Parameters:
bs
-- Returns:
- true if all undeleted atom bits in this model are in bs
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resetBoundCount
public void resetBoundCount() -
getBondCount
public int getBondCount() -
getChainCount
public int getChainCount(boolean countWater) -
getGroupCount
public int getGroupCount() -
getChainAt
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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
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fixIndicesM
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freeze
public boolean freeze() -
freezeM
protected void freezeM() -
setSimpleCage
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