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
(package private) int
private int
javajs.util.BS
tracks all presymmetry asymmetric unit atoms; atoms added using the ModelKit will add to this.final javajs.util.BS
Note that this bitset may or may not include bsAtomsDeletedfinal javajs.util.BS
private javajs.util.BS
protected int
Chain[]
(package private) int
(package private) float
(package private) int
int
(package private) int
long
int
(package private) boolean
boolean
int
(package private) int
boolean
boolean
boolean
boolean
a flag that, when false, indicates that the model has atoms in different regions of the Atom[] arrayboolean
(package private) boolean
(package private) String
(package private) String
javajs.util.SB
javajs.util.M4
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
(package private) javajs.util.P3
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescription(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
(package private) Chain
getChain
(int chainID) getChainAt
(int i) int
getChainCount
(boolean countWater) int
int
not actually accessed -- just pointing out what it isboolean
isContainedIn
(javajs.util.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)
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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
public javajs.util.M4 mat4mat4 tracks the rotation/translation of the full model using rotateSelected or translateSelected -
modelIndex
public int modelIndex -
fileIndex
int fileIndex -
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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dataFrames
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translation
javajs.util.P3 translation -
dataSourceFrame
int dataSourceFrame -
loadState
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loadScript
public javajs.util.SB loadScript -
hasRasmolHBonds
public boolean hasRasmolHBonds -
structureTainted
public boolean structureTainted -
isJmolDataFrame
public boolean isJmolDataFrame -
isTrajectory
boolean isTrajectory -
trajectoryBaseIndex
public int trajectoryBaseIndex -
altLocCount
public int altLocCount -
insertionCount
int insertionCount -
act
public int actatom count; includes deleted atoms only if not being nulled (Jmol 14.31 or below) -
bondCount
private int bondCount -
chainCount
protected int chainCount -
groupCount
public int groupCount -
hydrogenCount
public int hydrogenCount -
moleculeCount
public int moleculeCount -
biosymmetryCount
int biosymmetryCount -
firstAtomIndex
public int firstAtomIndex -
firstMoleculeIndex
int firstMoleculeIndex -
bsAtoms
public final javajs.util.BS bsAtomsNote that this bitset may or may not include bsAtomsDeleted -
bsAtomsDeleted
public final javajs.util.BS bsAtomsDeleted -
defaultRotationRadius
float defaultRotationRadius -
frameDelay
public long frameDelay -
selectedTrajectory
public int selectedTrajectory -
jmolData
String jmolData -
jmolFrameType
String jmolFrameType -
pdbID
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bsCheck
private javajs.util.BS bsCheck -
hasChirality
boolean hasChirality -
isOrderly
public boolean isOrderlya flag that, when false, indicates that the model has atoms in different regions of the Atom[] array -
bsAsymmetricUnit
public javajs.util.BS bsAsymmetricUnittracks 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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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
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() -
getBondCount
public int getBondCount() -
getChainCount
public int getChainCount(boolean countWater) -
calcSelectedGroupsCount
void calcSelectedGroupsCount(javajs.util.BS bsSelected) -
getGroupCount
public int getGroupCount() -
getChainAt
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getChain
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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) -
fixIndicesM
protected void fixIndicesM(int modelIndex, int nAtomsDeleted, javajs.util.BS bsDeleted) -
freeze
public boolean freeze() -
freezeM
protected void freezeM() -
setSimpleCage
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