Modifier and Type | Field and Description |
---|---|
int |
act |
int |
altLocCount |
protected Map<String,Object> |
auxiliaryInfo |
SymmetryInterface |
biosymmetry |
(package private) int |
biosymmetryCount |
private int |
bondCount |
BS |
bsAtoms |
BS |
bsAtomsDeleted |
private BS |
bsCheck |
protected int |
chainCount |
Chain[] |
chains |
(package private) Map<String,Integer> |
dataFrames |
(package private) int |
dataSourceFrame |
(package private) float |
defaultRotationRadius |
Map<String,Object> |
dssrCache |
(package private) int |
fileIndex |
int |
firstAtomIndex |
(package private) int |
firstMoleculeIndex |
long |
frameDelay |
int |
groupCount |
boolean |
hasRasmolHBonds |
int |
hydrogenCount |
(package private) int |
insertionCount |
boolean |
isBioModel |
boolean |
isJmolDataFrame |
boolean |
isModelKit |
boolean |
isPdbWithMultipleBonds |
(package private) boolean |
isTrajectory |
(package private) String |
jmolData |
(package private) String |
jmolFrameType |
javajs.util.SB |
loadScript |
String |
loadState |
javajs.util.M4 |
mat4
mat4 tracks the rotation/translation of the full model using rotateSelected or translateSelected
|
int |
modelIndex |
int |
moleculeCount |
ModelSet |
ms
BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT
FINALIZATION AND CREATE A MEMORY LEAK.
|
Orientation |
orientation |
String |
pdbID |
Properties |
properties |
int |
selectedTrajectory |
SymmetryInterface |
simpleCage |
boolean |
structureTainted |
int |
trajectoryBaseIndex |
(package private) javajs.util.P3 |
translation |
Constructor and Description |
---|
Model() |
Modifier and Type | Method and Description |
---|---|
(package private) void |
calcSelectedGroupsCount(BS bsSelected) |
void |
fixIndices(int modelIndex,
int nAtomsDeleted,
BS bsDeleted) |
protected void |
fixIndicesM(int modelIndex,
int nAtomsDeleted,
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 is
|
boolean |
isContainedIn(BS bs) |
void |
resetBoundCount() |
Model |
set(ModelSet modelSet,
int modelIndex,
int trajectoryBaseIndex,
String jmolData,
Properties properties,
Map<String,Object> auxiliaryInfo) |
public ModelSet ms
public javajs.util.M4 mat4
public int modelIndex
int fileIndex
public boolean isBioModel
public boolean isPdbWithMultipleBonds
public boolean isModelKit
public Chain[] chains
public SymmetryInterface simpleCage
public Orientation orientation
public Properties properties
public SymmetryInterface biosymmetry
javajs.util.P3 translation
int dataSourceFrame
public String loadState
public javajs.util.SB loadScript
public boolean hasRasmolHBonds
public boolean structureTainted
public boolean isJmolDataFrame
boolean isTrajectory
public int trajectoryBaseIndex
public int altLocCount
int insertionCount
public int act
private int bondCount
protected int chainCount
public int groupCount
public int hydrogenCount
public int moleculeCount
int biosymmetryCount
public int firstAtomIndex
int firstMoleculeIndex
public final BS bsAtoms
public final BS bsAtomsDeleted
float defaultRotationRadius
public long frameDelay
public int selectedTrajectory
String jmolData
String jmolFrameType
public String pdbID
private BS bsCheck
public Model set(ModelSet modelSet, int modelIndex, int trajectoryBaseIndex, String jmolData, Properties properties, Map<String,Object> auxiliaryInfo)
public int getTrueAtomCount()
public boolean isContainedIn(BS bs)
bs
- public void resetBoundCount()
public int getBondCount()
public int getChainCount(boolean countWater)
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 boolean freeze()
protected void freezeM()