Field Detail

• ms

  public ModelSet ms

  BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.

• mat4

  public javajs.util.M4 mat4

  mat4 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

  public Chain[] chains

• simpleCage

  public SymmetryInterface simpleCage

• dssrCache

  public java.util.Map<java.lang.String,​java.lang.Object> dssrCache

• orientation

  public Orientation orientation

• auxiliaryInfo

  protected java.util.Map<java.lang.String,​java.lang.Object> auxiliaryInfo

• properties

  public java.util.Properties properties

• biosymmetry

  public SymmetryInterface biosymmetry

• dataFrames

  java.util.Map<java.lang.String,​java.lang.Integer> dataFrames

• translation

  javajs.util.P3 translation

• dataSourceFrame

  int dataSourceFrame

• loadState

  public java.lang.String loadState

• 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 act

• 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 BS bsAtoms

• bsAtomsDeleted

  public final BS bsAtomsDeleted

• defaultRotationRadius

  float defaultRotationRadius

• frameDelay

  public long frameDelay

• selectedTrajectory

  public int selectedTrajectory

• jmolData

  java.lang.String jmolData

• jmolFrameType

  java.lang.String jmolFrameType

• pdbID

  public java.lang.String pdbID

• bsCheck

  private BS bsCheck

Constructor Detail

• Model

  public Model()

Method Detail

• 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)

• getTrueAtomCount

  public int getTrueAtomCount()

  not actually accessed -- just pointing out what it is

  Returns:

  true atom count

• isContainedIn

  public boolean isContainedIn​(BS bs)

  Parameters:

  bs -

  Returns:

  true if all undeleted atom bits in this model are in bs

• resetBoundCount

  public void resetBoundCount()

• getBondCount

  public int getBondCount()

• getChainCount

  public int getChainCount​(boolean countWater)

• calcSelectedGroupsCount

  void calcSelectedGroupsCount​(BS bsSelected)

• getGroupCount

  public int getGroupCount()

• getChainAt

  public Chain getChainAt​(int i)

• getChain

  Chain getChain​(int chainID)

• fixIndices

  public void fixIndices​(int modelIndex,
                         int nAtomsDeleted,
                         BS bsDeleted)

• fixIndicesM

  protected void fixIndicesM​(int modelIndex,
                             int nAtomsDeleted,
                             BS bsDeleted)

• freeze

  public boolean freeze()

• freezeM

  protected void freezeM()