Package org.jmol.modelset

Class Model

java.lang.Object
org.jmol.modelset.Model
Direct Known Subclasses:
BioModel
public class Model extends Object

  • Field Details

    • 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 Map<String,Object> dssrCache

    • orientation

      public Orientation orientation

    • auxiliaryInfo

      public Map<String,Object> auxiliaryInfo

    • properties

      public Properties properties

    • biosymmetry

      public SymmetryInterface biosymmetry

    • dataFrames

      Map<String,Integer> dataFrames

    • translation

      javajs.util.P3 translation

    • dataSourceFrame

      int dataSourceFrame

    • loadState

      public 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
      atom 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 bsAtoms
      Note 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

      public String pdbID

    • bsCheck

      private javajs.util.BS bsCheck

    • hasChirality

      boolean hasChirality

    • isOrderly

      public boolean isOrderly
      a flag that, when false, indicates that the model has atoms in different regions of the Atom[] array

    • bsAsymmetricUnit

      public javajs.util.BS bsAsymmetricUnit
      tracks all presymmetry asymmetric unit atoms; atoms added using the ModelKit will add to this.

  • Constructor Details

    • Model

      public Model()

  • Method Details

    • set

      public Model set(ModelSet modelSet, int modelIndex, int trajectoryBaseIndex, String jmolData, Properties properties, Map<String,Object> auxiliaryInfo)

    • getTrueAtomCount

      public int getTrueAtomCount()
      not actually accessed -- just pointing out what it is
      Returns:
      true atom count

    • isContainedIn

      public boolean isContainedIn(javajs.util.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(javajs.util.BS bsSelected)

    • getGroupCount

      public int getGroupCount()

    • getChainAt

      public Chain getChainAt(int i)

    • getChain

      Chain getChain(int chainID)

    • 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.

    • 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

      public void setSimpleCage(SymmetryInterface ucell)