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)