Package org.jmol.modelset

Class Trajectory

java.lang.Object
org.jmol.modelset.Trajectory
public class Trajectory extends Object

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    (package private) boolean
    isFractional
     
    (package private) ModelSet
    ms
     
    (package private) javajs.util.Lst<javajs.util.P3[]>
    steps
     
    private Viewer
    vwr
     

  • Constructor Summary

    Constructors
    Constructor
    Description
    Trajectory()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    (package private) void
    fixAtom(Atom a)
     
    void
    getFractional(Atom a, javajs.util.P3 ptTemp)
     
    void
    getModelBS(int modelIndex, javajs.util.BS bs)
    set bits for all trajectories associated with this model
    (package private) javajs.util.BS
    getModelsSelected()
     
    String
    getState()
     
    boolean
    hasMeasure(int[] measure)
     
    (package private) void
    morph(int m1, int m2, float f)
     
    void
    selectDisplayed(javajs.util.BS bs)
    Remove trajectories that are not currently displayed from the visible frames bitset.
    (package private) Trajectory
    set(Viewer vwr, ModelSet ms, javajs.util.Lst<javajs.util.P3[]> steps)
     
    private void
    setAtomPositions(int baseModelIndex, int modelIndex, javajs.util.P3[] t1, javajs.util.P3[] t2, float f, javajs.util.V3[] vibs, boolean isFractional)
    A generic way to set atom positions, possibly from trajectories but also possibly from an array.
    void
    setBaseModels(javajs.util.BS bsModels)
    set bits for all base models only
    (package private) void
    setModel(int modelIndex)
    The user has used the MODEL command to switch to a new set of atom coordinates Or has specified a trajectory in a select, display, or hide command.
    (package private) void
    setUnitCell(int imodel)
     

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Field Details

    • vwr

      private Viewer vwr

    • ms

      ModelSet ms

    • steps

      javajs.util.Lst<javajs.util.P3[]> steps

    • isFractional

      boolean isFractional

  • Constructor Details

    • Trajectory

      public Trajectory()

  • Method Details

    • set

      Trajectory set(Viewer vwr, ModelSet ms, javajs.util.Lst<javajs.util.P3[]> steps)

    • setUnitCell

      void setUnitCell(int imodel)

    • setModel

      void setModel(int modelIndex)
      The user has used the MODEL command to switch to a new set of atom coordinates Or has specified a trajectory in a select, display, or hide command. Assign the coordinates and the model index for this set of atoms
      Parameters:
      modelIndex -

    • setAtomPositions

      private void setAtomPositions(int baseModelIndex, int modelIndex, javajs.util.P3[] t1, javajs.util.P3[] t2, float f, javajs.util.V3[] vibs, boolean isFractional)
      A generic way to set atom positions, possibly from trajectories but also possibly from an array. Takes care of all associated issues of changing coordinates.
      Parameters:
      baseModelIndex -
      modelIndex -
      t1 -
      t2 -
      f -
      vibs -
      isFractional -

    • getModelsSelected

      javajs.util.BS getModelsSelected()

    • morph

      void morph(int m1, int m2, float f)

    • fixAtom

      void fixAtom(Atom a)

    • getFractional

      public void getFractional(Atom a, javajs.util.P3 ptTemp)

    • getState

      public String getState()

    • hasMeasure

      public boolean hasMeasure(int[] measure)

    • selectDisplayed

      public void selectDisplayed(javajs.util.BS bs)
      Remove trajectories that are not currently displayed from the visible frames bitset. when a trajectory is selected, the atom's modelIndex is switched to that of the selected trajectory even though the underlying model itself is not changed.
      Parameters:
      bs -

    • getModelBS

      public void getModelBS(int modelIndex, javajs.util.BS bs)
      set bits for all trajectories associated with this model
      Parameters:
      modelIndex -
      bs -

    • setBaseModels

      public void setBaseModels(javajs.util.BS bsModels)
      set bits for all base models only
      Parameters:
      bsModels -