Package org.jmol.modelset

Class Trajectory

  • public class Trajectory
extends java.lang.Object

    • Field Summary

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

    • Constructor Summary

      Constructors 
      Constructor Description
      Trajectory()  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      (package private) void fixAtom​(Atom a)  
      void getFractional​(Atom a, javajs.util.P3 ptTemp)  
      void getModelBS​(int modelIndex, BS bs)
      set bits for all trajectories associated with this model
      (package private) BS getModelsSelected()  
      java.lang.String getState()  
      boolean hasMeasure​(int[] measure)  
      (package private) void morph​(int m1, int m2, float f)  
      void selectDisplayed​(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​(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 Detail

      • steps

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

    • Constructor Detail

      • Trajectory

        public Trajectory()

    • Method Detail

      • 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

        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 java.lang.String getState()

      • hasMeasure

        public boolean hasMeasure​(int[] measure)

      • selectDisplayed

        public void selectDisplayed​(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,
                       BS bs)
        set bits for all trajectories associated with this model
        Parameters:
        modelIndex -
        bs -

      • setBaseModels

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