Package org.jmol.modelset
Class Trajectory
- java.lang.Object
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- org.jmol.modelset.Trajectory
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public class Trajectory extends java.lang.Object
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Constructor Summary
Constructors Constructor Description Trajectory()
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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, javajs.util.BS bs)
set bits for all trajectories associated with this model(package private) javajs.util.BS
getModelsSelected()
java.lang.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)
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Method Detail
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set
Trajectory set(Viewer vwr, ModelSet ms, javajs.util.Lst<javajs.util.P3[]> steps)
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setUnitCell
void setUnitCell(int imodel)
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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
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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
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getModelsSelected
javajs.util.BS getModelsSelected()
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morph
void morph(int m1, int m2, float f)
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fixAtom
void fixAtom(Atom a)
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getFractional
public void getFractional(Atom a, javajs.util.P3 ptTemp)
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getState
public java.lang.String getState()
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hasMeasure
public boolean hasMeasure(int[] measure)
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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
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getModelBS
public void getModelBS(int modelIndex, javajs.util.BS bs)
set bits for all trajectories associated with this model- Parameters:
modelIndex
-bs
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setBaseModels
public void setBaseModels(javajs.util.BS bsModels)
set bits for all base models only- Parameters:
bsModels
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