Package org.jmol.modelset
Class Trajectory
java.lang.Object
org.jmol.modelset.Trajectory
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Field Summary
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescription(package private) void
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
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
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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Field Details
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vwr
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ms
ModelSet ms -
steps
javajs.util.Lst<javajs.util.P3[]> steps -
isFractional
boolean isFractional
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Constructor Details
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Trajectory
public Trajectory()
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Method Details
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set
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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
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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() -
morph
void morph(int m1, int m2, float f) -
fixAtom
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getFractional
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getState
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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
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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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