Package jgromacs.analysis
Class Superposition
java.lang.Object
jgromacs.analysis.Superposition
Collection of methods for superposing structures
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic PointList
superposeTo
(PointList toBeSuperposed, PointList reference) Calculates the superposition of a point list to anotherstatic Structure
superposeTo
(Structure toBeSuperposed, IndexSet indices1, Structure reference, IndexSet indices2) Calculates the superposition of a structure to another using a subset of atoms for fittingstatic Structure
superposeTo
(Structure toBeSuperposed, Structure reference) Calculates the superposition of a structure to anotherstatic Trajectory
superposeTo
(Trajectory t, PointList reference) Calculates the superposition of each frame of a trajectory to a common reference framestatic Trajectory
superposeTo
(Trajectory t, Structure reference) Calculates the superposition of each frame of a trajectory to a common reference framestatic Trajectory
superposeTo
(Trajectory t, Structure reference, IndexSet indices) Calculates the superposition of each frame of a trajectory to a common reference frame using a subset of atoms for fittingstatic PointList
weightedSuperposeTo
(PointList toBeSuperposed, PointList reference, ArrayList<Double> weights) Calculates the weighted superposition of a point list to anotherstatic Structure
weightedSuperposeTo
(Structure toBeSuperposed, Structure reference, ArrayList<Double> weights) Calculates the weighted superposition of a structure to anotherstatic Trajectory
weightedSuperposeTo
(Trajectory t, PointList reference, ArrayList<Double> weights) Calculates the weighted superposition of each frame of a trajectory to a common reference framestatic Trajectory
weightedSuperposeTo
(Trajectory t, Structure reference, ArrayList<Double> weights) Calculates the weighted superposition of each frame of a trajectory to a common reference frame
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Constructor Details
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Superposition
public Superposition()
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Method Details
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superposeTo
Calculates the superposition of a point list to another- Parameters:
toBeSuperposed
- the point list to be superposedreference
- the reference point list- Returns:
- superposed points
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superposeTo
Calculates the superposition of a structure to another- Parameters:
toBeSuperposed
- the structure to be superposedreference
- the reference structure- Returns:
- superposed structure
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superposeTo
public static Structure superposeTo(Structure toBeSuperposed, IndexSet indices1, Structure reference, IndexSet indices2) Calculates the superposition of a structure to another using a subset of atoms for fitting- Parameters:
toBeSuperposed
- the structure to be superposedindices1
- first index setreference
- the reference structureindices2
- second index set- Returns:
- superposed structure
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superposeTo
Calculates the superposition of each frame of a trajectory to a common reference frame- Parameters:
t
- trajectory to be superposedreference
- reference point list- Returns:
- superposed trajectory
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superposeTo
Calculates the superposition of each frame of a trajectory to a common reference frame- Parameters:
t
- trajectory to be superposedreference
- reference structure- Returns:
- superposed trajectory
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superposeTo
Calculates the superposition of each frame of a trajectory to a common reference frame using a subset of atoms for fitting- Parameters:
t
- trajectory to be superposedreference
- reference structureindices
- index set- Returns:
- superposed trajectory
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weightedSuperposeTo
public static PointList weightedSuperposeTo(PointList toBeSuperposed, PointList reference, ArrayList<Double> weights) Calculates the weighted superposition of a point list to another- Parameters:
toBeSuperposed
- the point list to be superposedreference
- the reference point listweights
- vector of weights- Returns:
- superposed points
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weightedSuperposeTo
public static Structure weightedSuperposeTo(Structure toBeSuperposed, Structure reference, ArrayList<Double> weights) Calculates the weighted superposition of a structure to another- Parameters:
toBeSuperposed
- the structure to be superposedreference
- the reference structureweights
- vector of weights- Returns:
- superposed structure
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weightedSuperposeTo
public static Trajectory weightedSuperposeTo(Trajectory t, PointList reference, ArrayList<Double> weights) Calculates the weighted superposition of each frame of a trajectory to a common reference frame- Parameters:
t
- trajectory to be superposedreference
- reference point listweights
- vector of weights- Returns:
- superposed trajectory
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weightedSuperposeTo
public static Trajectory weightedSuperposeTo(Trajectory t, Structure reference, ArrayList<Double> weights) Calculates the weighted superposition of each frame of a trajectory to a common reference frame- Parameters:
t
- trajectory to be superposedreference
- reference structureweights
- vector of weights- Returns:
- superposed trajectory
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