Package jgromacs.analysis
Class Superposition
- java.lang.Object
-
- jgromacs.analysis.Superposition
-
public class Superposition extends java.lang.Object
Collection of methods for superposing structures
-
-
Constructor Summary
Constructors Constructor Description Superposition()
-
Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static 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, java.util.ArrayList<java.lang.Double> weights)
Calculates the weighted superposition of a point list to anotherstatic Structure
weightedSuperposeTo(Structure toBeSuperposed, Structure reference, java.util.ArrayList<java.lang.Double> weights)
Calculates the weighted superposition of a structure to anotherstatic Trajectory
weightedSuperposeTo(Trajectory t, PointList reference, java.util.ArrayList<java.lang.Double> weights)
Calculates the weighted superposition of each frame of a trajectory to a common reference framestatic Trajectory
weightedSuperposeTo(Trajectory t, Structure reference, java.util.ArrayList<java.lang.Double> weights)
Calculates the weighted superposition of each frame of a trajectory to a common reference frame
-
-
-
Method Detail
-
superposeTo
public static PointList superposeTo(PointList toBeSuperposed, PointList reference)
Calculates the superposition of a point list to another- Parameters:
toBeSuperposed
- the point list to be superposedreference
- the reference point list- Returns:
- superposed points
-
superposeTo
public static Structure superposeTo(Structure toBeSuperposed, Structure reference)
Calculates the superposition of a structure to another- Parameters:
toBeSuperposed
- the structure to be superposedreference
- the reference structure- Returns:
- superposed structure
-
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
-
superposeTo
public static Trajectory superposeTo(Trajectory t, PointList reference)
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
-
superposeTo
public static Trajectory superposeTo(Trajectory t, Structure reference)
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
-
superposeTo
public static 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 fitting- Parameters:
t
- trajectory to be superposedreference
- reference structureindices
- index set- Returns:
- superposed trajectory
-
weightedSuperposeTo
public static PointList weightedSuperposeTo(PointList toBeSuperposed, PointList reference, java.util.ArrayList<java.lang.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
-
weightedSuperposeTo
public static Structure weightedSuperposeTo(Structure toBeSuperposed, Structure reference, java.util.ArrayList<java.lang.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
-
weightedSuperposeTo
public static Trajectory weightedSuperposeTo(Trajectory t, PointList reference, java.util.ArrayList<java.lang.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
-
weightedSuperposeTo
public static Trajectory weightedSuperposeTo(Trajectory t, Structure reference, java.util.ArrayList<java.lang.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
-
-