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 and Description
Superposition()

Method Summary

Methods

Modifier and Type	Method and Description
static PointList	superposeTo(PointList toBeSuperposed, PointList reference) Calculates the superposition of a point list to another
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
static Structure	superposeTo(Structure toBeSuperposed, Structure reference) Calculates the superposition of a structure to another
static Trajectory	superposeTo(Trajectory t, PointList reference) Calculates the superposition of each frame of a trajectory to a common reference frame
static Trajectory	superposeTo(Trajectory t, Structure reference) Calculates the superposition of each frame of a trajectory to a common reference frame
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
static PointList	weightedSuperposeTo(PointList toBeSuperposed, PointList reference, java.util.ArrayList<java.lang.Double> weights) Calculates the weighted superposition of a point list to another
static Structure	weightedSuperposeTo(Structure toBeSuperposed, Structure reference, java.util.ArrayList<java.lang.Double> weights) Calculates the weighted superposition of a structure to another
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
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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Superposition

public Superposition()

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 superposed

reference - 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 superposed

reference - 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 superposed

indices1 - first index set

reference - the reference structure

indices2 - 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 superposed

reference - 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 superposed

reference - 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 superposed

reference - reference structure

indices - 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 superposed

reference - the reference point list

weights - 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 superposed

reference - the reference structure

weights - 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 superposed

reference - reference point list

weights - 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 superposed

reference - reference structure

weights - vector of weights

Returns:

superposed trajectory