jgromacs.analysis
Class Superposition

java.lang.Object
  extended by jgromacs.analysis.Superposition

public class Superposition
extends java.lang.Object

Collection of methods for superposing structures


Constructor Summary
Superposition()
           
 
Method Summary
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
equals, 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