jgromacs.analysis
Class Similarity

java.lang.Object
  jgromacs.analysis.Similarity

public class Similarity
extends java.lang.Object

Collection of methods for measuring structural similarity

Constructor Summary

Similarity()

Method Summary

static FrameIndexSet	findSimilarFramesDRMSD(Trajectory t, Jama.Matrix reference, double cutoff) Returns the list of frames in a trajectory that are more similar to a reference distance matrix (based on the dRMSD similarity measure) than a cutoff value
static FrameIndexSet	findSimilarFramesDRMSD(Trajectory t, PointList reference, double cutoff) Returns the list of frames in a trajectory that are more similar to a reference frame (based on the dRMSD similarity measure) than a cutoff value
static FrameIndexSet	findSimilarFramesRMSD(Trajectory t, PointList reference, double cutoff) Returns the set of frames in a trajectory that are more similar to a reference frame (based on the RMSD similarity measure) than a cutoff value
static Jama.Matrix	getDifferenceDistanceMatrix(PointList points1, PointList points2) Calculates the difference distance matrix between two point lists
static Jama.Matrix	getDifferenceDistanceMatrix(Structure s1, IndexSet indices1, Structure s2, IndexSet indices2) Calculates the atomic difference distance matrix between two sets of atoms defined by two index sets in two structures
static Jama.Matrix	getDifferenceDistanceMatrix(Structure s1, Structure s2) Calculates the atomic difference distance matrix between two structures
static double	getDRMSD(Jama.Matrix A, Jama.Matrix B) Calculates dRMSD similarity between two distance matrices
static double	getDRMSD(PointList A, PointList B) Calculates dRMSD similarity between two point lists
static double	getDRMSD(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB) Calculates dRMSD similarity between two groups of atoms
static double	getDRMSD(Structure A, Structure B) Calculates dRMSD similarity between two structures
static java.util.ArrayList<java.lang.Double>	getDRMSDiProfile(Jama.Matrix A, Jama.Matrix B) Calculates the dRMSDi profile between two distance matrices
static java.util.ArrayList<java.lang.Double>	getDRMSDiProfile(PointList A, PointList B) Calculates the dRMSDi profile between two point lists
static java.util.ArrayList<java.lang.Double>	getDRMSDiProfile(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB) Calculates the dRMSDi profile between two groups of atoms
static java.util.ArrayList<java.lang.Double>	getDRMSDiProfile(Structure A, Structure B) Calculates the dRMSDi profile between two structures
static PointList	getMedoidDRMSD(Trajectory t) Calculates the medoid frame of a trajectory using the dRMSD measure
static PointList	getMedoidRMSD(Trajectory t) Calculates the medoid frame of a trajectory using the RMSD measure
static double	getRMSD(PointList A, PointList B) Calculates RMSD similarity between two point lists
static double	getRMSD(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB) Calculates RMSD similarity between two groups of atoms
static double	getRMSD(Structure A, Structure B) Calculates RMSD similarity between two structures
static java.util.ArrayList<java.lang.Double>	getRMSDiProfile(PointList A, PointList B) Calculates the RMSDi profile between two point lists
static java.util.ArrayList<java.lang.Double>	getRMSDiProfile(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB) Calculates the RMSDi profile between two groups of atoms
static java.util.ArrayList<java.lang.Double>	getRMSDiProfile(Structure A, Structure B) Calculates the RMSDi profile between two structures
static java.util.ArrayList<java.lang.Double>	getRMSDiProfileNoSuperposition(PointList A, PointList B) Calculates the RMSDi profile between two point lists without superposition
static java.util.ArrayList<java.lang.Double>	getRMSDiProfileNoSuperposition(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB) Calculates the RMSDi profile between two groups of atoms without superposition
static java.util.ArrayList<java.lang.Double>	getRMSDiProfileNoSuperposition(Structure A, Structure B) Calculates the RMSDi profile between two structures without superposition
static double	getRMSDnoSuperposition(PointList A, PointList B) Calculates RMSD similarity between two point lists without doing superposition
static double	getRMSDnoSuperposition(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB) Calculates RMSD similarity between two groups of atoms without superposition
static double	getRMSDnoSuperposition(Structure A, Structure B) Calculates RMSD similarity between two structures without doing superposition
static Jama.Matrix	getSimilarityMatrixDRMSD(Trajectory t) Calculates the similarity matrix of all frames in a trajectory using the dRMSD measure
static Jama.Matrix	getSimilarityMatrixDRMSD(Trajectory t, IndexSet indices) Calculates the similarity matrix of all frames in a trajectory using the dRMSD measure taking into account only a subset of atoms
static Jama.Matrix	getSimilarityMatrixRMSD(Trajectory t) Calculates the similarity matrix of all frames in a trajectory using the RMSD measure
static Jama.Matrix	getSimilarityMatrixRMSD(Trajectory t, IndexSet indices) Calculates the similarity matrix of all frames in a trajectory using the RMSD measure taking into account only a subset of atoms
static Jama.Matrix	getSimilarityMatrixWDRMSD(Trajectory t, IndexSet indices, Jama.Matrix W) Calculates the similarity matrix of all frames in a trajectory using the wdRMSD (weighted dRMSD) measure taking into account only a subset of atoms
static Jama.Matrix	getSimilarityMatrixWDRMSD(Trajectory t, Jama.Matrix W) Calculates the similarity matrix of all frames in a trajectory using the wdRMSD (weighted dRMSD) measure
static java.util.ArrayList<java.lang.Double>	getSimilarityTimeSeriesDRMSD(Trajectory t, IndexSet indicesT, Structure R, IndexSet indicesR) Returns the time series of dRMSD in a trajectory with regards to a reference structure taking into account only a subset of atoms
static java.util.ArrayList<java.lang.Double>	getSimilarityTimeSeriesDRMSD(Trajectory t, PointList R) Returns the time series of dRMSD in a trajectory with regards to a reference point list
static java.util.ArrayList<java.lang.Double>	getSimilarityTimeSeriesDRMSD(Trajectory t, Structure R) Returns the time series of dRMSD in a trajectory with regards to a reference structure
static java.util.ArrayList<java.lang.Double>	getSimilarityTimeSeriesRMSD(Trajectory t, IndexSet indicesT, Structure R, IndexSet indicesR) Returns the time series of RMSD in a trajectory with regards to a reference structure taking into account only a subset of atoms
static java.util.ArrayList<java.lang.Double>	getSimilarityTimeSeriesRMSD(Trajectory t, PointList R) Returns the time series of RMSD in a trajectory with regards to a reference point list
static java.util.ArrayList<java.lang.Double>	getSimilarityTimeSeriesRMSD(Trajectory t, Structure R) Returns the time series of RMSD in a trajectory with regards to a reference structure
static java.util.ArrayList<java.lang.Double>	getSimilarityTimeSeriesWDRMSD(Trajectory t, IndexSet indicesT, Structure R, IndexSet indicesR, Jama.Matrix W) Returns the time series of wdRMSD (weighted dRMSD) in a trajectory with regards to a reference structure taking into account only a subset of atoms
static java.util.ArrayList<java.lang.Double>	getSimilarityTimeSeriesWDRMSD(Trajectory t, PointList R, Jama.Matrix W) Returns the time series of wdRMSD (weighted dRMSD) in a trajectory with regards to a reference point list
static java.util.ArrayList<java.lang.Double>	getSimilarityTimeSeriesWDRMSD(Trajectory t, Structure R, Jama.Matrix W) Returns the time series of wdRMSD (weighted dRMSD) in a trajectory with regards to a reference structure
static double	getWDRMSD(PointList A, PointList B, Jama.Matrix W) Calculates the wdRMSD (weighted dRMSD) similarity of two point lists
static double	getWDRMSD(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB, Jama.Matrix W) Calculates wdRMSD (weighted dRMSD) similarity between two groups of atoms
static double	getWDRMSD(Structure A, Structure B, Jama.Matrix W) Calculates the wdRMSD (weighted dRMSD) similarity of two structures
static java.util.ArrayList<java.lang.Double>	getWDRMSDiProfile(PointList A, PointList B, Jama.Matrix W) Calculates the wdRMSDi (weighted dRMSDi) profile between two point lists
static java.util.ArrayList<java.lang.Double>	getWDRMSDiProfile(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB, Jama.Matrix W) Calculates the wdRMSDi (weighted dRMSDi) profile between two groups of atoms
static java.util.ArrayList<java.lang.Double>	getWDRMSDiProfile(Structure A, Structure B, Jama.Matrix W) Calculates the wdRMSDi (weighted dRMSDi) profile between two structures

Methods inherited from class java.lang.Object

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

Constructor Detail

Similarity

public Similarity()

Method Detail

getRMSD

public static double getRMSD(PointList A,
                             PointList B)

Calculates RMSD similarity between two point lists

Parameters:

A - first point list

B - second point list

Returns:

RMSD

getRMSD

public static double getRMSD(Structure A,
                             Structure B)

Calculates RMSD similarity between two structures

Parameters:

A - first structure

B - second structure

Returns:

RMSD

getRMSD

public static double getRMSD(Structure A,
                             IndexSet indicesA,
                             Structure B,
                             IndexSet indicesB)

Calculates RMSD similarity between two groups of atoms

Parameters:

A - first structure

indicesA - index set of atoms in the first structure

B - second structure

indicesB - index set of atoms in the second structure

Returns:

RMSD

getRMSDiProfile

public static java.util.ArrayList<java.lang.Double> getRMSDiProfile(PointList A,
                                                                    PointList B)

Calculates the RMSDi profile between two point lists

Parameters:

A - first point list

B - second point list

Returns:

RMSDi profile

getRMSDiProfile

public static java.util.ArrayList<java.lang.Double> getRMSDiProfile(Structure A,
                                                                    Structure B)

Calculates the RMSDi profile between two structures

Parameters:

A - first structure

B - second structure

Returns:

RMSDi profile

getRMSDiProfile

public static java.util.ArrayList<java.lang.Double> getRMSDiProfile(Structure A,
                                                                    IndexSet indicesA,
                                                                    Structure B,
                                                                    IndexSet indicesB)

Calculates the RMSDi profile between two groups of atoms

Parameters:

A - first structure

indicesA - index set of atoms in the first structure

B - second structure

indicesB - index set of atoms in the second structure

Returns:

RMSDi profile

getRMSDnoSuperposition

public static double getRMSDnoSuperposition(PointList A,
                                            PointList B)

Calculates RMSD similarity between two point lists without doing superposition

Parameters:

A - first point list

B - second point list

Returns:

RMSD without superposition

getRMSDnoSuperposition

public static double getRMSDnoSuperposition(Structure A,
                                            Structure B)

Calculates RMSD similarity between two structures without doing superposition

Parameters:

A - first structure

B - second structure

Returns:

RMSD without superposition

getRMSDnoSuperposition

public static double getRMSDnoSuperposition(Structure A,
                                            IndexSet indicesA,
                                            Structure B,
                                            IndexSet indicesB)

Calculates RMSD similarity between two groups of atoms without superposition

Parameters:

A - first structure

indicesA - index set of atoms in the first structure

B - second structure

indicesB - index set of atoms in the second structure

Returns:

RMSD without superposition

getRMSDiProfileNoSuperposition

public static java.util.ArrayList<java.lang.Double> getRMSDiProfileNoSuperposition(PointList A,
                                                                                   PointList B)

Calculates the RMSDi profile between two point lists without superposition

Parameters:

A - first point list

B - second point list

Returns:

RMSDi profile without superposition

getRMSDiProfileNoSuperposition

public static java.util.ArrayList<java.lang.Double> getRMSDiProfileNoSuperposition(Structure A,
                                                                                   Structure B)

Calculates the RMSDi profile between two structures without superposition

Parameters:

A - first structure

B - second structure

Returns:

RMSDi profile without superposition

getRMSDiProfileNoSuperposition

public static java.util.ArrayList<java.lang.Double> getRMSDiProfileNoSuperposition(Structure A,
                                                                                   IndexSet indicesA,
                                                                                   Structure B,
                                                                                   IndexSet indicesB)

Calculates the RMSDi profile between two groups of atoms without superposition

Parameters:

A - first structure

indicesA - index set of atoms in the first structure

B - second structure

indicesB - index set of atoms in the second structure

Returns:

RMSDi profile without superposition

getDRMSD

public static double getDRMSD(Jama.Matrix A,
                              Jama.Matrix B)

Calculates dRMSD similarity between two distance matrices

Parameters:

A - first distance matrix

B - second distance matrix

Returns:

dRMSD

getDRMSD

public static double getDRMSD(PointList A,
                              PointList B)

Calculates dRMSD similarity between two point lists

Parameters:

A - first point list

B - second point list

Returns:

dRMSD

getDRMSD

public static double getDRMSD(Structure A,
                              Structure B)

Calculates dRMSD similarity between two structures

Parameters:

A - first structure

B - second structure

Returns:

dRMSD

getDRMSD

public static double getDRMSD(Structure A,
                              IndexSet indicesA,
                              Structure B,
                              IndexSet indicesB)

Calculates dRMSD similarity between two groups of atoms

Parameters:

A - first structure

indicesA - index set of atoms in the first structure

B - second structure

indicesB - index set of atoms in the second structure

Returns:

dRMSD

getDRMSDiProfile

public static java.util.ArrayList<java.lang.Double> getDRMSDiProfile(Jama.Matrix A,
                                                                     Jama.Matrix B)

Calculates the dRMSDi profile between two distance matrices

Parameters:

A - first distance matrix

B - second distance matrix

Returns:

dRMSDi profile

getDRMSDiProfile

public static java.util.ArrayList<java.lang.Double> getDRMSDiProfile(PointList A,
                                                                     PointList B)

Calculates the dRMSDi profile between two point lists

Parameters:

A - first point list

B - second point list

Returns:

dRMSDi profile

getDRMSDiProfile

public static java.util.ArrayList<java.lang.Double> getDRMSDiProfile(Structure A,
                                                                     Structure B)

Calculates the dRMSDi profile between two structures

Parameters:

A - first structure

B - second structure

Returns:

dRMSDi profile

getDRMSDiProfile

public static java.util.ArrayList<java.lang.Double> getDRMSDiProfile(Structure A,
                                                                     IndexSet indicesA,
                                                                     Structure B,
                                                                     IndexSet indicesB)

Calculates the dRMSDi profile between two groups of atoms

Parameters:

A - first structure

indicesA - index set of atoms in the first structure

B - second structure

indicesB - index set of atoms in the second structure

Returns:

dRMSDi profile

getWDRMSD

public static double getWDRMSD(PointList A,
                               PointList B,
                               Jama.Matrix W)

Calculates the wdRMSD (weighted dRMSD) similarity of two point lists

Parameters:

A - first point list

B - second point list

W - weight matrix

Returns:

wdRMSD

getWDRMSD

public static double getWDRMSD(Structure A,
                               Structure B,
                               Jama.Matrix W)

Calculates the wdRMSD (weighted dRMSD) similarity of two structures

Parameters:

A - first structure

B - second structure

W - weight matrix

Returns:

wdRMSD

getWDRMSD

public static double getWDRMSD(Structure A,
                               IndexSet indicesA,
                               Structure B,
                               IndexSet indicesB,
                               Jama.Matrix W)

Calculates wdRMSD (weighted dRMSD) similarity between two groups of atoms

Parameters:

A - first structure

indicesA - index set of atoms in the first structure

B - second structure

indicesB - index set of atoms in the second structure

W - weight matrix

Returns:

wdRMSD

getWDRMSDiProfile

public static java.util.ArrayList<java.lang.Double> getWDRMSDiProfile(PointList A,
                                                                      PointList B,
                                                                      Jama.Matrix W)

Calculates the wdRMSDi (weighted dRMSDi) profile between two point lists

Parameters:

A - first point list

B - second point list

W - weight matrix

Returns:

wdRMSDi profile

getWDRMSDiProfile

public static java.util.ArrayList<java.lang.Double> getWDRMSDiProfile(Structure A,
                                                                      Structure B,
                                                                      Jama.Matrix W)

Calculates the wdRMSDi (weighted dRMSDi) profile between two structures

Parameters:

A - first structure

B - second structure

W - weight matrix

Returns:

wdRMSDi profile

getWDRMSDiProfile

public static java.util.ArrayList<java.lang.Double> getWDRMSDiProfile(Structure A,
                                                                      IndexSet indicesA,
                                                                      Structure B,
                                                                      IndexSet indicesB,
                                                                      Jama.Matrix W)

Calculates the wdRMSDi (weighted dRMSDi) profile between two groups of atoms

Parameters:

A - first structure

indicesA - index set of atoms in the first structure

B - second structure

indicesB - index set of atoms in the second structure

W - weight matrix

Returns:

wdRMSDi profile

getSimilarityMatrixRMSD

public static Jama.Matrix getSimilarityMatrixRMSD(Trajectory t)

Calculates the similarity matrix of all frames in a trajectory using the RMSD measure

Parameters:

t - trajectory

Returns:

similarity matrix

getSimilarityMatrixRMSD

public static Jama.Matrix getSimilarityMatrixRMSD(Trajectory t,
                                                  IndexSet indices)

Calculates the similarity matrix of all frames in a trajectory using the RMSD measure taking into account only a subset of atoms

Parameters:

t - trajectory

indices - index set of atoms

Returns:

similarity matrix

getSimilarityMatrixDRMSD

public static Jama.Matrix getSimilarityMatrixDRMSD(Trajectory t)

Calculates the similarity matrix of all frames in a trajectory using the dRMSD measure

Parameters:

t - trajectory

Returns:

similarity matrix

getSimilarityMatrixDRMSD

public static Jama.Matrix getSimilarityMatrixDRMSD(Trajectory t,
                                                   IndexSet indices)

Calculates the similarity matrix of all frames in a trajectory using the dRMSD measure taking into account only a subset of atoms

Parameters:

t - trajectory

indices - index set of atoms

Returns:

similarity matrix

getSimilarityMatrixWDRMSD

public static Jama.Matrix getSimilarityMatrixWDRMSD(Trajectory t,
                                                    Jama.Matrix W)

Calculates the similarity matrix of all frames in a trajectory using the wdRMSD (weighted dRMSD) measure

Parameters:

t - trajectory

W - weight matrix

Returns:

similarity matrix

getSimilarityMatrixWDRMSD

public static Jama.Matrix getSimilarityMatrixWDRMSD(Trajectory t,
                                                    IndexSet indices,
                                                    Jama.Matrix W)

Calculates the similarity matrix of all frames in a trajectory using the wdRMSD (weighted dRMSD) measure taking into account only a subset of atoms

Parameters:

t - trajectory

indices - index set of atoms

W - weight matrix

Returns:

similarity matrix

getSimilarityTimeSeriesRMSD

public static java.util.ArrayList<java.lang.Double> getSimilarityTimeSeriesRMSD(Trajectory t,
                                                                                PointList R)

Returns the time series of RMSD in a trajectory with regards to a reference point list

Parameters:

t - trajectory

R - reference point list

Returns:

time series of RMSD

getSimilarityTimeSeriesRMSD

public static java.util.ArrayList<java.lang.Double> getSimilarityTimeSeriesRMSD(Trajectory t,
                                                                                Structure R)

Returns the time series of RMSD in a trajectory with regards to a reference structure

Parameters:

t - trajectory

R - reference structure

Returns:

time series of RMSD

getSimilarityTimeSeriesRMSD

public static java.util.ArrayList<java.lang.Double> getSimilarityTimeSeriesRMSD(Trajectory t,
                                                                                IndexSet indicesT,
                                                                                Structure R,
                                                                                IndexSet indicesR)

Returns the time series of RMSD in a trajectory with regards to a reference structure taking into account only a subset of atoms

Parameters:

t - trajectory

indicesT - index set of atoms in the trajectory

R - reference structure

indicesR - index set of atoms in the reference structure

Returns:

time series of RMSD

getSimilarityTimeSeriesDRMSD

public static java.util.ArrayList<java.lang.Double> getSimilarityTimeSeriesDRMSD(Trajectory t,
                                                                                 PointList R)

Returns the time series of dRMSD in a trajectory with regards to a reference point list

Parameters:

t - trajectory

R - reference point list

Returns:

time series of dRMSD

getSimilarityTimeSeriesDRMSD

public static java.util.ArrayList<java.lang.Double> getSimilarityTimeSeriesDRMSD(Trajectory t,
                                                                                 Structure R)

Returns the time series of dRMSD in a trajectory with regards to a reference structure

Parameters:

t - trajectory

R - reference structure

Returns:

time series of dRMSD

getSimilarityTimeSeriesDRMSD

public static java.util.ArrayList<java.lang.Double> getSimilarityTimeSeriesDRMSD(Trajectory t,
                                                                                 IndexSet indicesT,
                                                                                 Structure R,
                                                                                 IndexSet indicesR)

Returns the time series of dRMSD in a trajectory with regards to a reference structure taking into account only a subset of atoms

Parameters:

t - trajectory

indicesT - index set of atoms in the trajectory

R - reference structure

indicesR - index set of atoms in the reference structure

Returns:

time series of dRMSD

getSimilarityTimeSeriesWDRMSD

public static java.util.ArrayList<java.lang.Double> getSimilarityTimeSeriesWDRMSD(Trajectory t,
                                                                                  PointList R,
                                                                                  Jama.Matrix W)

Returns the time series of wdRMSD (weighted dRMSD) in a trajectory with regards to a reference point list

Parameters:

t - trajectory

R - reference point list

W - weight matrix

Returns:

time series of wdRMSD

getSimilarityTimeSeriesWDRMSD

public static java.util.ArrayList<java.lang.Double> getSimilarityTimeSeriesWDRMSD(Trajectory t,
                                                                                  Structure R,
                                                                                  Jama.Matrix W)

Returns the time series of wdRMSD (weighted dRMSD) in a trajectory with regards to a reference structure

Parameters:

t - trajectory

R - reference structure

W - weight matrix

Returns:

time series of wdRMSD

getSimilarityTimeSeriesWDRMSD

public static java.util.ArrayList<java.lang.Double> getSimilarityTimeSeriesWDRMSD(Trajectory t,
                                                                                  IndexSet indicesT,
                                                                                  Structure R,
                                                                                  IndexSet indicesR,
                                                                                  Jama.Matrix W)

Returns the time series of wdRMSD (weighted dRMSD) in a trajectory with regards to a reference structure taking into account only a subset of atoms

Parameters:

t - trajectory

indicesT - index set of atoms in the trajectory

R - reference structure

indicesR - index set of atoms in the reference structure

W - weight matrix

Returns:

time series of wdRMSD

getDifferenceDistanceMatrix

public static Jama.Matrix getDifferenceDistanceMatrix(PointList points1,
                                                      PointList points2)

Calculates the difference distance matrix between two point lists

Parameters:

points1 - first point list

points2 - second point list

Returns:

difference distance matrix

getDifferenceDistanceMatrix

public static Jama.Matrix getDifferenceDistanceMatrix(Structure s1,
                                                      Structure s2)

Calculates the atomic difference distance matrix between two structures

Parameters:

s1 - first structure

s2 - second structure

Returns:

difference distance matrix

getDifferenceDistanceMatrix

public static Jama.Matrix getDifferenceDistanceMatrix(Structure s1,
                                                      IndexSet indices1,
                                                      Structure s2,
                                                      IndexSet indices2)

Calculates the atomic difference distance matrix between two sets of atoms defined by two index sets in two structures

Parameters:

s1 - first structure

indices1 - first index set

s2 - second structure

indices2 - second index set

Returns:

difference distance matrix

findSimilarFramesRMSD

public static FrameIndexSet findSimilarFramesRMSD(Trajectory t,
                                                  PointList reference,
                                                  double cutoff)

Returns the set of frames in a trajectory that are more similar to a reference frame (based on the RMSD similarity measure) than a cutoff value

Parameters:

t - trajectory

reference - reference frame

cutoff - similarity cutoff

Returns:

frame index set

findSimilarFramesDRMSD

public static FrameIndexSet findSimilarFramesDRMSD(Trajectory t,
                                                   PointList reference,
                                                   double cutoff)

Returns the list of frames in a trajectory that are more similar to a reference frame (based on the dRMSD similarity measure) than a cutoff value

Parameters:

t - trajectory

reference - reference frame

cutoff - similarity cutoff

Returns:

frame list

findSimilarFramesDRMSD

public static FrameIndexSet findSimilarFramesDRMSD(Trajectory t,
                                                   Jama.Matrix reference,
                                                   double cutoff)

Returns the list of frames in a trajectory that are more similar to a reference distance matrix (based on the dRMSD similarity measure) than a cutoff value

Parameters:

t - trajectory

reference - reference distance matrix

cutoff - similarity cutoff

Returns:

frame list

getMedoidRMSD

public static PointList getMedoidRMSD(Trajectory t)

Calculates the medoid frame of a trajectory using the RMSD measure

Parameters:

t - trajectory

Returns:

medoid frame

getMedoidDRMSD

public static PointList getMedoidDRMSD(Trajectory t)

Calculates the medoid frame of a trajectory using the dRMSD measure

Parameters:

t - trajectory

Returns:

medoid frame