jgromacs.analysis

Class Distances

java.lang.Object

jgromacs.analysis.Distances

public class Distances
extends java.lang.Object

Collection of methods for analysing distances

Field Summary

Fields

Modifier and Type	Field and Description
static int	ALPHACARBON
static int	CLOSEST
static int	CLOSESTHEAVY

Constructor Summary

Constructors

Constructor and Description
Distances()

Method Summary

Modifier and Type	Method and Description
static Atom	findClosestAtom(Structure s, IndexSet atomset, IndexSet referenceset) Returns the atom from a given atom set that is closest to a reference set of atoms
static PointList	findFrameWhereClosest(Trajectory t, int atomindex1, int atomindex2) Returns the frame in which two atoms are closest to each other in a simulation
static PointList	findFrameWhereMostDistant(Trajectory t, int atomindex1, int atomindex2) Returns the frame in which two atoms are most distant from each other in a simulation
static Jama.Matrix	getAtomicDistanceMatrix(Structure s) Calculates the distance matrix of all atoms in a structure
static Jama.Matrix	getAtomicDistanceMatrix(Structure s, IndexSet indices) Calculates the distance matrix of atoms of given indices in a structure
static Jama.Matrix	getAtomicDistanceMatrix(Structure s, IndexSet indices1, IndexSet indices2) Calculates the distance matrix between two sets of atoms
static IndexSet	getAtomIndicesInRadius(Structure s, Atom atom, double radius) Returns the index set of atoms in a structure that are closer to a reference atom than a given radius
static IndexSet	getAtomIndicesInRadius(Structure s, IndexSet referenceindices, double radius) Returns the index set of atoms in a structure that are closer to a reference set of atoms than a given radius
static IndexSet	getAtomIndicesInRadius(Structure s, IndexSet atomIndices, IndexSet referenceIndices, double radius) Returns the index set of atoms from a set of atoms that are closer to a reference set than a given radius
static IndexSet	getAtomIndicesInRadius(Structure s, Point3D point, double radius) Returns the index set of atoms in a structure that are closer to a reference point than a given radius
static Jama.Matrix	getContactMatrix(PointList points, double cutoff) Calculates the contact matrix from a point list
static Jama.Matrix	getContactMatrix(Structure s, int distanceBetween, double cutoff) Calculates the contact matrix of residues in a structure by the given method
static Jama.Matrix	getContactOfMeanMatrix(Trajectory t, int distanceBetween, double cutoff) Calculates the contact matrix based on the mean residue distance matrix in a trajectory
static Jama.Matrix	getDistanceMatrix(PointList points) Calculates the distance matrix from a point list
static double	getDistanceOfAtomToAtomSet(Structure s, int atomindex, IndexSet referenceset) Calculates the distance of an atom to a reference set of atoms (i.e.
static double	getDistanceOfTwoAtomSets(Structure s, IndexSet indices1, IndexSet indices2) Calculates the distance between two sets of atoms (i.e.
static double	getDistanceRange(Trajectory t, int atomindex1, int atomindex2) Returns the range (max-min) of the distance of two atoms in a trajectory
static java.util.ArrayList<java.lang.Double>	getDistanceTimeSeries(Trajectory t, IndexSet indices1, IndexSet indices2) Returns the time series of the distance of two sets of atoms in a trajectory
static java.util.ArrayList<java.lang.Double>	getDistanceTimeSeries(Trajectory t, int atomindex, IndexSet referenceset) Returns the time series of the distance of a single atom and a set of atoms in a trajectory
static java.util.ArrayList<java.lang.Double>	getDistanceTimeSeries(Trajectory t, int atomindex1, int atomindex2) Returns the time series of the distance of two atoms in a trajectory
static FrameIndexSet	getFramesWhereAtomIsCloseToPoint(Trajectory t, int atomindex, Point3D point, double cutoff) Returns the list of frames in the trajectory where an atoms is closer to a reference point than a given cutoff
static FrameIndexSet	getFramesWhereAtomIsDistantFromPoint(Trajectory t, int atomindex, Point3D point, double cutoff) Returns the list of frames in the trajectory where an atoms is more distant from a reference point than a given cutoff
static FrameIndexSet	getFramesWhereAtomsAreClose(Trajectory t, int atomindex1, int atomindex2, double cutoff) Returns the list of frames in a trajectory where two atoms are closer to each other than the given cutoff
static FrameIndexSet	getFramesWhereAtomsAreDistant(Trajectory t, int atomindex1, int atomindex2, double cutoff) Returns the list of frames in a trajectory where two atoms are more distant from each other than the given cutoff
static Jama.Matrix	getFrequencyContactMatrix(Trajectory t, int distanceBetween, double cutoff, double frequency) Calculates the contact matrix of residues where two residues are said to be in contact if they are in contact in at least the given percentage of frames of the trajectory
static double	getMaximalDistance(Trajectory t, int atomindex1, int atomindex2) Returns the maximal distance of two atoms in a trajectory
static Jama.Matrix	getMeanAtomicDistanceMatrix(Trajectory t) Calculates the mean distance matrix of all atoms in a trajectory
static Jama.Matrix	getMeanAtomicDistanceMatrix(Trajectory t, IndexSet indices) Calculates the mean distance matrix of atoms of given indices in a trajectory
static double	getMeanDistance(Trajectory t, int atomindex1, int atomindex2) Returns the mean of the distance of two atoms in a trajectory
static Jama.Matrix	getMeanResidueDistanceMatrix(Trajectory t, int distanceBetween) Calculates the mean distance matrix of residues in a trajectory by the given method
static double	getMinimalDistance(Trajectory t, int atomindex1, int atomindex2) Returns the minimal distance of two atoms in a trajectory
static Jama.Matrix	getResidueDistanceMatrix(Structure s, int distanceBetween) Calculates the distance matrix of residues in a structure by the given method
static double	getVarianceOfDistance(Trajectory t, int atomindex1, int atomindex2) Returns the variance of the distance of two atoms in a trajectory

Methods inherited from class java.lang.Object

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

Field Detail

ALPHACARBON

public static final int ALPHACARBON

See Also:

Constant Field Values

CLOSEST

public static final int CLOSEST

See Also:

Constant Field Values

CLOSESTHEAVY

public static final int CLOSESTHEAVY

See Also:

Constant Field Values

Constructor Detail

Distances

public Distances()

Method Detail

getDistanceMatrix

public static Jama.Matrix getDistanceMatrix(PointList points)

Calculates the distance matrix from a point list

Parameters:

points - point list

Returns:

distance matrix

getAtomicDistanceMatrix

public static Jama.Matrix getAtomicDistanceMatrix(Structure s)

Calculates the distance matrix of all atoms in a structure

Parameters:

s - structure

Returns:

distance matrix

getAtomicDistanceMatrix

public static Jama.Matrix getAtomicDistanceMatrix(Structure s,
                                                  IndexSet indices)

Calculates the distance matrix of atoms of given indices in a structure

Parameters:

s - structure

indices - index set

Returns:

distance matrix

getAtomicDistanceMatrix

public static Jama.Matrix getAtomicDistanceMatrix(Structure s,
                                                  IndexSet indices1,
                                                  IndexSet indices2)

Calculates the distance matrix between two sets of atoms

Parameters:

s - structure

indices1 - index set 1

indices2 - index set 2

Returns:

distance matrix

getResidueDistanceMatrix

public static Jama.Matrix getResidueDistanceMatrix(Structure s,
                                                   int distanceBetween)

Calculates the distance matrix of residues in a structure by the given method

Parameters:

s - structure

distanceBetween - which atoms are used for calculating the distances (ALPHACARBON: alpha carbon atoms, CLOSEST: closest atoms of two residues, CLOSESTHEAVY: closest heavy atoms of two residues)

Returns:

distance matrix

getMeanAtomicDistanceMatrix

public static Jama.Matrix getMeanAtomicDistanceMatrix(Trajectory t)

Calculates the mean distance matrix of all atoms in a trajectory

Parameters:

t - trajecotry

Returns:

mean distance matrix

getMeanAtomicDistanceMatrix

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

Calculates the mean distance matrix of atoms of given indices in a trajectory

Parameters:

t - trajecotry

indices - index set

Returns:

mean distance matrix

getMeanResidueDistanceMatrix

public static Jama.Matrix getMeanResidueDistanceMatrix(Trajectory t,
                                                       int distanceBetween)

Calculates the mean distance matrix of residues in a trajectory by the given method

Parameters:

t - trajectory

distanceBetween - which atoms are used for calculating the distances (ALPHACARBON: alpha carbon atoms, CLOSEST: closest atoms of two residues, CLOSESTHEAVY: closest heavy atoms of two residues)

Returns:

mean distance matrix

getContactMatrix

public static Jama.Matrix getContactMatrix(PointList points,
                                           double cutoff)

Calculates the contact matrix from a point list

Parameters:

points - point list

cutoff - distance cutoff

Returns:

contact matrix

getContactMatrix

public static Jama.Matrix getContactMatrix(Structure s,
                                           int distanceBetween,
                                           double cutoff)

Calculates the contact matrix of residues in a structure by the given method

Parameters:

s - structure

distanceBetween - which atoms are used for calculating the distances (ALPHACARBON: alpha carbon atoms, CLOSEST: closest atoms of two residues, CLOSESTHEAVY: closest heavy atoms of two residues)

cutoff - distance cutoff

Returns:

contact matrix

getContactOfMeanMatrix

public static Jama.Matrix getContactOfMeanMatrix(Trajectory t,
                                                 int distanceBetween,
                                                 double cutoff)

Calculates the contact matrix based on the mean residue distance matrix in a trajectory

Parameters:

t - trajectory

distanceBetween - which atoms are used for calculating the distances (ALPHACARBON: alpha carbon atoms, CLOSEST: closest atoms of two residues, CLOSESTHEAVY: closest heavy atoms of two residues)

cutoff - distance cutoff

Returns:

contact matrix

getFrequencyContactMatrix

public static Jama.Matrix getFrequencyContactMatrix(Trajectory t,
                                                    int distanceBetween,
                                                    double cutoff,
                                                    double frequency)

Calculates the contact matrix of residues where two residues are said to be in contact if they are in contact in at least the given percentage of frames of the trajectory

Parameters:

t - trajectory

distanceBetween - which atoms are used for calculating the distances (ALPHACARBON: alpha carbon atoms, CLOSEST: closest atoms of two residues, CLOSESTHEAVY: closest heavy atoms of two residues)

cutoff - distance cutoff

frequency - minimal frequency of frames in which two residues are in contact

Returns:

contact matrix

getDistanceTimeSeries

public static java.util.ArrayList<java.lang.Double> getDistanceTimeSeries(Trajectory t,
                                                                          int atomindex1,
                                                                          int atomindex2)

Returns the time series of the distance of two atoms in a trajectory

Parameters:

t - trajectory

atomindex1 - index of first atom

atomindex2 - index of second atom

Returns:

time series of distance

getDistanceTimeSeries

public static java.util.ArrayList<java.lang.Double> getDistanceTimeSeries(Trajectory t,
                                                                          int atomindex,
                                                                          IndexSet referenceset)

Returns the time series of the distance of a single atom and a set of atoms in a trajectory

Parameters:

t - trajectory

atomindex - index of atom

referenceset - index set of reference atoms

Returns:

time series of distance

getDistanceTimeSeries

public static java.util.ArrayList<java.lang.Double> getDistanceTimeSeries(Trajectory t,
                                                                          IndexSet indices1,
                                                                          IndexSet indices2)

Returns the time series of the distance of two sets of atoms in a trajectory

Parameters:

t - trajectory

indices1 - first index set

indices2 - second index set

Returns:

time series of distance

getMeanDistance

public static double getMeanDistance(Trajectory t,
                                     int atomindex1,
                                     int atomindex2)

Returns the mean of the distance of two atoms in a trajectory

Parameters:

t - trajectory

atomindex1 - index of first atom

atomindex2 - index of second atom

Returns:

mean of distance

getVarianceOfDistance

public static double getVarianceOfDistance(Trajectory t,
                                           int atomindex1,
                                           int atomindex2)

Returns the variance of the distance of two atoms in a trajectory

Parameters:

t - trajectory

atomindex1 - index of first atom

atomindex2 - index of second atom

Returns:

variance of distance

getMinimalDistance

public static double getMinimalDistance(Trajectory t,
                                        int atomindex1,
                                        int atomindex2)

Returns the minimal distance of two atoms in a trajectory

Parameters:

t - trajectory

atomindex1 - index of first atom

atomindex2 - index of second atom

Returns:

minimal distance

getMaximalDistance

public static double getMaximalDistance(Trajectory t,
                                        int atomindex1,
                                        int atomindex2)

Returns the maximal distance of two atoms in a trajectory

Parameters:

t - trajectory

atomindex1 - index of first atom

atomindex2 - index of second atom

Returns:

maximal distance

getDistanceRange

public static double getDistanceRange(Trajectory t,
                                      int atomindex1,
                                      int atomindex2)

Returns the range (max-min) of the distance of two atoms in a trajectory

Parameters:

t - trajectory

atomindex1 - index of first atom

atomindex2 - index of second atom

Returns:

size of distance interval

getAtomIndicesInRadius

public static IndexSet getAtomIndicesInRadius(Structure s,
                                              Point3D point,
                                              double radius)

Returns the index set of atoms in a structure that are closer to a reference point than a given radius

Parameters:

s - structure

point - reference point

radius - distance radius

Returns:

atom indices

getAtomIndicesInRadius

public static IndexSet getAtomIndicesInRadius(Structure s,
                                              Atom atom,
                                              double radius)

Returns the index set of atoms in a structure that are closer to a reference atom than a given radius

Parameters:

s - structure

atom - reference atom

radius - distance radius

Returns:

atom indices

getAtomIndicesInRadius

public static IndexSet getAtomIndicesInRadius(Structure s,
                                              IndexSet referenceindices,
                                              double radius)

Returns the index set of atoms in a structure that are closer to a reference set of atoms than a given radius

Parameters:

s - structure

referenceindices - index set of reference atoms

radius - distance radius

Returns:

atom indices

getAtomIndicesInRadius

public static IndexSet getAtomIndicesInRadius(Structure s,
                                              IndexSet atomIndices,
                                              IndexSet referenceIndices,
                                              double radius)

Returns the index set of atoms from a set of atoms that are closer to a reference set than a given radius

Parameters:

s - structure

atomIndices - index set of atoms tested

referenceIndices - index set of reference atoms

radius - distance radius

Returns:

atom indices

findFrameWhereClosest

public static PointList findFrameWhereClosest(Trajectory t,
                                              int atomindex1,
                                              int atomindex2)

Returns the frame in which two atoms are closest to each other in a simulation

Parameters:

t - trajectory

atomindex1 - index of first atom

atomindex2 - index of second atom

Returns:

frame of trajectory

findFrameWhereMostDistant

public static PointList findFrameWhereMostDistant(Trajectory t,
                                                  int atomindex1,
                                                  int atomindex2)

Returns the frame in which two atoms are most distant from each other in a simulation

Parameters:

t - trajectory

atomindex1 - index of first atom

atomindex2 - index of second atom

Returns:

frame of trajectory

getDistanceOfAtomToAtomSet

public static double getDistanceOfAtomToAtomSet(Structure s,
                                                int atomindex,
                                                IndexSet referenceset)

Calculates the distance of an atom to a reference set of atoms (i.e. the minimum of all pairwise distances)

Parameters:

s - structure

atomindex - index of atom

referenceset - index set of reference atoms

Returns:

minimal distance

getDistanceOfTwoAtomSets

public static double getDistanceOfTwoAtomSets(Structure s,
                                              IndexSet indices1,
                                              IndexSet indices2)

Calculates the distance between two sets of atoms (i.e. the minimum of all pairwise distances)

Parameters:

s - structure

indices1 - first index set

indices2 - second index set

Returns:

minimal distance

findClosestAtom

public static Atom findClosestAtom(Structure s,
                                   IndexSet atomset,
                                   IndexSet referenceset)

Returns the atom from a given atom set that is closest to a reference set of atoms

Parameters:

s - structure

atomset - index set of atoms

referenceset - index set of reference atoms

Returns:

closest atom

getFramesWhereAtomsAreClose

public static FrameIndexSet getFramesWhereAtomsAreClose(Trajectory t,
                                                        int atomindex1,
                                                        int atomindex2,
                                                        double cutoff)

Returns the list of frames in a trajectory where two atoms are closer to each other than the given cutoff

Parameters:

t - trajectory

atomindex1 - index of first atom

atomindex2 - index of second atom

cutoff - distance cutoff

Returns:

frame list

getFramesWhereAtomsAreDistant

public static FrameIndexSet getFramesWhereAtomsAreDistant(Trajectory t,
                                                          int atomindex1,
                                                          int atomindex2,
                                                          double cutoff)

Returns the list of frames in a trajectory where two atoms are more distant from each other than the given cutoff

Parameters:

t - trajectory

atomindex1 - index of first atom

atomindex2 - index of second atom

cutoff - distance cutoff

Returns:

frame list

getFramesWhereAtomIsCloseToPoint

public static FrameIndexSet getFramesWhereAtomIsCloseToPoint(Trajectory t,
                                                             int atomindex,
                                                             Point3D point,
                                                             double cutoff)

Returns the list of frames in the trajectory where an atoms is closer to a reference point than a given cutoff

Parameters:

t - trajectory

atomindex - index of atom

point - reference point

cutoff - distance cutoff

Returns:

frame list

getFramesWhereAtomIsDistantFromPoint

public static FrameIndexSet getFramesWhereAtomIsDistantFromPoint(Trajectory t,
                                                                 int atomindex,
                                                                 Point3D point,
                                                                 double cutoff)

Returns the list of frames in the trajectory where an atoms is more distant from a reference point than a given cutoff

Parameters:

t - trajectory

atomindex - index of atom

point - reference point

cutoff - distance cutoff

Returns:

frame list