Class Distances


  • public class Distances
    extends java.lang.Object
    Collection of methods for analysing distances
    • 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