Class Distances

java.lang.Object
jgromacs.analysis.Distances

public class Distances extends Object
Collection of methods for analysing distances
  • Field Details

  • Constructor Details

    • Distances

      public Distances()
  • Method Details

    • 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 ArrayList<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 ArrayList<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 ArrayList<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