Package jgromacs.analysis

Class Angles

java.lang.Object
jgromacs.analysis.Angles
public class Angles extends Object
Collection of methods for analysing angles

  • Constructor Details

    • Angles

      public Angles()

  • Method Details

    • getAngleBetweenVectors

      public static Angle getAngleBetweenVectors(Point3D v1, Point3D v2)
      Calculates the angle between two vectors
      Parameters:
      v1 - first vector
      v2 - second vector
      Returns:
      angle between vectors

    • getAngleBetweenPlanes

      public static Angle getAngleBetweenPlanes(Point3D A, Point3D B, Point3D C, Point3D D)
      Calculates the angle between two planes defined by points A, B, C and points B, C, D
      Parameters:
      A - point A
      B - point B
      C - point C
      D - point D
      Returns:
      angle between planes

    • getDihedralPhi

      public static Angle getDihedralPhi(Structure s, int i)
      Calculates dihedral angle Phi of residue #i of a structure
      Parameters:
      s - structure
      Returns:
      dihedral angle Phi

    • getDihedralPsi

      public static Angle getDihedralPsi(Structure s, int i)
      Calculates dihedral angle Psi of residue #i of a structure
      Parameters:
      s - structure
      Returns:
      dihedral angle Psi

    • getDihedralOmega

      public static Angle getDihedralOmega(Structure s, int i)
      Calculates dihedral angle Omega of residue #i of a structure
      Parameters:
      s - structure
      Returns:
      dihedral angle Omega

    • getDihedralChi1

      public static Angle getDihedralChi1(Structure s, int i)
      Calculates side chain dihedral angle Chi1 of residue #i of a structure The residue can be ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER,THR,TRP,TYR or VAL
      Parameters:
      s - structure
      Returns:
      dihedral angle Chi1

    • getDihedralChi2

      public static Angle getDihedralChi2(Structure s, int i)
      Calculates side chain dihedral angle Chi2 of residue #i of a structure The residue can only be ARG,ASN,ASP,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,TRP or TYR
      Parameters:
      s - structure
      Returns:
      dihedral angle Chi2

    • getDihedralChi3

      public static Angle getDihedralChi3(Structure s, int i)
      Calculates side chain dihedral angle Chi3 of residue #i of a structure The residue can only be ARG,GLN,GLU,LYS or MET
      Parameters:
      s - structure
      Returns:
      dihedral angle Chi3

    • getDihedralChi4

      public static Angle getDihedralChi4(Structure s, int i)
      Calculates side chain dihedral angle Chi4 of residue #i of a structure The residue can only be ARG or LYS
      Parameters:
      s - structure
      Returns:
      dihedral angle Chi4

    • getDihedralChi5

      public static Angle getDihedralChi5(Structure s, int i)
      Calculates side chain dihedral angle Chi5 of residue #i of a structure The residue can only be ARG
      Parameters:
      s - structure
      Returns:
      dihedral angle Chi5

    • getDihedralPhiTimeSeries

      public static ArrayList<Angle> getDihedralPhiTimeSeries(Trajectory t, int i)
      Calculates the time series of dihedral angle Phi of residue #i over a trajectory
      Parameters:
      t - trajectory
      Returns:
      time series of Phi

    • getDihedralPsiTimeSeries

      public static ArrayList<Angle> getDihedralPsiTimeSeries(Trajectory t, int i)
      Calculates the time series of dihedral angle Psi of residue #i over a trajectory
      Parameters:
      t - trajectory
      Returns:
      time series of Psi

    • getDihedralOmegaTimeSeries

      public static ArrayList<Angle> getDihedralOmegaTimeSeries(Trajectory t, int i)
      Calculates the time series of dihedral angle Omega of residue #i over a trajectory
      Parameters:
      t - trajectory
      Returns:
      time series of Omega

    • getDihedralChi1TimeSeries

      public static ArrayList<Angle> getDihedralChi1TimeSeries(Trajectory t, int i)
      Calculates the time series of dihedral angle Chi1 of residue #i over a trajectory The residue can be ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER,THR,TRP,TYR or VAL
      Parameters:
      t - trajectory
      Returns:
      time series of Chi1

    • getDihedralChi2TimeSeries

      public static ArrayList<Angle> getDihedralChi2TimeSeries(Trajectory t, int i)
      Calculates the time series of dihedral angle Chi2 of residue #i over a trajectory The residue can only be ARG,ASN,ASP,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,TRP or TYR
      Parameters:
      t - trajectory
      Returns:
      time series of Chi2

    • getDihedralChi3TimeSeries

      public static ArrayList<Angle> getDihedralChi3TimeSeries(Trajectory t, int i)
      Calculates the time series of dihedral angle Chi3 of residue #i over a trajectory The residue can only be ARG,GLN,GLU,LYS or MET
      Parameters:
      t - trajectory
      Returns:
      time series of Chi3

    • getDihedralChi4TimeSeries

      public static ArrayList<Angle> getDihedralChi4TimeSeries(Trajectory t, int i)
      Calculates the time series of dihedral angle Chi4 of residue #i over a trajectory The residue can only be ARG or LYS
      Parameters:
      t - trajectory
      Returns:
      time series of Chi4

    • getDihedralChi5TimeSeries

      public static ArrayList<Angle> getDihedralChi5TimeSeries(Trajectory t, int i)
      Calculates the time series of dihedral angle Chi5 of residue #i over a trajectory The residue can only be ARG
      Parameters:
      t - trajectory
      Returns:
      time series of Chi5

    • getTorsionAngleTimeSeries

      public static ArrayList<Angle> getTorsionAngleTimeSeries(Trajectory t, int atom1, int atom2, int atom3, int atom4)
      Calculates the time series of torsion angle over a trajectory defined by four atoms
      Parameters:
      t - trajectory
      atom1 - index of first atom
      atom2 - index of second atom
      atom3 - index of third atom
      atom4 - index of fourth atom
      Returns:
      time series of torsion angle

    • getRamachandranPlot

      public static Jama.Matrix getRamachandranPlot(Structure s)
      Calculates the Ramachandran Plot of a structure
      Parameters:
      s - structure (a polypeptide chain)
      Returns:
      (N-2)x2 matrix of (phi,psi) pairs