Class Angles


  • public class Angles
    extends java.lang.Object
    Collection of methods for analysing angles
    • Constructor Summary

      Constructors 
      Constructor Description
      Angles()  
    • Constructor Detail

      • Angles

        public Angles()
    • Method Detail

      • 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 java.util.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 java.util.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 java.util.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 java.util.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 java.util.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 java.util.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 java.util.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 java.util.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 java.util.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