jgromacs.analysis

Class Angles

java.lang.Object

jgromacs.analysis.Angles

public class Angles
extends java.lang.Object

Collection of methods for analysing angles

Constructor Summary

Constructors

Constructor and Description
Angles()

Method Summary

Modifier and Type	Method and Description
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
static Angle	getAngleBetweenVectors(Point3D v1, Point3D v2) Calculates the angle between two vectors
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
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
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
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
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
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
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
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
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
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
static Angle	getDihedralOmega(Structure s, int i) Calculates dihedral angle Omega of residue #i of a structure
static java.util.ArrayList<Angle>	getDihedralOmegaTimeSeries(Trajectory t, int i) Calculates the time series of dihedral angle Omega of residue #i over a trajectory
static Angle	getDihedralPhi(Structure s, int i) Calculates dihedral angle Phi of residue #i of a structure
static java.util.ArrayList<Angle>	getDihedralPhiTimeSeries(Trajectory t, int i) Calculates the time series of dihedral angle Phi of residue #i over a trajectory
static Angle	getDihedralPsi(Structure s, int i) Calculates dihedral angle Psi of residue #i of a structure
static java.util.ArrayList<Angle>	getDihedralPsiTimeSeries(Trajectory t, int i) Calculates the time series of dihedral angle Psi of residue #i over a trajectory
static Jama.Matrix	getRamachandranPlot(Structure s) Calculates the Ramachandran Plot of a structure
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

Methods inherited from class java.lang.Object

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

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