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java.lang.Object jgromacs.analysis.Angles
public class Angles
Collection of methods for analysing angles
Constructor Summary | |
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Angles()
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Method Summary | |
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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 |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public Angles()
Method Detail |
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public static Angle getAngleBetweenVectors(Point3D v1, Point3D v2)
v1
- first vectorv2
- second vector
public static Angle getAngleBetweenPlanes(Point3D A, Point3D B, Point3D C, Point3D D)
A
- point AB
- point BC
- point CD
- point D
public static Angle getDihedralPhi(Structure s, int i)
s
- structure
public static Angle getDihedralPsi(Structure s, int i)
s
- structure
public static Angle getDihedralOmega(Structure s, int i)
s
- structure
public static Angle getDihedralChi1(Structure s, int i)
s
- structure
public static Angle getDihedralChi2(Structure s, int i)
s
- structure
public static Angle getDihedralChi3(Structure s, int i)
s
- structure
public static Angle getDihedralChi4(Structure s, int i)
s
- structure
public static Angle getDihedralChi5(Structure s, int i)
s
- structure
public static java.util.ArrayList<Angle> getDihedralPhiTimeSeries(Trajectory t, int i)
t
- trajectory
public static java.util.ArrayList<Angle> getDihedralPsiTimeSeries(Trajectory t, int i)
t
- trajectory
public static java.util.ArrayList<Angle> getDihedralOmegaTimeSeries(Trajectory t, int i)
t
- trajectory
public static java.util.ArrayList<Angle> getDihedralChi1TimeSeries(Trajectory t, int i)
t
- trajectory
public static java.util.ArrayList<Angle> getDihedralChi2TimeSeries(Trajectory t, int i)
t
- trajectory
public static java.util.ArrayList<Angle> getDihedralChi3TimeSeries(Trajectory t, int i)
t
- trajectory
public static java.util.ArrayList<Angle> getDihedralChi4TimeSeries(Trajectory t, int i)
t
- trajectory
public static java.util.ArrayList<Angle> getDihedralChi5TimeSeries(Trajectory t, int i)
t
- trajectory
public static java.util.ArrayList<Angle> getTorsionAngleTimeSeries(Trajectory t, int atom1, int atom2, int atom3, int atom4)
t
- trajectoryatom1
- index of first atomatom2
- index of second atomatom3
- index of third atomatom4
- index of fourth atom
public static jama.Matrix getRamachandranPlot(Structure s)
s
- structure (a polypeptide chain)
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