public class Angles
extends java.lang.Object
Constructor and Description |
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Angles() |
Modifier and Type | Method and Description |
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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
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static Angle |
getAngleBetweenVectors(Point3D v1,
Point3D v2)
Calculates the angle between two vectors
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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
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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
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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
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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
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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
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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
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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
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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
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static Angle |
getDihedralOmega(Structure s,
int i)
Calculates dihedral angle Omega of residue #i of a structure
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static java.util.ArrayList<Angle> |
getDihedralOmegaTimeSeries(Trajectory t,
int i)
Calculates the time series of dihedral angle Omega of residue #i over a trajectory
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static Angle |
getDihedralPhi(Structure s,
int i)
Calculates dihedral angle Phi of residue #i of a structure
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static java.util.ArrayList<Angle> |
getDihedralPhiTimeSeries(Trajectory t,
int i)
Calculates the time series of dihedral angle Phi of residue #i over a trajectory
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static Angle |
getDihedralPsi(Structure s,
int i)
Calculates dihedral angle Psi of residue #i of a structure
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static java.util.ArrayList<Angle> |
getDihedralPsiTimeSeries(Trajectory t,
int i)
Calculates the time series of dihedral angle Psi of residue #i over a trajectory
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static Jama.Matrix |
getRamachandranPlot(Structure s)
Calculates the Ramachandran Plot of a structure
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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
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public static Angle getAngleBetweenVectors(Point3D v1, Point3D v2)
v1
- first vectorv2
- second vectorpublic static Angle getAngleBetweenPlanes(Point3D A, Point3D B, Point3D C, Point3D D)
A
- point AB
- point BC
- point CD
- point Dpublic static Angle getDihedralPhi(Structure s, int i)
s
- structurepublic static Angle getDihedralPsi(Structure s, int i)
s
- structurepublic static Angle getDihedralOmega(Structure s, int i)
s
- structurepublic static Angle getDihedralChi1(Structure s, int i)
s
- structurepublic static Angle getDihedralChi2(Structure s, int i)
s
- structurepublic static Angle getDihedralChi3(Structure s, int i)
s
- structurepublic static Angle getDihedralChi4(Structure s, int i)
s
- structurepublic static Angle getDihedralChi5(Structure s, int i)
s
- structurepublic static java.util.ArrayList<Angle> getDihedralPhiTimeSeries(Trajectory t, int i)
t
- trajectorypublic static java.util.ArrayList<Angle> getDihedralPsiTimeSeries(Trajectory t, int i)
t
- trajectorypublic static java.util.ArrayList<Angle> getDihedralOmegaTimeSeries(Trajectory t, int i)
t
- trajectorypublic static java.util.ArrayList<Angle> getDihedralChi1TimeSeries(Trajectory t, int i)
t
- trajectorypublic static java.util.ArrayList<Angle> getDihedralChi2TimeSeries(Trajectory t, int i)
t
- trajectorypublic static java.util.ArrayList<Angle> getDihedralChi3TimeSeries(Trajectory t, int i)
t
- trajectorypublic static java.util.ArrayList<Angle> getDihedralChi4TimeSeries(Trajectory t, int i)
t
- trajectorypublic static java.util.ArrayList<Angle> getDihedralChi5TimeSeries(Trajectory t, int i)
t
- trajectorypublic 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 atompublic static Jama.Matrix getRamachandranPlot(Structure s)
s
- structure (a polypeptide chain)