Package jgromacs.analysis
Class Angles
- java.lang.Object
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- jgromacs.analysis.Angles
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public class Angles extends java.lang.Object
Collection of methods for analysing angles
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Constructor Summary
Constructors Constructor Description Angles()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method 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, Dstatic Angle
getAngleBetweenVectors(Point3D v1, Point3D v2)
Calculates the angle between two vectorsstatic 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 VALstatic 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 VALstatic 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 TYRstatic 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 TYRstatic 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 METstatic 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 METstatic 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 LYSstatic 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 LYSstatic Angle
getDihedralChi5(Structure s, int i)
Calculates side chain dihedral angle Chi5 of residue #i of a structure The residue can only be ARGstatic 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 ARGstatic Angle
getDihedralOmega(Structure s, int i)
Calculates dihedral angle Omega of residue #i of a structurestatic java.util.ArrayList<Angle>
getDihedralOmegaTimeSeries(Trajectory t, int i)
Calculates the time series of dihedral angle Omega of residue #i over a trajectorystatic Angle
getDihedralPhi(Structure s, int i)
Calculates dihedral angle Phi of residue #i of a structurestatic java.util.ArrayList<Angle>
getDihedralPhiTimeSeries(Trajectory t, int i)
Calculates the time series of dihedral angle Phi of residue #i over a trajectorystatic Angle
getDihedralPsi(Structure s, int i)
Calculates dihedral angle Psi of residue #i of a structurestatic java.util.ArrayList<Angle>
getDihedralPsiTimeSeries(Trajectory t, int i)
Calculates the time series of dihedral angle Psi of residue #i over a trajectorystatic Jama.Matrix
getRamachandranPlot(Structure s)
Calculates the Ramachandran Plot of a structurestatic 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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Method Detail
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getAngleBetweenVectors
public static Angle getAngleBetweenVectors(Point3D v1, Point3D v2)
Calculates the angle between two vectors- Parameters:
v1
- first vectorv2
- second vector- Returns:
- angle between vectors
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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 AB
- point BC
- point CD
- point D- Returns:
- angle between planes
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
- trajectoryatom1
- index of first atomatom2
- index of second atomatom3
- index of third atomatom4
- index of fourth atom- Returns:
- time series of torsion angle
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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
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