Package jgromacs.analysis
Class Angles
java.lang.Object
jgromacs.analysis.Angles
Collection of methods for analysing angles
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic 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 VALgetDihedralChi1TimeSeries
(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 TYRgetDihedralChi2TimeSeries
(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 METgetDihedralChi3TimeSeries
(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 LYSgetDihedralChi4TimeSeries
(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 ARGgetDihedralChi5TimeSeries
(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 structuregetDihedralOmegaTimeSeries
(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 structuregetDihedralPhiTimeSeries
(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 structuregetDihedralPsiTimeSeries
(Trajectory t, int i) Calculates the time series of dihedral angle Psi of residue #i over a trajectorystatic Jama.Matrix
Calculates the Ramachandran Plot of a structuregetTorsionAngleTimeSeries
(Trajectory t, int atom1, int atom2, int atom3, int atom4) Calculates the time series of torsion angle over a trajectory defined by four atoms
-
Constructor Details
-
Angles
public Angles()
-
-
Method Details
-
getAngleBetweenVectors
Calculates the angle between two vectors- Parameters:
v1
- first vectorv2
- second vector- Returns:
- angle between vectors
-
getAngleBetweenPlanes
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
-
getDihedralPhi
Calculates dihedral angle Phi of residue #i of a structure- Parameters:
s
- structure- Returns:
- dihedral angle Phi
-
getDihedralPsi
Calculates dihedral angle Psi of residue #i of a structure- Parameters:
s
- structure- Returns:
- dihedral angle Psi
-
getDihedralOmega
Calculates dihedral angle Omega of residue #i of a structure- Parameters:
s
- structure- Returns:
- dihedral angle Omega
-
getDihedralChi1
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
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
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
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
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
Calculates the time series of dihedral angle Phi of residue #i over a trajectory- Parameters:
t
- trajectory- Returns:
- time series of Phi
-
getDihedralPsiTimeSeries
Calculates the time series of dihedral angle Psi of residue #i over a trajectory- Parameters:
t
- trajectory- Returns:
- time series of Psi
-
getDihedralOmegaTimeSeries
Calculates the time series of dihedral angle Omega of residue #i over a trajectory- Parameters:
t
- trajectory- Returns:
- time series of Omega
-
getDihedralChi1TimeSeries
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
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
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
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
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 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
-
getRamachandranPlot
Calculates the Ramachandran Plot of a structure- Parameters:
s
- structure (a polypeptide chain)- Returns:
- (N-2)x2 matrix of (phi,psi) pairs
-