PROFASI  Version 1.5
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prf::Valine Class Reference

Valine. More...

#include <valine.hh>

Inheritance diagram for prf::Valine:
Inheritance graph

Additional Inherited Members

- Public Member Functions inherited from prf::AminoAcid
AtomNitrogen ()
 Reference to backbone nitrogen.
AtomCalpha ()
 Reference to Calpha.
AtomCprime ()
 Reference to C' atom.
AtomHca ()
 Reference to H alpha, or first H attached to C alpha.
AtomCbeta ()
 Reference to C beta.
AtomOc ()
 Reference to O attached to C'.
Atomsidechain_atom (int i)
 Reference to i'th side chain atom.
Atomlabeled_atom (std::string alabel)
 Reference to any atom in the amino acid through its PDB label.
Atomat (std::string alabel)
 Look up and return reference to Atom with a certain label.
double Chi (int i) const
 Side chain torsional DOF numbered from 0.
double Phi () const
 Ramachandran Phi angle about the bond N-CA in the residue.
double Psi () const
 Ramachandran Psi angle about the bond CA-C in the residue.
double Omega () const
 Peptide bond angle between this and the next residue.
void Chi (int i, double x)
 Set side chain torsional DOF.
void Phi (double x)
 Set Ramachandran Phi angle.
void Psi (double x)
 Set Ramachandran Psi angle.
void Omega (double x)
 Set omega angle between this and the next residue.
void calcPhiPsi (double &phv, double &psv) const
 Calculate Ramachandran angles from current 3D coordinates.
bool is_helical () const
 Do the current backbone angles fall in the helix region ?
bool is_strand () const
 Do the current backbone angles fall in the beta strand region ?
void WritePDB (int &atindx, char ch_id, int aaindx, FILE *fp)
 Writes into a PDB file.
void WritePDB2 (int &atindx, char ch_id, int aaindx, FILE *fp)
 Write PDB with heavy atoms first.
double get_coord (int i)
 phi, psi, omega and side chain chi angles
void set_coord (int i, double x)
 Assign to i'th DOF in amino acid.
int n_coord () const
 3+number of side chain angles
double get_dof (int i)
 True degrees of freedom in the residue.
void set_dof (int i, double x)
 Assign to i'th true DOF in amino acid.
int n_dof () const
 Number of true degrees of freedom in the residue.
int rotDof_assign_and_reconstruct (int il, double mgd, int &a0, int &a1)
 Assign to (sidechain) dof i, and return the range of moved atoms.
int rotDof_assign (int il, double mgd)
 Assign to (sidechain) dof i, but don't recalculate any coordinates.
double get_rotDof (int il)
 Value of the i'th (sidechain) dof.
void nodes_reconnect ()
 Reassign atom offsets to the nodes.

Detailed Description

Geometry of valine : an asymmetric tetrahedron (CH), and two tetrahedral nodes with completely symmetric "outgoing" bonds (CH3).

The documentation for this class was generated from the following files:

PROFASI: Protein Folding and Aggregation Simulator, Version 1.5
© (2005-2016) Anders Irbäck and Sandipan Mohanty
Documentation generated on Mon Jul 18 2016 using Doxygen version 1.8.2