PROFASI  Version 1.5
Protected Member Functions | List of all members
prf::HydrogenBond Class Reference

HydrogenBond base class from which the HBMM and HBMS classes are derived. More...

#include <HydrogenBond.hh>

Inheritance diagram for prf::HydrogenBond:
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Protected Member Functions

double hb_pair (Dipole &don, Dipole &acc, int excl1, int excl2)
 Bare hydrogen bond function between two dipoles.
 

Detailed Description

The HydrogenBond base class implements the basic functional form of the hydrogen bond terms in PROFASI. The terms represented by HBMM and HBMS make use of backbone NH and CO dipoles. It is convenient to store information about them in one place.

Member Function Documentation

double prf::HydrogenBond::hb_pair ( Dipole &  don,
Dipole &  acc,
int  excl1,
int  excl2 
)
protected

hb_pair, in version 1.1 of profasi, calculates the interaction between a pair of dipoles. Dipoles now know which ligand and chain they are on. hp_pair makes use of this information to decide whether or not to use periodic boundary conditions. Since by contruction in profasi, no pair of atoms in a single protein can have a distance greater than one box length, periodic distance measure is not used if both dipoles are in the same chain. The ligand index is used to enforce the suppression of hydrogen bonds between neighbouring residues. The dipoles belonging to neighbouring peptide units do not participate in hydrogen bonding. For each dipole, there is therefore an excluded region in the list of dipoles. The region is given in relative ligand indices with respect to the ligand contributing the donor. If excl1 is -2 and excl2 is 0, it means, the contribution is 0 for acceptor ligand indices idon-2, idon-1 and idon.


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