Class Torsion

A class to contain the atom numbers for each torsion

Instance Methods

[hide private]

__init__(self, a1, a2, a3, a4, cms, lig_atoms, results=None, calc_tors=True)

set_color(self, col)

get_color(self)

set_ligand_from(self, lfrom)

set_ligand_to(self, lto)

get_angles(self)

set_rbpotential(self, rbp)

get_potential(self)

__str__(self)

_convert_index_to_asl(self, index_list)

_get_utt_potential(self, atom_list)
Given atom_list (i,j,k,l), to get a full potential around j-k in st, we need to also look at all the atoms connected to j and k, and reconstruct UTT

_get_energy(self, tor, angle)

_get_potential(self, st, atom_list)

init_ff(self, st, atom_list)
This function initializes torsion force field parameters relevant to the ligand.

Class Variables

[hide private]

dih = None
hash(x)

Method Details

[hide private]

init_ff(self, st, atom_list)

This function initializes torsion force field parameters relevant to the ligand. Ligand is defined by a list of atoms.

Parameters:

st (structure.Structure) - structure object for all molecules
atom_list (list) - list of ligand atom indices