schrodinger.application.desmond.torsion_related module¶

class schrodinger.application.desmond.torsion_related.TorsionPotential(a1, a2, a3, a4, cms, lig_atoms, results=None, calc_tors=True)[source]¶

Bases: object

A class to contain the atom numbers for each torsion

dih = None¶

__init__(a1, a2, a3, a4, cms, lig_atoms, results=None, calc_tors=True)[source]¶

set_color(col)[source]¶

get_color()[source]¶

set_ligand_from(lfrom)[source]¶

set_ligand_to(lto)[source]¶

get_angles()[source]¶

set_rbpotential(rbp)[source]¶

get_potential()[source]¶

init_ff(st, atom_list)[source]¶

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

class schrodinger.application.desmond.torsion_related.BondRotator(st, rb_atoms, angle_diff=10, ff=16, debug=False, canonicalize=True, sampling=True)[source]¶

Bases: object

perform RB scan

__init__(st, rb_atoms, angle_diff=10, ff=16, debug=False, canonicalize=True, sampling=True)[source]¶

potential(conf=None, degree=True)[source]¶

get potential energy corresponding to ‘conf’ :param conf: conformation in degrees to get corresponding potential :type conf: float

:rtype float

search_and_scan(ct)[source]¶: Get best profile by using fast3d to generate multiple initial coordinates. self.results to contain the best profile.

getRotEnergy(offset=False)[source]¶

schrodinger.application.desmond.torsion_related.get_old2new(st, prop='i_m_original_index')[source]¶: Get dictionary for atom-level property ‘prop’ as a key, and return it’s new atom index (aid)

exception schrodinger.application.desmond.torsion_related.IncompleteFragmentError[source]¶

Bases: Exception

__init__(*args, **kwargs)¶

args¶

with_traceback()¶: Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

schrodinger.application.desmond.torsion_related.get_rb_potential(cms_model, lig_aids, a1, a2, a3, a4)[source]¶

schrodinger.application.desmond.torsion_related.rb_potential_from_struct(lig_st, tor_sys_idx)[source]¶

Creates bond rotator object to calculate torsional potential for a given structure. The input structure should have ‘ORIGINAL_INDEX’ property.

Parameters

lig_st (structure.Structure) – ligand structure
tor_sys_idx (list[int]) – list of atom indices to define torsion

Returns

bond rotator object

Return type

BondRotator

schrodinger.application.desmond.torsion_related.get_rb_torsions_potential(cms_model, lig_aids, a1, a2, a3, a4)[source]¶