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)

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)

Initialize self. See help(type(self)) for accurate signature.

set_color(col)

get_color()

set_ligand_from(lfrom)

set_ligand_to(lto)

get_angles()

set_rbpotential(rbp)

get_potential()

init_ff(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

class schrodinger.application.desmond.torsion_related.BondRotator(st, rb_atoms, angle_diff=10, ff=16, debug=False, canonicalize=True, prime_hmc=True, hmc_steps=20, is_fep=False)

Bases: object

perform RB scan

__init__(st, rb_atoms, angle_diff=10, ff=16, debug=False, canonicalize=True, prime_hmc=True, hmc_steps=20, is_fep=False)

Parameters:is_fep – Prime license is not checkout for FEP system.

potential(conf=None, degree=True)

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

:rtype float

run_hmc(nsteps=20, max_confs=10)

Run Prime’s Hybrid Monte Carlo (HMC), return top output cts that will be ‘deduplicated’ by energy and rmsd. :param nsteps: Number of MC steps :param max_confs: Number of maximum conformers to return :rtype: list(structure.Structure)

prime_search_and_scan(nsteps=20)

Get best profile by using Prime HMC to generate multiple initial coordinates. Modify self.results to reflect the best profile.

getRotEnergy(offset=False)

schrodinger.application.desmond.torsion_related.get_old2new(st, prop='i_m_original_index')

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

Bases: Exception

__init__

Initialize self. See help(type(self)) for accurate signature.

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)

schrodinger.application.desmond.torsion_related.get_rb_torsions_potential(cms_model, lig_aids, a1, a2, a3, a4)