schrodinger.application.desmond.torsion_related module

class schrodinger.application.desmond.torsion_related.TorsionPotential(a1: int, a2: int, a3: int, a4: int, cms_model: Cms, lig_atoms: list[int], results=None, calc_tors=True)

Bases: object

A class to contain the atom numbers for each torsion

dih = None

__init__(a1: int, a2: int, a3: int, a4: int, cms_model: Cms, lig_atoms: list[int], results=None, calc_tors=True)

Initialize a torsion potential object for a four-atom dihedral.

Parameters:

• a1 – First atom index in the torsion

• a2 – Second atom index in the torsion (central bond atom 1)

• a3 – Third atom index in the torsion (central bond atom 2)

• a4 – Fourth atom index in the torsion

• cms_model – CMS model containing the full system

• lig_atoms – Ligand atom indices in the full system

• results – Optional precomputed results payload

• calc_tors – Whether to compute torsion potential on initialization

set_color(col)

get_color()

set_ligand_from(lfrom)

set_ligand_to(lto)

get_angles()

set_rbpotential(rbp)

get_potential()

init_ff(st: Structure, atom_list: list[int])

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

Parameters:

• st – structure object for all molecules

• atom_list – list of ligand atom indices

class schrodinger.application.desmond.torsion_related.BondRotator(st: Structure, rb_atoms: list[int], angle_diff: int = 10, opls_version: int = 16, debug: bool = False, canonicalize: bool = True, sampling: bool = True)

Bases: object

perform RB scan

__init__(st: Structure, rb_atoms: list[int], angle_diff: int = 10, opls_version: int = 16, debug: bool = False, canonicalize: bool = True, sampling: bool = True)

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

search_and_scan(st: Structure)

Get best profile by using fast3d to generate multiple initial coordinates. self.results to contain 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

schrodinger.application.desmond.torsion_related.get_rb_potential(cms_model: Structure, lig_aids: list[int], a1: int, a2: int, a3: int, a4: int, opls_version: int = 16)

schrodinger.application.desmond.torsion_related.get_rb_torsions_potential(cms_model: Structure, lig_aids: list[int], a1: int, a2: int, a3: int, a4: int) → list[float]

Calculate torsion potential for a four-atom dihedral using force field parameters.

This function computes the torsion potential energy profile by creating a TorsionPotential object and returning the calculated potential values.

Parameters:

• cms_model – CMS model object containing the molecular structure

• lig_aids – List of ligand atom indices

• a1 – First atom index in the torsion

• a2 – Second atom index in the torsion (central bond atom 1)

• a3 – Third atom index in the torsion (central bond atom 2)

• a4 – Fourth atom index in the torsion

Returns:

Torsion potential values rounded to 3 decimal places