From bcd4e10e848c31a3223581a5003761bb1787b098 Mon Sep 17 00:00:00 2001 From: bieniekmat Date: Tue, 1 Aug 2023 17:37:37 +0100 Subject: [PATCH] Using the neater .to_openmm() in the new openff-toolkit --- fegrow/receptor.py | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/fegrow/receptor.py b/fegrow/receptor.py index feee2d4f..fc21ac91 100644 --- a/fegrow/receptor.py +++ b/fegrow/receptor.py @@ -1,20 +1,20 @@ from copy import deepcopy from typing import List, Tuple -import parmed +import numpy from openmmforcefields.generators import SystemGenerator from pdbfixer import PDBFixer +import parmed from rdkit import Chem from rdkit.Geometry.rdGeometry import Point3D -from tqdm import tqdm from typing_extensions import Literal +from tqdm import tqdm -from .package import RMol from openmmml import MLPotential -import numpy +from .package import RMol + -# fix for new openmm versions try: from openmm import app, openmm, unit, Platform except (ImportError, ModuleNotFoundError): @@ -201,10 +201,8 @@ def optimise_in_receptor( for i, conformer in enumerate( tqdm(openff_mol.conformers, desc="Optimising conformer: ", ncols=80) ): - # make the ligand coords - lig_vec = unit.Quantity([c.m.tolist() for c in conformer], unit=unit.angstrom) + complex_coords = numpy.concatenate([receptor_coords, conformer.to_openmm()]) - complex_coords = receptor_coords + lig_vec # set the initial positions simulation.context.setPositions(complex_coords) # now minimize the energy