Using the neater .to_openmm() in the new openff-toolkit

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