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import warnings
from rdkit import Chem
from rdkit.Chem.rdForceFieldHelpers import UFFOptimizeMolecule, UFFHasAllMoleculeParams
from src.data import sanifix
def uff_relax(mol, max_iter=200):
"""
Uses RDKit's universal force field (UFF) implementation to optimize a
molecule.
"""
if not UFFHasAllMoleculeParams(mol):
warnings.warn('UFF parameters not available for all atoms. '
'Returning None.')
return None
try:
more_iterations_required = UFFOptimizeMolecule(mol, maxIters=max_iter)
if more_iterations_required:
warnings.warn(f'Maximum number of FF iterations reached. '
f'Returning molecule after {max_iter} relaxation steps.')
except RuntimeError:
return None
return mol
def add_hydrogens(rdmol):
return Chem.AddHs(rdmol, addCoords=(len(rdmol.GetConformers()) > 0))
def get_largest_fragment(rdmol):
mol_frags = Chem.GetMolFrags(rdmol, asMols=True, sanitizeFrags=False)
largest_frag = max(mol_frags, default=rdmol, key=lambda m: m.GetNumAtoms())
# try:
# Chem.SanitizeMol(largest_frag)
# except ValueError:
# return None
return largest_frag
def process_all(rdmol, largest_frag=True, adjust_aromatic_Ns=True, relax_iter=0):
"""
Apply all filters and post-processing steps. Returns a new molecule.
Returns:
RDKit molecule or None if it does not pass the filters or processing
fails
"""
# Only consider non-trivial molecules
if rdmol.GetNumAtoms() < 1:
return None
# Create a copy
mol = Chem.Mol(rdmol)
# try:
# Chem.SanitizeMol(mol)
# except ValueError:
# warnings.warn('Sanitization failed. Returning None.')
# return None
if largest_frag:
mol = get_largest_fragment(mol)
# if mol is None:
# return None
if adjust_aromatic_Ns:
mol = sanifix.fix_mol(mol)
if mol is None:
return None
# if add_hydrogens:
# mol = add_hydrogens(mol)
if relax_iter > 0:
mol = uff_relax(mol, relax_iter)
if mol is None:
return None
try:
Chem.SanitizeMol(mol)
except ValueError:
warnings.warn('Sanitization failed. Returning None.')
return None
return mol
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