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adaptive number_of_conformers #4

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adaptive number_of_conformers #4

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15 changes: 14 additions & 1 deletion structural/molecule.py
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Original file line number Diff line number Diff line change
Expand Up @@ -512,6 +512,19 @@ def get_molecule_infos_from_smiles_with_batched_conformers(smiles, number_of_con
enforceChirality=True,
numThreads=-1)

number_of_conformers_ = number_of_conformers
while m.GetNumConformers() < number_of_conformers:
number_of_conformers_ *= 2
AllChem.EmbedMultipleConfs(
m,
numConfs=number_of_conformers_,
maxAttempts=max_attempts,
pruneRmsThresh=.1,
useExpTorsionAnglePrefs=True,
useBasicKnowledge=True,
enforceChirality=True,
numThreads=-1)

if addhs_in_post and add_hs:
m = Chem.AddHs(m, addCoords=True, )
for i in range(number_of_conformers):
Expand Down Expand Up @@ -1115,4 +1128,4 @@ def crippen_multi(sdf_file, smiles, num_conf=50, add_hs=True, iterations=50, max
(score, rmsd, trans) = p2p_alignment(smiles_mol, sdf_mol, iterations=iterations)
Chem.rdMolTransforms.TransformConformer(smiles_mol.GetConformer(0), trans)
molinfo = MoleculeInfo.from_molblock(Chem.MolToMolBlock(smiles_mol), smiles)
yield (score, rmsd, trans), molinfo
yield (score, rmsd, trans), molinfo