Braden BradenDKelly

A Knight who says Ni. BSc. MSc. Chemical Engineering PhD. Biophysics I try to code in Julia. I like molecular simulation and thermodynamics.

BradenDKelly / conf_gen.py

Created November 23, 2021 18:15 — forked from tdudgeon/conf_gen.py

Conformer generation using RDKit

	import sys
	from rdkit import Chem
	from rdkit.Chem import AllChem, TorsionFingerprints
	from rdkit.ML.Cluster import Butina


	def gen_conformers(mol, numConfs=100, maxAttempts=1000, pruneRmsThresh=0.1, useExpTorsionAnglePrefs=True, useBasicKnowledge=True, enforceChirality=True):
	ids = AllChem.EmbedMultipleConfs(mol, numConfs=numConfs, maxAttempts=maxAttempts, pruneRmsThresh=pruneRmsThresh, useExpTorsionAnglePrefs=useExpTorsionAnglePrefs, useBasicKnowledge=useBasicKnowledge, enforceChirality=enforceChirality, numThreads=0)
	return list(ids)