Hi,
I wanted to know if it was possible to do the same thing as in the
cookbook (1) but for conformer optimization : optimize each conformer
generated but in parallel.
I want to optimize conformer generation for one molecule, because it
will be a one molecule job script on a webserver.
I tried with that (part of ) code :
|def optimize(mol, id):||
|| AllChem.UFFOptimizeMolecule(mol, confId=id)||
||
||def main ():||
||
|| global options, args||
||
|| max_workers=4||
||
|| input_file = args.input||
|| sdf_output_file = args.output||
||
|| n = args.nbconf||
||
|| writer = Chem.SDWriter(sdf_output_file)||
||
|| suppl = Chem.SDMolSupplier(input_file)||
||
|| for mol in suppl:||
|| try:||
|| mol = Chem.AddHs(mol)||
|| ids = AllChem.EmbedMultipleConfs(mol, numConfs=n)||
|| ids = list(ids)||
|| # for id in ids:||
|| # AllChem.UFFOptimizeMolecule(mol, confId=id)||
|| except:||
|| raise||
||
|| try:||
|| with futures.ProcessPoolExecutor(max_workers=max_workers)
as executor:||
|| # Submit a set of asynchronous jobs||
|| jobs = []||
|| try:||
|| for id in ids:||
|| job = executor.submit(optimize, mol, id)||
|| jobs.append(job)||
|| except:||
|| raise||
||
|| for job in futures.as_completed(jobs):||
|| for id in ids:||
|| writer.write(mol, confId=id)||
|| writer.close()||
|| except:||
|| raise|
But with nbconf = 10, it generate 100 conformers. So i suspect something
wrong with the optimization function and the job management.
(1) http://www.rdkit.org/docs/Cookbook.html#parallel-conformation-generation
Thank you.
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