Hi Wandré and Axel,
Thank you both !
I ended up adding this to my code:
if not mol: continue
Which works well for me
Carlos
________________________________
From: Wandré <wandrevel...@gmail.com>
Sent: Tuesday, January 23, 2018 4:29 AM
To: Carlos Faerman
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Errors with RDKit
Hi Carlos,
Simmilar to Axel, in my code I use
if mol is None: return False (if you are using a function to read each SDF file)
if mol is None: continue (to force the next loop)
--
Wandré Nunes de Pinho Veloso
Professor Assistente - Unifei - Campus Avançado de Itabira-MG
Doutorando em Bioinformática - Universidade Federal de Minas Gerais - UFMG
Pesquisador do INSILICO - Grupo Interdisciplinar em Simulação e Inteligência
Computacional - UNIFEI
Membro do Grupo de Pesquisa Assinaturas Biológicas da FIOCRUZ
Membro do Grupo de Pesquisa Bioinformática Estrutural da UFMG
Laboratório de Bioinformática e Sistemas - LBS, DCC, UFMG
2018-01-23 0:59 GMT-02:00 Carlos Faerman
<i...@chemvisen.com<mailto:i...@chemvisen.com>>:
Hello,
My code is very simple:
suppl4 = Chem.SDMolSupplier("/Volumes/MyPassportForMac/chembl_23.sdf")
i = 0
for mol in suppl4:
smile = Chem.MolToSmiles(mol,isomericSmiles=True)
fingerpri = get_fp_rdkit(mol)
namenmol = mol.GetProp("_Name")
patron[namenmol]=fingerpri
print (i,namenmol,smile)
outfile.write('{} {} {}\n'.format(namenmol,smile,fingerpri))
i = i+1
I know that a few molecules in Chembl_23.sdf have wrong valences.
Is there a way to skip these molecules when these errors are found?
671231 CHEMBL1254908 O=C(NCCN1CCC2(CC1)C(=O)NCN2c1cccc(Cl)c1)c1cc2cc(F)ccc2[nH]1
[21:18:16] Explicit valence for atom # 35 N, 5, is greater than permitted
[21:18:16] ERROR: Could not sanitize molecule ending on line 48940986
[21:18:16] ERROR: Explicit valence for atom # 35 N, 5, is greater than permitted
Traceback (most recent call last):
File "calculate-fingerprints.py", line 23, in <module>
smile = Chem.MolToSmiles(mol,isomericSmiles=True)
Boost.Python.ArgumentError: Python argument types in
rdkit.Chem.rdmolfiles.MolToSmiles(NoneType)
did not match C++ signature:
MolToSmiles(RDKit::ROMol mol, bool isomericSmiles=False, bool
kekuleSmiles=False, int rootedAtAtom=-1, bool canonical=True, bool
allBondsExplicit=False, bool allHsExplicit=False)
The "culprit" molecule seems to be
CHEMBL450200
-My question to this forum:
Please suggest a way to modify the code to skip the wrong molecule(s) instead
of abruptly ending the run
Thank you,
Carlos Faerman
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