Re: [Rdkit-discuss] Errors with RDKit

[Wandré <wan...@gm...>]

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 <in...@ch...>:

> 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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