Re: [Rdkit-discuss] Errors with RDKit

[Axel P. <axe...@gm...>]

Hi Carlos,


insert this in your loop:


if not mol: continue



Kind regards,

Axel


On 23.01.2018 03:59, Carlos Faerman wrote:
>
> 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
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss