Hi Mike,
The usual incantation when working with suppliers, and this is shown in a
lot of sample code, is to check to see if the molecule that is returned is
None (which indicates a problem processing it).
The simple way to do this, and to report the error molecules to stdout (you
can change this) is:
for i,mol in enumerate(supplier):
if mol is None:
print(supplier.GetItemText(i))
continue
do_whatever_you_want(mol)
If you're using the [] notation to retrieve a molecule from the supplier
(as in your example above), you just need to do a check like:
mol = suppl[0]
if mol is None:
there_is_a_problem()
else:
do_whatever_you_want()
-greg
On Tue, Sep 24, 2019 at 4:53 PM <mi...@novadatasolutions.co.uk> wrote:
> Hello RDKit gurus,
>
>
>
> I've found an interesting issue with V2000 SDF files which have a carbon
> marked as "Either or unmarked stereocentre", a 3 in the atom-block.
>
>
>
> The enclosed molecule throws these errors – note also that the word
> “begining" is spelt wrong in the stderr.
>
>
>
> Is there a way to “try-catch” when I run these commands, as the program
> crashes when it hits a molecule it can not pass.
>
> suppl = Chem.SDMolSupplier(‘sdf_file.sdf’)
>
> Chem.MolTo-whatever(suppl[x])
>
>
>
> So that if a molecule fails here it can be sent to sdterr?
>
>
>
> Thanks,
>
> mike
>
>
>
> Python command line:
>
>
>
> ****
>
> Pre-condition Violation
>
> bad dir
>
> Violation occurred on line 1755 in file
> /opt/conda/conda-bld/rdkit_1561471048963/work/Code/GraphMol/Chirality.cpp
>
> Failed Expression: dir == Bond::ENDUPRIGHT || dir == Bond::ENDDOWNRIGHT
>
> ****
>
>
>
> [14:34:59] Unexpected error hit on line 317044
>
> [14:34:59] ERROR: moving to the begining of the next molecule
>
> Traceback (most recent call last):
>
> File "AllChem_prop.py", line 178, in <module>
>
> main()
>
> File "AllChem_prop.py", line 170, in main
>
> calc_values = calc_SDF(file_names)
>
> File "AllChem_prop.py", line 105, in calc_SDF
>
> orig = Chem.MolToSmiles(suppl[i])
>
> Boost.Python.ArgumentError: Python argument types in
>
> rdkit.Chem.rdmolfiles.MolToSmiles(NoneType)
>
> did not match C++ signature:
>
> MolToSmiles(RDKit::ROMol mol, bool isomericSmiles=True, bool
> kekuleSmiles=False, int rootedAtAtom=-1, bool canonical=True, bool
> allBondsExplicit=False, bool allHsExplicit=False, bool doRandom=False)
>
>
>
>
>
>
>
> Jupyter-notebook
>
>
>
> ArgumentError Traceback (most recent call last)
>
> <ipython-input-400-56f3f05e3048> in <module>
>
> 1 suppl = Chem.SDMolSupplier('enamine_fail_3.sdf')
>
> ----> 2 Chem.MolToSmiles(suppl[0],kekuleSmiles=True)
>
> 3 Chem.rdDepictor.Compute2DCoords(suppl[0])
>
> 4 Draw.MolToImage(suppl[0], size=(300, 300))
>
>
>
> ArgumentError: Python argument types in
>
> rdkit.Chem.rdmolfiles.MolToSmiles(NoneType)
>
> did not match C++ signature:
>
> MolToSmiles(RDKit::ROMol mol, bool isomericSmiles=True, bool
> kekuleSmiles=False, int rootedAtAtom=-1, bool canonical=True, bool
> allBondsExplicit=False, bool allHsExplicit=False, bool doRandom=False)
>
>
>
>
>
>
>
>
>
>
>
> Dr Mike Mazanetz, FRSC
>
> Director
>
>
>
> Honorary Lecturer
>
> School of Natural and Computing Sciences
>
> University of Aberdeen
>
>
>
> +44 (0) 141 533 0930
>
> +44 (0) 7780 672509
>
> mi...@novadatasolutions.co.uk
>
> www.novadatasolutions.co.uk
>
> skype michael.mazanetz
>
>
>
> NovaData Solutions Ltd.
>
> PO Box 639
>
> Abingdon-on-Thames
>
> Oxfordshire
>
> OX14 9JD
>
> United Kingdom
>
>
>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
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