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
enamine_fail_3.sdf
Description: chemical/mdl-sdfile
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