bad params pointer

[Sean Cutler]

Any idea what might be causing this? I can send a link to the sdf file that I’m processing if that’s useful. Below is the traceback.
Sean

Traceback (most recent call last):
File "run_gypsum_dl.py", line 220, in <module>
prepare_molecules(INPUTS)
File "/home/sean/Downloads/gypsum_dl-1.1.2/gypsum_dl/Start.py", line 230, in prepare_molecules
execute_gypsum_dl(contnrs, params)
File "/home/sean/Downloads/gypsum_dl-1.1.2/gypsum_dl/Start.py", line 275, in execute_gypsum_dl
prepare_smiles(contnrs, params)
File "/home/sean/Downloads/gypsum_dl-1.1.2/gypsum_dl/Steps/SMILES/PrepareSmiles.py", line 64, in prepare_smiles
parallelizer_obj)
File "/home/sean/Downloads/gypsum_dl-1.1.2/gypsum_dl/Steps/SMILES/AddHydrogens.py", line 116, in add_hydrogens
contnrs, results, max_variants_per_compound, thoroughness
File "/home/sean/Downloads/gypsum_dl-1.1.2/gypsum_dl/ChemUtils.py", line 163, in bst_for_each_contnr_no_opt
mols, max_variants_per_compound, thoroughness
File "/home/sean/Downloads/gypsum_dl-1.1.2/gypsum_dl/ChemUtils.py", line 64, in pick_lowest_enrgy_mols
mol.make_first_3d_conf_no_min() # Make sure at least one conformer
File "/home/sean/Downloads/gypsum_dl-1.1.2/gypsum_dl/MyMol.py", line 272, in make_first_3d_conf_no_min
self.add_conformers(1, 1e60, False)
File "/home/sean/Downloads/gypsum_dl-1.1.2/gypsum_dl/MyMol.py", line 577, in add_conformers
new_conf = MyConformer(self)
File "/home/sean/Downloads/gypsum_dl-1.1.2/gypsum_dl/MyMol.py", line 747, in init
ff = AllChem.UFFGetMoleculeForceField(self.mol)
RuntimeError: Pre-condition Violation
bad params pointer
Violation occurred on line 75 in file Code/ForceField/UFF/AngleBend.cpp
Failed Expression: at2Params
RDKIT: 2017.09.1
BOOST: 1_63

[Jacob Durrant]

Hi Sean. Thanks for your message. I’ve never seen this error before. It appears to be a problem with RDKit, one of Gypsum-DL’s dependencies. Can you share the specific SMILES string that led to this error so I can debug? Thanks.

[Sean Cutler]

This error arose while processing a virtual library built from ZINC building blocks. I’m not exactly sure which compound was to blame, but I will narrow it down and post a SMILEs string for a problematic compound in a bit.

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