- This topic has 2 replies, 1 voice, and was last updated 3 years, 9 months ago by Sean Cutler.
- January 23, 2020 at 6:51 pm #12143Sean CutlerGuest
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.
Traceback (most recent call last):
File "run_gypsum_dl.py", line 220, in <module>
File "/home/sean/Downloads/gypsum_dl-1.1.2/gypsum_dl/Start.py", line 230, in prepare_molecules
File "/home/sean/Downloads/gypsum_dl-1.1.2/gypsum_dl/Start.py", line 275, in execute_gypsum_dl
File "/home/sean/Downloads/gypsum_dl-1.1.2/gypsum_dl/Steps/SMILES/PrepareSmiles.py", line 64, in prepare_smiles
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
- February 22, 2020 at 2:12 am #12597Jacob DurrantKeymaster
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.
- February 22, 2020 at 4:10 am #12605Sean CutlerGuest
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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