bad params pointer

  • This topic has 2 replies, 1 voice, and was last updated 7 months ago by Sean Cutler.
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    • #12143
      Sean Cutler
      Guest

      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

    • #12597
      Jacob Durrant
      Keymaster

      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.

    • #12605
      Sean Cutler
      Guest

      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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