Problems decomposing some compounds
I'm having some trouble with a small subset of several thousand SMILES compounds that I'm trying to calculate the formation energies of (undecomposable_smiles.csv)
Do you have any insight into why this might be the case?
I'm using an outdated version of equilibrator (from last year sometime), but not sure if this issue would go away from updated to v0.4.
Thanks
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GroupDecompositionError Traceback (most recent call last)
<ipython-input-203-768ed8d87879> in <module>
----> 1 lc.get_compounds("C1(CC(OC(C(C1)=O)CO)O)=O")
.../equilibrator_assets/local_compound_cache.py in get_compounds(self, _mol_strings, mol_format)
128
129 compounds = get_or_create_compound(
--> 130 self.ccache, _mol_strings, mol_format
131 )
132
/.../equilibrator_assets/generate_compound.py in get_or_create_compound(ccache, _mol_strings, mol_format)
152 if len(misses) > 0:
153 result_df.loc[misses, "compound"] = create_compound(
--> 154 result_df.loc[misses, "mol_string"].tolist()
155 )
156
.../equilibrator_assets/generate_compound.py in create_compound(_mol_strings, mol_format)
92 mol = molecule.Molecule.FromSmiles(row.compound.smiles)
93 decomposition = group_decomposer.Decompose(
---> 94 mol, ignore_protonations=False, raise_exception=True
95 )
96 row.compound.group_vector = decomposition.AsVector()
.../equilibrator_assets/group_decompose.py in Decompose(self, mol, ignore_protonations, raise_exception)
623 if raise_exception and decomposition.unassigned_nodes:
624 raise GroupDecompositionError(
--> 625 f"Unable to decompose {mol} into groups", decomposition
626 )
627
GroupDecompositionError: Unable to decompose <openbabel.openbabel.OBMol; proxy of <Swig Object of type 'OpenBabel::OBMol *' at 0x7f8f3dacbd80> > into groups