Closed drc007 closed 2 years ago
SGenheden
commented
2 years ago Hello
Thanks for the feedback.
You are very correct, this should be catched much earlier.
If you are interested, I would welcome a PR, after some discussion where to put this check. Otherwise, it will be added in a future release.
/ Sam
SGenheden
commented
2 years ago Fixed on master and will be included in release 3.4.0
When running aizynthcli it will now skip target molecules that are not sanitizable
drc007
commented
2 years ago Great. Another option is to check the structures in advance. I've put a very simple Jupyter Notebook here https://www.macinchem.org/reviews/rdkitcheck/sdfOrsmicheck.php
Hi, I got this error for a molecule (a nitro group drawn incorrectly) this lead to a subsequent file not found error.
Traceback (most recent call last): File "/Users/chrisswain/miniconda3/envs/aizynth-env/lib/python3.8/site-packages/aizynthfinder/chem/mol.py", line 175, in sanitize AllChem.SanitizeMol(self.rd_mol) rdkit.Chem.rdchem.AtomValenceException: Explicit valence for atom # 19 N, 4, is greater than permitted
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/Users/chrisswain/miniconda3/envs/aizynth-env/bin/aizynthcli", line 8, in
sys.exit(main())
File "/Users/chrisswain/miniconda3/envs/aizynth-env/lib/python3.8/site-packages/aizynthfinder/interfaces/aizynthcli.py", line 270, in main
func(
File "/Users/chrisswain/miniconda3/envs/aizynth-env/lib/python3.8/site-packages/aizynthfinder/interfaces/aizynthcli.py", line 183, in _process_multi_smiles
search_time = finder.tree_search()
File "/Users/chrisswain/miniconda3/envs/aizynth-env/lib/python3.8/site-packages/aizynthfinder/aizynthfinder.py", line 187, in tree_search
is_solved = self.tree.one_iteration()
File "/Users/chrisswain/miniconda3/envs/aizynth-env/lib/python3.8/site-packages/aizynthfinder/search/mcts/search.py", line 116, in one_iteration
leaf.expand()
File "/Users/chrisswain/miniconda3/envs/aizynth-env/lib/python3.8/site-packages/aizynthfinder/search/mcts/node.py", line 234, in expand
) = self._expansion_policy(self.state.expandable_mols)
File "/Users/chrisswain/miniconda3/envs/aizynth-env/lib/python3.8/site-packages/aizynthfinder/context/policy/policies.py", line 50, in call
return self.get_actions(molecules)
File "/Users/chrisswain/miniconda3/envs/aizynth-env/lib/python3.8/site-packages/aizynthfinder/context/policy/policies.py", line 68, in get_actions
possible_actions, priors = self[name].get_actions(molecules)
File "/Users/chrisswain/miniconda3/envs/aizynth-env/lib/python3.8/site-packages/aizynthfinder/context/policy/expansion_strategies.py", line 120, in get_actions
all_transforms_prop = self._predict(mol, model)
File "/Users/chrisswain/miniconda3/envs/aizynth-env/lib/python3.8/site-packages/aizynthfinder/context/policy/expansion_strategies.py", line 161, in _predict
fp_arr = _make_fingerprint(mol, model)
File "/Users/chrisswain/miniconda3/envs/aizynth-env/lib/python3.8/site-packages/aizynthfinder/context/policy/utils.py", line 18, in _make_fingerprint
fingerprint = obj.fingerprint(radius=2, nbits=len(model))
File "/Users/chrisswain/miniconda3/envs/aizynth-env/lib/python3.8/site-packages/aizynthfinder/chem/mol.py", line 128, in fingerprint
self.sanitize()
File "/Users/chrisswain/miniconda3/envs/aizynth-env/lib/python3.8/site-packages/aizynthfinder/chem/mol.py", line 179, in sanitize
raise MoleculeException(f"Unable to sanitize molecule ({self.smiles})")
aizynthfinder.utils.exceptions.MoleculeException: Unable to sanitize molecule (n1(c(=O)[nH]c2c(c1=O)c(c(s2)C(=O)N(C)C)C)c1c(N(=O)O)cccc1 ID20001)