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mcs07 / MolVS

Molecule Validation and Standardization
https://molvs.readthedocs.io/
MIT License
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Unable to standardize some PubChem molecules #39

Open VladislavChernykh opened 3 years ago

VladislavChernykh commented 3 years ago

Hello,

I was using molvs standardizer on PubChem molecules and found out several molecules that cannot be standardized:

  1. SMILES: CC(S(=O)CC1=CC=C(C=C1)C(S(=O)CC2=CC=C(C=C2)C(S(=O)CC3=CC=C(C=C3)C(S(=O)C4=CC=C(C=C4)Br)S(=O)C5=CC=C(C=C5)Br)S(=O)CC6=CC=C(C=C6)C(S(=O)C7=CC=C(C=C7)Br)S(=O)C8=CC=C(C=C8)Br)S(=O)CC9=CC=C(C=C9)C(S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)CC1=CC=C(C=C1)C(S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br

Link: https://pubchem.ncbi.nlm.nih.gov/compound/59827358

  1. SMILES: CC1=CC=C(C=C1)C(S(=O)CC2=CC=C(C=C2)C(S(=O)CC3=CC=C(C=C3)C(S(=O)CC4=CC=C(C=C4)C(S(=O)C5=CC=C(C=C5)Br)S(=O)C6=CC=C(C=C6)Br)S(=O)CC7=CC=C(C=C7)C(S(=O)C8=CC=C(C=C8)Br)S(=O)C9=CC=C(C=C9)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)CC1=CC=C(C=C1)C(S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br

Link: https://pubchem.ncbi.nlm.nih.gov/compound/59827349

Code to reproduce:

from rdkit import Chem
from molvs import Standardizer

smiles = "CC1=CC=C(C=C1)C(S(=O)CC2=CC=C(C=C2)C(S(=O)CC3=CC=C(C=C3)C(S(=O)CC4=CC=C(C=C4)C(S(=O)C5=CC=C(C=C5)Br)S(=O)C6=CC=C(C=C6)Br)S(=O)CC7=CC=C(C=C7)C(S(=O)C8=CC=C(C=C8)Br)S(=O)C9=CC=C(C=C9)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)CC1=CC=C(C=C1)C(S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br"
mol = Chem.MolFromSmiles(smiles)
res = Standardizer().standardize(mol)

It seems that the flow goes into an infinite loop in function _apply_transform() (normalize.py). After 10 minutes of transformation still got no result.

Thanks, Vladislav

UnixJunkie commented 3 years ago

It might be nice to do this on the whole pubchem, to flag all erroneous molecules at once.