mcs07/MolVS

Unable to standardize some PubChem molecules

VladislavChernykh opened this issue · 1 comments

VladislavChernykh commented

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

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