Open eloyfelix opened 1 year ago
Error occured only after
indigo.setOption("pKa-model", "advanced")
Whithout this options - no error occured
Current realization cannot ionize molecule in advanced mode if it contains any aromatic atom. Please use dearomatize before ionize.
Moved to Refined Backlog since no fix over 5 versions
I was willing to play a bit with pKa models in Indigo when I found this issue.
Steps to Reproduce
Same happens for other SMILES like paracetamol
CC(=O)Nc1ccc(O)cc1
. I imagined there is some generalized issue.Expected behavior Molecule to be ionized.
Actual behavior Indigo throwing a connectivity error.
Indigo version
Indigo built from: https://github.com/epam/Indigo/commit/2d696a21414e2c9cdb5952bcba21e0f7139a975f
Additional context It would be also nice to have some extended documentation about the pKa models in Indigo. There is a lack of open source pKa calculators and having the ones in Indigo better documented I think it could bring some users. I would be happy to compare the results with current ChEMBL pKa calcualted values.