Chirality remove issue

[peiyaoli]

Hi, first of all, thanks for open this pipeline which is really helpful for our molecule standardization work.

We came up one question regarding chiralty remove.

Input SMILES: O=C(O)[C@@H]1O[B-]2(O[C@H]1C(=O)O)O[C@@H](C(=O)O)[C@H](C(=O)O)O2

after "standardize_mol" and "get_parent_mol", the output molecule is:

OUT SMILES: O=C(O)C1O[B-]2(O[C@H]1C(=O)O)O[C@@H](C(=O)O)[C@H](C(=O)O)O2

It looks like only one chiralty has been removed.

@greglandrum How to resolve this issue? Many thanks...

[greglandrum]

I can reproduce this with standardize_mol():

In [8]: res = standardizer.standardize_mol(Chem.MolFromSmiles('O=C(O)[C@@H]1O[B-]2(O[C@H]1C(=O)O)O[C@@H](C(=O)O)[C@H](C(=O)O)O2'
   ...: ))
[11:21:57] Running Normalizer
[11:21:57] Running Uncharger

In [9]: Chem.MolToSmiles(res)
Out[9]: 'O=C(O)C1O[B-]2(O[C@H]1C(=O)O)O[C@@H](C(=O)O)[C@H](C(=O)O)O2'

but not with get_parent_mol():

In [5]: res,_ = standardizer.get_parent_mol(Chem.MolFromSmiles('O=C(O)[C@@H]1O[B-]2(O[C@H]1C(=O)O)O[C@@H](C(=O)O)[C@H](C(=O)O)O2
   ...: '))
[11:20:57] Running Uncharger
[11:20:57] Running Uncharger

In [6]: Chem.MolToSmiles(res)
Out[6]: 'O=C(O)[C@@H]1O[B-]2(O[C@H]1C(=O)O)O[C@@H](C(=O)O)[C@H](C(=O)O)O2'

I will look into it.

[greglandrum]

Ok, found it. The problem here is with flatten_tartrate_mol()
Fix on its way

[greglandrum]

The problem here is caused by errors in the flatten_tartrate() function, which has multiple problems.

[greglandrum]

Thanks for reporting this @peiyaoli !

[peiyaoli]

Welcome~

[eloyfelix]

Many thanks @peiyaoli for reporting and @greglandrum for the PR! :)

We are planing release a new version of the package for ChEMBL30.

Related to the new version... @greglandrum: will the new RDKit version builds ship with InChI 1.06?

[greglandrum]

Related to the new version... @greglandrum: will the new RDKit version builds ship with InChI 1.06?

That's definitely something we should do for the 2021.09 release.
Here's the issue: rdkit/rdkit#4322

[eloyfelix]

that's great, many thanks again