datamol

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Datamol does not provide any cli yet. It might be useful to have some for basic operations like IO and conversion.

hadim

https://github.com/rdkit/rdkit/pull/7004 added a deprecation warning for several functions related to Morgan Fingerprints. Running ``` dm.to_fp("CCCCC") ``` Gives: ``` "please use MorganGenerator" ```

cwognum

Git codecov action is not properly set. See the action: https://github.com/datamol-io/datamol/actions/runs/9451401081 ``` Codecov: Failed to properly create commit: The process '/home/runner/work/_actions/codecov/codecov-action/v4/dist/codecov' failed with exit code 1 ```

zhu0619

Adding JSON I/O for molecules

1

Sometimes it is convenient to exchange molecules in JSON format rather than SMILES or `.sdf` files. Fortunately, `rdChem.Mol` JSON is already implemented in `rdkit.Chem.rdMolInterchange.MolsToJSON` and `rdkit.Chem.rdMolInterchange.JSONToMols`. This can be implemented...

isty2e

Conformer generation error with specific RDKit version

1

**Description:** The following code to generate conformers using `datamol` works fine with RDKit version `2022.09.5`, but fails with RDKit version `2024.03.1`. This inconsistency might be due to changes in RDKit...

SergeiNikolenko

Fixing does not appear to work for inferring valence & formal charge states from molecules from some PDB files

4

Thank you for this nice library! I'm have a question re fixing 'broken' Mols by inferring the correct valences and charges that I was hoping `datamol` could fix for me....

Croydon-Brixton