RDKit Integration

[jvansan]

Hello,

I am wondering if the documentation of this project should reflect the fact that much of this API has been integrated into newer version of the RDKit?

[UnixJunkie]

I think that the part that does tautomer choosing is not part of rdkit.

[msteijaert]

@UnixJunkie, which part do you mean exactly?

If I compare https://github.com/rdkit/rdkit/tree/master/rdkit/Chem/MolStandardize and https://github.com/mcs07/MolVS/tree/master/molvs, it seems like all modules (except for the commandline interface in cli.py) have been copied into RDKit. Does this also mean that the RDKit repository is the primary location for further development. @mcs07 or @greglandrum , can you comment on this?

I agree with @jvansan that it would be good to mention this in the documentation of this project.

[UnixJunkie]

@susanhleung should know if this has been completely integrated into rdkit

[UnixJunkie]

@msteijaert the CLI is in rdkit/Contrib/MolVS/molvs_cli.py

[greglandrum]

I believe the RDKit now has a complete C++ implementation of the functionality provided by MolVS, including picking a canonical tautomer.

An aside: the python code in https://github.com/rdkit/rdkit/tree/master/rdkit/Chem/MolStandardize is legacy and should be removed.

[msteijaert]

Thanks for the clarification! So, if I understand correctly, the recommended python interface is now documented here: http://www.rdkit.org/docs/source/rdkit.Chem.MolStandardize.rdMolStandardize.html? Indeed I see most of the MolVS functionality there. However, I do not see the Standardizer.isotope_parent reflected there. As an alternative, I use the the following to remove all isotope from my rdchem.Mol object: _ = [atom.SetIsotope(0) for atom in mol.GetAtoms()]