Greg Landrum

Sure: ``` In [3]: m = Chem.MolFromSmiles('C[C@H]([F:1])[F:2]') In [4]: m.GetAtomWithIdx(1).GetPropsAsDict() Out[4]: {'__computedProps': , '_CIPRank': 1, '_ChiralityPossible': 1, '_CIPCode': 'R'} In [6]: for at in m.GetAtoms(): at.SetAtomMapNum(0) In [8]: Chem.AssignStereochemistry(m,force=True,cleanIt=True,flagPossibleStereoCenters=True) In...

If you just want to clear the computed properties on the molecule and all atoms and bonds, you can do: ``` In [10]: m.ClearComputedProps() In [11]: m.GetAtomWithIdx(1).GetPropsAsDict() Out[11]: {'__computedProps': }...

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...

> I also noticed that this function will not standardize tautomeric forms. I guess it just doesn't do what I thought it would. > Correct. This code does not do...

@gpatbrady, those messages are coming from the RDKit core. The incantation to disable the RDKit info log is: ``` from rdkit import RDLogger RDLogger.DisableLog("rdApp.info") ```

Hi @nbosc , Which python version/OS are you using? Do you have conda-forge in your list of channels? I was able to install the package in a new conda environment...

Yeah, I think pointing people to conda-forge totally makes sense. We should update the docs... PR on its way.

@eloyfelix : if you agree that this is a reasonable idea, I will go ahead and implement it and add a couple tests for it.

Ok. I will try to get a PR done in the next couple days. As usual, writing the tests will be the majority of the effort. :-)

`MolToFile()` is still using the old drawing code as far as I can tell. Agreed that a general cleanup of the contents of the rdkit.Chem.Draw module is necessary. And should...