Greg Landrum
Greg Landrum
@ptosco when I try to review this with either the github interface or in VS Code I still see a bunch of changes unconnected to the RGD work. Can you...
@ptosco yeah, it really helps to have the PRs as compact as possible.
How did you install the RDKit?
If conda doesn't automatically update, you can install the newer version by specifying it: `mamba install rdkit=2024.03` or `conda install rdkit=2024.03`
If you want to consider neighboring atoms, you need to use the keyword argument `includeNeighbors`: ``` In [4]: smi='C' ...: mol = Chem.MolFromSmiles(smi) ...: mol=Chem.AddHs(mol) ...: nAtoms = mol.GetNumAtoms() ...:...
There are valid use cases for both alternatives: sometimes you want the number of hydrogens that aren't actually in the graph (these are logically known as "implicit hydrogens" but the...
good point. I will try to get that done before the next release.
Hi @pechersky, Thanks for testing out the beta of the new release! Since the atropisomer support is new, this is new territory for us, but I believe that what happens...
The origin of the RDKit values is, unfortunately, "lost in antiquity". Updating these values to something that has a reference would be a nice enhancement for a future RDKit version.
It's defined here: https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/atomic_data.cpp