Lester Hedges
Lester Hedges
Thanks, after refactoring this all looks good. I'll deal with the Sire release this week then give this another once over before doing the BioSimSpace side of things.
Hi there. What's `b`? ``` NameError: name 'b' is not defined ```
I don't think your assertion that the parametrised molecule retains the stereochemistry is correct. If I do the following then everything is fine: ```python import BioSimSpace as BSS # Create...
This is now fixed in #331.
Hmm, I see. It's strange that things look okay using the `view2d` function, since that's literally using Sire to convert to RDKit behind the scenes. Looking at the code [here](https://github.com/OpenBioSim/sire/blob/a18452ea0da87632285d55cf7ee2d7413e1871b9/src/sire/mol/_smiles.py#L190-L213)...
In this sense, the view is a bit misleading since the stereochemistry is not part of the BioSimSpace molecule and wouldn't (necessarily) be present when using the Sire-to-RDKit converter.
Great, glad it was helpful.
Is it okay to close this issue? I've implemented the code to preserve the SMILES information in the molecule when that was the source of input to the parametrisation. One...
Hi there, thanks for the question. This is how the Gro87 atom records are generated: ```cpp auto write_line = [&](int iatm) { // the atom number is iatm+1 int atmnum...
Oh, and just to say that an easier way to edit is using the new Sire API. (My brain is still hardcoded to use the old API.) ```python # Create...