I believe I've covered the issues you've raised, but let me know if not.
I'll also mention this on Twitter to see if anyone has anything to add.
https://github.com/openbabel/documentation/pull/15
On Tue, 11 Feb 2020 at 19:54, Noel O'Boyle wrote:
> Hi Stefano,
>
> When you call GetConfig() you
Hi Stefano,
When you call GetConfig() you are setting the winding yourself. I see now
that this wasn't clear. By default, you are saying "give me the atoms in
clockwise order looking from atom x". In other words, you will never need
to check the winding of a config - you will always know it -
Hi Noel,
indeed, that was my initial attempt to figure out how to deal with stereogenic centers,
and I still didn't have a decent understanding of Id vs Idx.
Incidentally, this is particularly clear in your documentation.
I have one suggestion.
In the section about the inversion of
Just a note on the code above. Many years ago Tim replaced the
stereochemistry handling, and I helped a bit. But vestiges of the original
handling were left lying around to avoid breaking the API. I guess we
thought we'd remove them sooner than we did, as looking back it makes no
sense to have
Excellent suggestions for examples and/or areas of focus. I'll refer back
to these as I work through the docs.
Actually now I remember that it was your earlier email Stefano that
prompted me to write these docs. I started at the time, but lost the file,
and/or moved jobs, etc.
On Thu, 6 Feb 2020
Noel,
this is great! I've been following the stereochemistry issue for a while in the mailing
list and you addressed pretty much all the key aspects.
One thing that seems to be missing is the discussion on how to invert chirality. In the
past I've tried writing code to enumerate all possible
Yes, Naruki and I were running into confusion when using these classes for the
distance geometry implementation.
The key challenge is that we'd want to save the expected stereo configuration
around atoms and bonds - and then when generating 3D coordinates, test to see
if the generated
Hi there,
I've been very slowly pulling together some docs on using the API for
stereo. I remember someone on the list a few months back discussing
difficulties with this part of the library - if anyone has any particular
examples they'd like me to discuss, this would be a good time to mention
