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 enantiomers of molecules with
unspecified chiral centers or to explicitly invert the defined ones.
An issue found while digging into that was that OBAtom.HasChiralitySpecified(), and
facade.GetTetrahedralStereo(idx).IsSpecified() were giving conflicting results.
It's been a while since I tested it, but the code was this:
====================
import pybel
ob = pybel.ob
mols = [ 'OCC1OC(O)C(O)C(O)C1O',
'OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@@H]1O']
for smi in mols:
print "\nMOL->", smi
m = pybel.readstring('smi', smi).OBMol
m.FindChiralCenters()
facade = ob.OBStereoFacade(m)
for a in ob.OBMolAtomIter(m):
if a.IsChiral():
idx = a.GetIdx()
print "ATOM", a.GetIdx(), a.IsChiral(),
a.HasChiralitySpecified(),
print facade.GetTetrahedralStereo(idx-1).IsSpecified()
=======================
It would be interesting to test it with the latest development code and see if there are
still issues.
Thas
On 2020-02-05 14:51, Geoffrey Hutchison wrote:
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
configurations match the expected ones.
I think we can probably go through the code and examine, but if you have suggestions on
how to save the expected configs for future comparison, that would be great.
-Geoff
On Feb 5, 2020, at 4:30 PM, Noel O'Boyle <[email protected]
<mailto:[email protected]>> wrote:
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 them.
Progress so far:
https://github.com/baoilleach/documentation/blob/stereo/Stereochemistry/stereo.rst
Regards,
- Noel
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Center for Computational Structural Biology
Dept. of Integrative Structural
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