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 stereochemistry, it would be helpful if the example
would show how to read the current winding.
For example, would this work?
--
if config.winding == ob.OBStereo.Clockwise:
print("Clockwise winding")
elif config.winding==ob.OBStereo.AntiClockwise:
print("Anti-clockwise winding")
else: # elif config.winding==ob.OBStereoUnknownWinding: ?
print("Undefined winding winding")
--
Also, I know the support for non-tetrahedral chirality is not complete, but I'm wondering
if there a way to use the OBStereo.Type with the facade to infer if it is recognized or not.
Thanks!
S
On 2020-02-09 12:36, Noel O'Boyle wrote:
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 them lying around confusing everyone.
Anyway, now with version 3.0, mol.FindChiralCenters() and atom.HasChiralitySpecified()
have both been removed. atom.IsChiral() I kept (though I thought about removing it also)
but changed the code so that it's now a convenience function that just calls the functions
in the modern API.
And just to note that you should avoid subtracting 1 from the Idx to get the Id. Right now
it works, but we don't guarantee that relationship, and it certainly won't be true if you
delete atoms. Better to get the atom and then call GetId().
- Noel
On Thu, 6 Feb 2020 at 06:58, Stefano Forli <fo...@scripps.edu <mailto:fo...@scripps.edu>>
wrote:
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 <baoille...@gmail.com
<mailto:baoille...@gmail.com>
>> <mailto:baoille...@gmail.com <mailto:baoille...@gmail.com>>> 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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--
Stefano Forli, PhD
Assistant Professor
Center for Computational Structural Biology
Dept. of Integrative Structural
and Computational Biology, MB-112A
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037-1000, USA.
tel: +1 (858)784-2055
fax: +1 (858)784-2860
email: fo...@scripps.edu <mailto:fo...@scripps.edu>
http://www.scripps.edu/~forli/
--
Stefano Forli, PhD
Assistant Professor
Center for Computational Structural Biology
Dept. of Integrative Structural
and Computational Biology, MB-112A
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037-1000, USA.
tel: +1 (858)784-2055
fax: +1 (858)784-2860
email: fo...@scripps.edu
http://www.scripps.edu/~forli/
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