In fact, my mistake was to assume the config object would be build accordingly to
Cahn-Ingold-Prelog rules, hence my misunderstanding when the winding showed up identical.
I've read the documentation and tried with refs, and yes, it works as expected (same
results as with the winding with less confusion).
Although, I still think there is a problem.
I've started looking into the winding issue because I was generating enantiomers for this
structure:
C1C2=CC(=C(C=C2C3C1(COC4=C3C=CC(=C4O)O)O)O)O
Altering either the winding or the reference atoms, the resulting structures
are identical:
Oc1cc2C[C@]3([C@H](c2cc1O)c1ccc(c(c1OC3)O)O)O error.smi
Oc1cc2C[C@@]3([C@H](c2cc1O)c1ccc(c(c1OC3)O)O)O working.smi
When generating the 3D structure of 'error.smi', there's a warning (using either obabel or
Python v.2.3.2):
$ obabel -ismi error.smi -omol2 --gen3D 1> /dev/null
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 1 stereocenter(s) in this molecule ()
with Atom Ids as follows: 5
and the 3D structure generated is identical to the one generated using the opposite
chirality ('working.smi'). I thought it was a misuse of the winding that generated the
wrong SMILES, but it's not the case.
I've tested generating 2D structures using -opng and results show that they are indeed
valid SMILES and shown with the proper wedging (see attached).
At this point I suspect an issue with the builder when generating 3D structures.
This is only one example of many that I have. When processing a library of ~700 compounds,
I get this error for about 30 of them.
Not sure if this is a bug, so I'll wait for confirmation before opening a new
report.
Let me know if you need more examples, I'll be glad to send them.
Thanks a lot for the support,
S
On 02/17/2015 12:22 PM, Noel O'Boyle wrote:
The config object represents the usual way chemists communicate
stereochemistry in a diagram; looking either from/towards a particular
atom, atoms X, Y and Z are arranged clockwise/anticlockwise.
Your code is correctly inverting the stereo. If you invert the
'winding', and keep everything else the same, then you get the
opposite chirality. (Another way is if you swap two of the refs, and
keep everything else the same, then you get the opposite chirality.)
The docs are at
http://openbabel.org/api/2.3/structOpenBabel_1_1OBTetrahedralStereo_1_1Config.shtml
- Noel
On 17 February 2015 at 19:13, Stefano Forli <fo...@scripps.edu> wrote:
Noel,
thanks for the clarification.
It makes sense now, but it means that I'm using the wrong tool for what I
want to do.
In a previous discussion[1] I was suggested to use this code to alter the
chirality of a tetrahedral stereocenter, since OBTetrahedralStereo.Invert()
doesn't seem to be available in Python.
What would you recommend to identify a chiral center configuration and
invert it in Python?
Thanks,
S
[1] http://sourceforge.net/p/openbabel/mailman/message/32475236/
On 02/17/2015 01:50 AM, Noel O'Boyle wrote:
Hi,
Hope you don't mind but...
1. Should GetId() not GetIdx()-1
2. Should be "HasTetrahedralStereo(idx)"
Regarding the main question, the config objects are correct, but the
stereo definition consist of three parts (see the API docs): view,
winding and refs. You were just looking at the winding. The refs are
in a different order in each case.
Regards,
- Noel
On 17 February 2015 at 00:53, Stefano Forli <fo...@scripps.edu> wrote:
Hi,
I can't understand the way in which chiral winding is handled by
OpenBabel.
I wrote a small test script in Python (attached) to try to clarify the
concept. The output is:
ClC(I)Br -> WINDING [1->2] -> ClC(I)Br
Cl[C@H](I)Br -> WINDING [1->2] -> Cl[C@@H](I)Br
Cl[C@@H](I)Br -> WINDING [1->2] -> Cl[C@H](I)Br
The winding is always perceived as 1, and this is wrong by definition
(right?)
Setting the winding to 2 generates the other enantiomer, independently
from
the starting point.
Both atom.IsClockwise() and atom.IsAntiClockwise() return False, showing
that chirality is not perceived (uncomment the last line to test it).
Is this expected, or there is a way to perceive it properly?
Thanks,
S
--
Stefano Forli, PhD
Staff Scientist
Molecular Graphics Laboratory
Dept. of Integrative Structural
and Computational Biology, MB-112F
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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Stefano Forli, PhD
Staff Scientist
Molecular Graphics Laboratory
Dept. of Integrative Structural
and Computational Biology, MB-112F
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/
--
Stefano Forli, PhD
Staff Scientist
Molecular Graphics Laboratory
Dept. of Integrative Structural
and Computational Biology, MB-112F
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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