This limitation of the 3D builder is described in the docs and also
flagged up by the warning message:
https://open-babel.readthedocs.org/en/latest/3DStructureGen/SingleConformer.html#obbuilder
We have an idea what to add to get around this (distance geometry),
but no-one has done it yet.
Regards,
- Noel
On 18 February 2015 at 22:48, Stefano Forli <fo...@scripps.edu> wrote:
> 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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>>>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>>>
>>>
>>> --
>>> 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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