Actually, I think that this particular is most easily solved as Chris has
suggested, using regular ring closure digits. The deferred ring closures
(&) are currently not accepted by OB, and I guess aren't really needed in
any case. We should get them working though. They are a feature of SMILES
that is not very well documented.
We have support for RXN, but the question is not about representing
reactions but generating molecules.
I have just written up a proposal to change how we handle reactions in Open
Babel. If/when this is in place, it would be worth revisiting support for
reaction transformations. In the meanwhile, if you are aware of any
problems with OBChemTsfm, we'd appreciate if you could file an issue.
Regards,
- Noel
On 1 February 2018 at 00:16, Stefano Forli <fo...@scripps.edu> wrote:
> My experience with simulating reactions with OpenBabel was mostly
> unsuccessful.
> I've tried using OBChemTsfm to atoms, but I couldn't have it to work even
> by adding one atom at the time.
>
> The most straightforward way to deal with a library enumeration would be
> to have support for the RXN format, which can be used to describe any
> arbitrary reaction. For that, I've found pretty easy to work with Indigo
> and RDKit.
>
> On the other hand, I'm not familiar with the "&" notation Noel is
> referring to.
> If there's some documentation on the matter, please let me know!
>
> Thanks,
>
> S
>
> On 01/30/2018 11:59 AM, Nicolas Cheron wrote:
>
>> Please allow me to do shameless self-promotion. I have developped an
>> open-source program (using OpenBabel) that aims at creating de novo ligands
>> by directly growing them in the active site of a target protein. You can
>> also use it without the protein (I have called it FOG2) : you can define a
>> core molecule (so-called seed), choose from which atom you will grow new
>> molecules, and the program will create new molecules by adding fragments to
>> the seed in a "rational" way. If you want more details, let me know, I can
>> explain it.
>>
>> The links: http://pubs.acs.org/doi/10.1021/acs.jmedchem.5b00886,
>> https://sourceforge.net/projects/opengrowth/
>>
>> Nicolas
>>
>>
>>
>> 2018-01-30 20:53 GMT+01:00 Chris Swain <sw...@mac.com <mailto:
>> sw...@mac.com>>:
>>
>> Hi,
>>
>> It depends on the transformations you want to undertake. I did a very
>> quick library
>> build about 20 years ago using SMILES strings. Just have dummy atoms
>> with unique
>> letters where you want to add functional groups then just do a text
>> find and replace
>> with the desired SMILES of the building block you want to add (which
>> can of course
>> contain dummy atoms). Then run through OpenBabel to generate
>> canonical SMILES. I
>> generated a 10 million molecule library doing this.
>>
>> Cheers,
>>
>> Chris
>>
>> On 30 Jan 2018, at 19:45, openbabel-discuss-request@list
>>> s.sourceforge.net
>>> <mailto:openbabel-discuss-requ...@lists.sourceforge.net> wrote:
>>>
>>> Message: 1
>>> Date: Tue, 30 Jan 2018 15:25:38 +0000 (UTC)
>>> From: Siavoush Dastmalchi <siavous...@yahoo.com <mailto:
>>> siavous...@yahoo.com>>
>>> To: "openbabel-disc...@lists.sf.net <mailto:openbabel-discuss@list
>>> s.sf.net>"
>>> <openbabel-disc...@lists.sf.net <mailto:openbabel-discuss@list
>>> s.sf.net>>
>>> Subject: [Open Babel] using Open Babel for virtual library generation
>>> Message-ID: <1885905137.1937075.1517325938...@mail.yahoo.com
>>> <mailto:1885905137.1937075.1517325938...@mail.yahoo.com>>
>>> Content-Type: text/plain; charset="utf-8"
>>>
>>> Dear List,
>>> I was wondering if it is possible to use OB for virtual library
>>> generation. For
>>> example adding building blocks in a file to different sites of a
>>> core structure in a
>>> combinatorial manner.
>>> Many thanks in advance for you help.
>>> Cheers,Siavoush
>>> -------------- next part --------------
>>> An HTML attachment was scrubbed...
>>>
>>
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>>
> --
>
> Stefano Forli, PhD
>
> Assistant Professor
> 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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