Hi Siavoush,
To my understanding, in OBChemTsfm::Init (phmodel.cpp, around line 208),
there's only options to delete atoms, change the atomic number or charge,
or modify bonds.
If your combinations have very simple rules, you might be able to use a
workaround in Open Babel to get around these limitations. I've been using
dot-separated smiles to graft functional groups onto specific attachment
points. See Table 3.7.1 of OpenSMILES for an example:
http://opensmiles.org/opensmiles.html#_other_uses_of_ring_numbers_and_dot_bond
The disadvantage is that directly manipulating SMILES as strings is messy
and considerably less flexible than SMARTS (e.g. rdkit's
ReactionFromSmarts).
Cheers,
Ben
On Tue, Jan 30, 2018 at 12:50 PM, Stefano Forli <fo...@scripps.edu> wrote:
> Hi Siavoush,
>
> I've tried a few times with OpenBabel, but since there is no support for
> actual chemical reactions, its essentially impossible to do.
>
> At least for me, the best way to handle the problem is to use the RXN
> format, which can be used to describe any chemical reactions. For that you
> might want to consider alternatives such as RDKit or Indigo.
>
> Hope this helps,
>
> S
>
>
> On 01/30/2018 07:25 AM, Siavoush Dastmalchi via OpenBabel-discuss wrote:
>
>> 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
>>
>>
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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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