Re: [Rdkit-discuss] reading multiple conformers from file

[Thomas E. <te...@gm...>]

Hello Greg,

Is the canonical SMILES string always unique for every isomer and
tautomerization state of a molecule? If yes, then I have already written a
function to load multiple molecules and their conformers, which I can share
it here.

best
Thomas

PS: thanks to David for pointing this out.



On 27 October 2016 at 05:20, Greg Landrum <gre...@gm...> wrote:

> Hi Thomas,
>
> You're right, reading multiple conformations out of an SDF does seem like
> one of those common operations. Unfortunately the RDKit does not currently
> support it in an easy way.
>
> A python implementation of this would be a good topic for Friday's UGM
> hackathon, we can see if anyone finds it interesting enough to work on.
>
> -greg
>
>
> On Tue, Oct 25, 2016 at 2:16 AM, Thomas Evangelidis <te...@gm...>
> wrote:
>
>> Hello everyone,
>>
>> I am a new user of RDkit and I was looking in the documentation for an
>> easy way to load multiple conformers from a structure file like .sdf. The
>> code must 1) distinguish between different protonation states of the same
>> molecule,  2) create a new Mol() object for each protonation state and load
>> into it the respective conformers.
>>
>> Apparently I can work out a solution for 1) using mol.GetProp('_Name'), mol.GetNumAtoms, mol.GetNumBonds
>> and other properties, but I was wondering if there is any more straight
>> forward way to do it.
>> For 2) I guess I must iterate over all molecules in the input file,
>> create new Mol() objects (one for each protonation state of each ligand)
>> and add conformers to these new Mol() objects. Again this sounds easily
>> programmable, but sounds like a very common operation, thus I was wondering
>> if it has been implemented in a function.
>>
>> thanks in advance
>> Thomas
>>
>>
>> --
>>
>> ======================================================================
>>
>> Thomas Evangelidis
>>
>> Research Specialist
>> CEITEC - Central European Institute of Technology
>> Masaryk University
>> Kamenice 5/A35/1S081,
>> 62500 Brno, Czech Republic
>>
>> email: te...@ph...
>>
>>           te...@gm...
>>
>>
>> website: https://sites.google.com/site/thomasevangelidishomepage/
>>
>>
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>


-- 

======================================================================

Thomas Evangelidis

Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic

email: te...@ph...

          te...@gm...


website: https://sites.google.com/site/thomasevangelidishomepage/