It would seem that a major issue with RDKit's multiconformer file is the
inability to associate structure-level and atom-level properties with
conformations. t's not quite orthogonal to the question of how to read,
say, a multiconformer SD file into RDKit's multiconformer format, because
the conformers in said SD file could contain such properties, and
information would be lost.
-P.
On Thu, Oct 27, 2016 at 6:20 AM, Thomas Evangelidis <teva...@gmail.com>
wrote:
> 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 <greg.land...@gmail.com> 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 <teva...@gmail.com>
>> 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: tev...@pharm.uoa.gr
>>>
>>> teva...@gmail.com
>>>
>>>
>>> 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: tev...@pharm.uoa.gr
>
> teva...@gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
>
> ------------------------------------------------------------
> ------------------
> The Command Line: Reinvented for Modern Developers
> Did the resurgence of CLI tooling catch you by surprise?
> Reconnect with the command line and become more productive.
> Learn the new .NET and ASP.NET CLI. Get your free copy!
> http://sdm.link/telerik
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
------------------------------------------------------------------------------
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Did the resurgence of CLI tooling catch you by surprise?
Reconnect with the command line and become more productive.
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http://sdm.link/telerik
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