The RDKit has support for the TPL format, an old BioCad/MSI/Accelrys format.
It's easy to imagine something better, but this is at least already there
and there could be other software that speaks it:
https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/FileParsers/test_data/cmpd2.tpl
I'd still like to do a decent JSON format and adding multi-confs to that
would be logical
On Thu, Oct 27, 2016 at 6:58 AM, David Cosgrove <davidacosgrov...@gmail.com>
wrote:
> I've been wondering if, now that you can get decent conformations from
> RDKit, it would be worth devising a multi-conformation file format to make
> reading multi-conf molecules faster for vs purposes. In my experience,
> pulling all the conformers out of an ascii file such as an sdf can become
> the RDS for pharmacophore searchimg. Something to think about at the
> hackathon maybe and certainly something that deserves a new email thread.
>
> Dave
>
>
> On Thursday, 27 October 2016, 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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>>
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