I would 2nd the suggestion of continuing to push a JSON format forward that
natively supports multiple conformers.
I've never seen automatic recombination of an SDF work %100 of the time, it's
fraught with corner cases. It's also abysmally slow and takes a huge amount of
disk space.
-Bruce
> On Oct 30, 2016, at 5:21 PM, Brian Kelley <fustiga...@gmail.com> wrote:
>
> Rdkit already has a way to serialize conformers, the binary pickle format!
>
> Perhaps we should make a file extension for multiple molecules. Say ".rdk"
> and call it a day. Like inchi the source code is the reference :)
>
> ----
> Brian Kelley
>
>> On Oct 27, 2016, at 2:05 AM, Greg Landrum <greg.land...@gmail.com> wrote:
>>
>> 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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