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

[Thomas Evangelidis]

Hello,

I was just wondering, has there been any progress on the multi-conformer
sdf file reader since last year?

best
Thomas


On 27 October 2016 at 05:20, Greg Landrum  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 
> 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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>


-- 

==

Dr Thomas Evangelidis

Post-doctoral Researcher
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/2S049,
62500 Brno, Czech Republic

email: tev...@pharm.uoa.gr

  teva...@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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[Rdkit-discuss] Periodic RMSD and C++ API Ubuntu Repo Updates?

[Patrick Avery]

Hi Greg,

I know proteins are sometimes used within periodic boundaries. We aren't
using proteins, but we will be using molecules within crystals. I was
wondering if there is a way in RDKit to calculate RMSD between two periodic
systems (such as two crystals, each containing molecules), and if not, if
there is a way to generate some kind of fingerprint? I know the RMSD and
fingerprinting methods exist for molecules, but I'm not sure if there are
ones for periodic conditions. Note that we may have multiple "molecules"
inside each crystal.

Also, we were running tests with RDKit using Python, but since our program
is written in C++, I think it is easier to integrate it with the C++ API. I
already have an integration set-up that includes the proper headers and
links the proper libraries for our needs. But I had to compile RDKit myself
to do so. I noticed there are repositories for RDKit (like on Ubuntu), but
it looks like they are not up-to-date (some of the functions I need are not
yet present). I was wondering if those will get updated sometime in the
future?

The updated repositories aren't necessary (because I can always have others
compile RDKit themselves if they need to compile our program), but they're
nice to have because they speed up the process.

Thanks,
Patrick
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