- I've had this on my to-do list for a few months now, implementing the
algorithm described in this paper. I think the force-field energy
minimization routines already present in the RDKit can be utilized for this
pretty easily. The only part that I don't think is set up already
Incorporating and "industrialising" Matt's MolVS tautomer and
standardizer code?
http://molvs.readthedocs.io/en/latest/index.html
On 15/01/18 07:09, Greg Landrum wrote:
Dear all,
We've been invited again to participate in the OpenChemistry
application for Google Summer of Code.
In order
Agreed. Good support for reading and writing mol2 format would indeed be
useful.
But not convinced this alone is sexy enough for GSoC.
Could there be something in a more general project to bridge the
compound (mol/smiles), sequence (protein/nucleotide seq + alignments)
and structure
On 01/15/2018 02:43 PM, Tim Dudgeon wrote:
> Could there be something in a more general project to bridge the
> compound (mol/smiles), sequence (protein/nucleotide seq + alignments)
> and structure (pdb/mmcif/mmtf) worlds?
FWIW PDB builds everything up from structure because they can derive
On 01/16/2018 06:43 AM, Dimitri Maziuk wrote:
> On 01/15/2018 02:43 PM, Tim Dudgeon wrote:
>
>> Could there be something in a more general project to bridge the
>> compound (mol/smiles), sequence (protein/nucleotide seq + alignments)
>> and structure (pdb/mmcif/mmtf) worlds?
>
> FWIW PDB builds
Thanks for the detailed reply
>
> The fact that this isn't happening for you indicates that you are reading
> the molecules in without sanitizing them - the mol file parser calls
> assignStereochemistry() by default if you sanitize. Are you sure that you
> should be disabling sanitization?
>
>
I
On 01/16/2018 05:51 AM, Tim Dudgeon wrote:
> Incorporating and "industrialising" Matt's MolVS tautomer and
> standardizer code?
> http://molvs.readthedocs.io/en/latest/index.html
If we can vote, I would vote for this one.
> On 15/01/18 07:09, Greg Landrum wrote:
>> Dear all,
>>
>> We've been
On Mon, Jan 15, 2018 at 9:50 AM, Francois BERENGER <
beren...@bioreg.kyushu-u.ac.jp> wrote:
> Supporting mol2 files as input would be nice.
>
Do you mean as output? You can already (in a limited way) read them.
-greg
There is already some code out there, people have worked on it and
> several
Supporting mol2 files as input would be nice.
There is already some code out there, people have worked on it and
several people would like to have the feature...
On 01/15/2018 04:09 PM, Greg Landrum wrote:
> Dear all,
>
> We've been invited again to participate in the OpenChemistry application
Dear RDKitters,
here is a project idea for GSoC 2018 (actually brought up by Greg during
the Hackathon of RDKitUGM2016):
Project: RDKit lite
Brief explanation:
Create a minimal version of the RDKit that only contains basic
functionality (like MolFrom/ToSmiles and substructure search
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