I know this isn't a particularly sexy job for a budding cheminformatician
but...

Work on the Python documentation!!!

I love rdKit and occasionally think I'm pretty savvy but I can't tell you
how often I'm scrolling through the documentation (or source) and either:

a) discover something that exists but doesn't have anything documentation
but the function signature
or
b) discover some some functionality that exists (and i've wanted) but
didn't know it was there!

I think this mailing list and Greg do a superb job of keeping the community
informed and creating and maintaining the codebase but I think having some
more "Pythonic" API documentation would be great.

One shining example is the scikit-learn documentation
<http://scikit-learn.org/stable/documentation.html> that has a quick start,
tutorials etc.  and then in the well categorized and explanatory API ref
has links for examples in the User Guide (akin to the "Getting Started with
the RDKit in Python" doc) .

Just my 2 cents!

Thanks for all the hard work as always,
Cam


On Mon, Jan 15, 2018 at 12:52 PM <
rdkit-discuss-requ...@lists.sourceforge.net> wrote:

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>    1. Re: RDKit and Google Summer of Code 2018 (Jason Biggs)
>    2. Re: RDKit and Google Summer of Code 2018 (Tim Dudgeon)
>    3. Re: RDKit and Google Summer of Code 2018 (Tim Dudgeon)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 15 Jan 2018 09:20:48 -0600
> From: Jason Biggs <jasondbi...@gmail.com>
> To: Greg Landrum <greg.land...@gmail.com>
> Cc: RDKit Discuss <rdkit-discuss@lists.sourceforge.net>
> Subject: Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018
> Message-ID:
>         <CAOOMBER8jrLNg-f7zyBQdPYvsH1mH351k7NK9chyHzBhV4=
> f...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
>    - 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
> would be
>    applying a constant force to all atoms to force them into the xy plane.
>
> Fr?czek, T., "Simulation-Based Algorithm for Two-Dimensional Chemical
> Structure Diagram Generation of Complex Molecules and Ligand?Protein
> Interactions." J. Chem. Inf. Model. 2016, 56, 2320-2335, DOI:
> 10.1021/acs.jcim.6b00391.
>
>
>
>    - Another idea would be to add in point-group symmetry detection.  I'm
>    using the Symmetrizer java library, described here
>    https://www.ncbi.nlm.nih.gov/pubmed/22549414, and pretty happy with it
>    overall.  One could re-implement it in C++, or include the jar in the
>    External folder and write python wrappers.
>
>
> Jason Biggs
>
>
> On Mon, Jan 15, 2018 at 1:09 AM, Greg Landrum <greg.land...@gmail.com>
> wrote:
>
> > Dear all,
> >
> > We've been invited again to participate in the OpenChemistry application
> > for Google Summer of Code.
> >
> > In order to participate we need ideas for projects and mentors to go
> along
> > with them.
> >
> > The current list of RDKit ideas is being maintained here:
> > http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas
> >
> > (Note: at the point that I'm pressing "send", that's still a copy of last
> > year's project ideas).
> >
> > If you're willing to be a mentor (please ask me about the ~5 hours/week
> > required here) or have ideas, please reply to this thread.
> >
> > Best,
> > -greg
> >
> > ------------------------------------------------------------
> > ------------------
> > Check out the vibrant tech community on one of the world's most
> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> > _______________________________________________
> > Rdkit-discuss mailing list
> > Rdkit-discuss@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
> >
> >
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> ------------------------------
>
> Message: 2
> Date: Mon, 15 Jan 2018 20:43:12 +0000
> From: Tim Dudgeon <tdudgeon...@gmail.com>
> To: rdkit-discuss@lists.sourceforge.net
> Subject: Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018
> Message-ID: <af1e586c-a633-b851-e382-c479ee549...@gmail.com>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
> 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 (pdb/mmcif/mmtf) worlds?
> OK, so that's far too much to ask for, but is there something that could
> be plucked out from there that is useful and achievable?
>
> Tim
>
>
> On 15/01/18 09:19, Greg Landrum wrote:
> >
> >
> > On Mon, Jan 15, 2018 at 9:50 AM, Francois BERENGER
> > <beren...@bioreg.kyushu-u.ac.jp
> > <mailto: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 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
> >     > for Google Summer of Code.
> >     >
> >     > In order to participate we need ideas for projects and mentors to
> go
> >     > along with them.
> >     >
> >     > The current list of RDKit ideas is being maintained here:
> >     >
> >     http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas
> >     <http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas>
> >     >
> >     > (Note: at the point that I'm pressing "send", that's still a copy
> of
> >     > last year's project ideas).
> >     >
> >     > If you're willing to be a mentor (please ask me about the ~5
> >     hours/week
> >     > required here) or have ideas, please reply to this thread.
> >     >
> >     > Best,
> >     > -greg
> >     >
> >     >
> >     >
> >
>  
> ------------------------------------------------------------------------------
> >     > Check out the vibrant tech community on one of the world's most
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> >     >
> >     >
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> >
> >
>  
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> >     Rdkit-discuss@lists.sourceforge.net
> >     <mailto:Rdkit-discuss@lists.sourceforge.net>
> >     https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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> >
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Check out the vibrant tech community on one of the world's most
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> Message: 3
> Date: Mon, 15 Jan 2018 20:51:52 +0000
> From: Tim Dudgeon <tdudgeon...@gmail.com>
> To: rdkit-discuss@lists.sourceforge.net
> Subject: Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018
> Message-ID: <129d77fb-5461-800c-ffd0-43a542a60...@gmail.com>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
> 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 to participate we need ideas for projects and mentors to go
> > along with them.
> >
> > The current list of RDKit ideas is being maintained here:
> > http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas
> >
> > (Note: at the point that I'm pressing "send", that's still a copy of
> > last year's project ideas).
> >
> > If you're willing to be a mentor (please ask me about the ~5
> > hours/week required here) or have ideas, please reply to this thread.
> >
> > Best,
> > -greg
> >
> >
> >
> ------------------------------------------------------------------------------
> > Check out the vibrant tech community on one of the world's most
> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> >
> >
> > _______________________________________________
> > Rdkit-discuss mailing list
> > Rdkit-discuss@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
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