How about setting up a donation fund on rdkit.org to pay for summer
students to document code?  For companies that benefited from using RDKit,
it is a worthy cause to pay it forward.

___________________
JW Feng, Ph.D.
Denali Therapeutics Inc.
151 Oyster Point Blvd, 2nd Floor, South San Francisco, CA 94080 | (650)
270-0628

On Wed, Feb 7, 2018 at 12:24 PM, <
rdkit-discuss-requ...@lists.sourceforge.net> wrote:

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> Today's Topics:
>
>    1. Re: RDKit and Google Summer of Code 2018 (Greg Landrum)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 7 Feb 2018 21:23:46 +0100
> From: Greg Landrum <greg.land...@gmail.com>
> To: Cameron Pye <cameron....@gmail.com>
> Cc: RDKit Discuss <rdkit-discuss@lists.sourceforge.net>
> Subject: Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018
> Message-ID:
>         <CAD4fdRT4e+gp0Hsi6KojPQfmirwx6JO3P5QVrbhD4XrXJG=
> o...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> A quick one on this as part of me digging out from the pile of email I
> should have replied to.
>
> Cameron's suggestion is a really good one, but unfortunately GSoC is really
> about coding projects, so it doesn't work here.
>
> But we should still talk about ways to improve the docs.
>
> I agree that this is a really important task but it's also a bit
> overwhelming and difficult to know where to start. This is too bad since
> it's something you don't need to be a coder to approach; more or less any
> RDKit user could contribute. Believe it or not, just having people point
> out pieces of code that could be (better) documented is already useful -
> I'm sure I'm not the only developer who has forgotten which bits of code
> they've left un(der)documented. I often have 10-15 minute slots of time
> that I could use for writing docs, but it really helps to know which pieces
> should be done first.
>
> I would love to hear suggestions for ways that we can make it easier for
> people to submit improved documentation or pointers to pieces of code that
> could use better documentation and then to let people know that these
> options exist. It needs to be something other than "send email to the list"
> though.
>
> It's currently pretty easy to submit bug reports/feature requests using the
> github interface. These could either provide suggested docs/doc changes or
> point to functions/methods/classes that could be better documented. The
> github guys just added the ability to specify different types of issue
> templates, I could look into doing one of these for documentation requests.
>
> -greg
>
>
>
> On Wed, Jan 24, 2018 at 7:38 PM, Cameron Pye <cameron....@gmail.com>
> wrote:
>
> >  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-request@lists.
> > sourceforge.net> wrote:
> >
> >> Send Rdkit-discuss mailing list submissions to
> >>         rdkit-discuss@lists.sourceforge.net
> >>
> >> To subscribe or unsubscribe via the World Wide Web, visit
> >>         https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
> >> or, via email, send a message with subject or body 'help' to
> >>         rdkit-discuss-requ...@lists.sourceforge.net
> >>
> >> You can reach the person managing the list at
> >>         rdkit-discuss-ow...@lists.sourceforge.net
> >>
> >> When replying, please edit your Subject line so it is more specific
> >> than "Re: Contents of Rdkit-discuss digest..."
> >>
> >>
> >> Today's Topics:
> >>
> >>    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
> >> >
> >> >
> >> -------------- next part --------------
> >> An HTML attachment was scrubbed...
> >>
> >> ------------------------------
> >>
> >> 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
> >> >     > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> >> >     >
> >> >     >
> >> >     >
> >> >     > _______________________________________________
> >> >     > Rdkit-discuss mailing list
> >> >     > Rdkit-discuss@lists.sourceforge.net
> >> >     <mailto:Rdkit-discuss@lists.sourceforge.net>
> >> >     > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
> >> >     <https://lists.sourceforge.net/lists/listinfo/rdkit-discuss>
> >> >     >
> >> >
> >> >     -----------------------------------------------------------
> >> -------------------
> >> >     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
> >> >     <mailto:Rdkit-discuss@lists.sourceforge.net>
> >> >     https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
> >> >     <https://lists.sourceforge.net/lists/listinfo/rdkit-discuss>
> >> >
> >> >
> >> >
> >> >
> >> > ------------------------------------------------------------
> >> ------------------
> >> > Check out the vibrant tech community on one of the world's most
> >> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> >> >
> >> >
> >> > _______________________________________________
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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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> >> Check out the vibrant tech community on one of the world's most
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> >>
> >
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