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:
>
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>>
>> 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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>> > Rdkit-discuss@lists.sourceforge.net
>> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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>> An HTML attachment was scrubbed...
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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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>> **********************************************
>>
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