Re: [Rdkit-discuss] What is RDkit?

[Noel O'B. <bao...@gm...>]

On 12/09/2007, Greg Landrum <gre...@gm...> wrote:
> Hi Noel,
>
> Sorry for the very slow posting of your message and reply; I was on
> vacation until yesterday and needed to approve your posting since you
> aren't subscribed to the discuss list; that shouldn't be a problem
> from now on.

Don't worry about it. Hope you had a good holiday.

> On 8/27/07, Noel O'Boyle <bao...@gm...> wrote:
> > Any chance of more info on what RDkit contains? E.g. an API, or a
> > website. Although Open Source projects are infamous for incomplete
> > documentation, you seem to have taken this to an extreme :-)
>
> ah hah! that's where you're wrong! :-)
> We actually do have have some documentation, we just don't have any
> obvious links to it from sourceforge. This is an oversight on my part
> and something I will clear up.
>
> There are some useful links here:
> http://www.rdkit.org/
> specifically to the overview PDF:
> http://www.rdkit.org/RDKit_Overview.pdf
> and some (automatically generated and somewhat out of date) API documentation:
> http://www.rdkit.org/C++_Docs

Just a note: you can point the SF home page to go to whatever website you want.

> There's also an introduction to using the code from Python on
> sourceforge that provides something of an overview of the
> functionality:
> http://downloads.sourceforge.net/rdkit/GettingStartedInPython.pdf

Great! I'll read up on it.

> > I'm involved in other open source cheminformatics packages (via the
> > BlueObelisk, with varying degrees of documentation it must be
> > admitted) so it would be good to know to what extent there is overlap,
> > and whether we could share code, etc...
>
> My last look at blue obelisk was, admittedly, a while ago, but I
> somehow got the impression at the time that it was pretty
> Java-centric. Is this true?

I can understand your impression. I'm not into Java though. The other
side is the C++ code of OpenBabel, and Python code for various things
(e.g. GaussSum, cclib for comp chem, and Python bindings for
OpenBabel). Also, the BO is involved in sharing chemical data, e.g.
names of elements, atomic weights and so on, so that we don't keep
having to re-enter this information in different software. (Check out
Blue Obelisk Data Repository on google). Interoperability is also one
of our goals.

In the end, the BO is a loosely coupled bunch of chemists/computer
scientists with largely the same goals but lots of different ideas
about getting there. In short, I recommend subscribing to the mailing
list, or the RSS feed, checking out the wiki, and keeping an eye on
things. There's a couple of very interesting blogs too, if I do say so
myself..

Noel

> Regards,
> -greg
>