On 13/09/2007, Greg Landrum <greg.land...@gmail.com> wrote: > On 9/13/07, Noel O'Boyle <baoille...@gmail.com> wrote: > > So on to the questions: > > (1) Can I believe my eyes? Is this really open source? A lot of the > > Python code has a very restrictive copyright statement right at the > > start (see Windows release, AllChem.py for example) > > The "All rights reserved" is, in my opinion, superseded by the > license.txt file (which is BSD, except for the GUI components, which > are GPL due to Qt license restrictions). It's really open source and > it's as open as we could make it without going public domain (I > consider the BSD license to be far more open than the GPL, which is > quite restrictive IMO).
I would definitely encourage you to replace the "All rights reserved" to be replaced with something more friendly. I'll check out some codes I'm involved with and suggest a change. > > (4) Why haven't you publicised RDKit, if you don't mind me asking? For > > example, there is an excellent (if I do say so myself) website called > > Linux4Chemistry which lists the excellent (if you do say so yourself) > > YaEHMOP. Also there's the CCL mailing list. I only found RDKit because > > of trawling through the SF software map. Is this, um, shyness, > > intentional? > > There are many components to the answer to this question. Some are: > 1) Promotion isn't something I enjoy or am particularly good at. > 2) I'm kind of afraid of having more users. I do a lot of this as a > free-time project and I'm afraid of spending all my time answering > questions. This is, of course, a bit stupid because if the whole open > source thing works then other people will pitch in and help with those > questions. For that to happen I need those other people as users, > which requires that I find them, which... it's a Catch 22 Well...don't worry about the publicisation...you can leave that to me (I feel a blog post coming on :-) ) As regards too much time answering questions, cheminformatics toolkits are a pretty niche interest. Also, I try to avoid answering any question twice; i.e. I update the documentation if someone doesn't know how to do something, and you can always send them over to OpenBabel if they don't behave. But it'd be wrong to think that people will pitch in to answer questions - they don't. They are more forthcoming finding bugs though, which is useful too. > > (5) You may/not be aware but Numeric is deprecrated to the extent that > > it is not available for Python 2.5 on Windows. I had to replace a > > couple of "import Numeric"s with "from numpy import oldnumeric as > > Numeric", but this is only a temporary solution. > > The Numeric thing is a definite problem (though it works fine for me > with Python2.5 under windows). I made an attempt a while ago to port > the code to use numpy, but was immediately frustrated by the lack of > documentation available (unless you buy the book) and the very > aggressive response of the community when I complained about this. I'll help if I can, but I'd be relying on the unittests to ensure correctness. > > (6) It'd be nice to have an installer for the Python stuff...I've done > > this for OpenBabel. It's pretty easy. > > If you care to share how you did this, I'd be happy to learn. It's a nice > idea. Will do. In fact, the one major flaw with promoting your toolkit is that it's not clear how it's installed on Windows or on Linux. You might want to consider writing this up. > > (12) Interested in easily converting a ROMol to an OBMol and vice > > versa? I am. It'd be trivial to do this at the Python level. We could > > coordinate a bit to make the methods somewhat symmetrical. It would > > make it easy to unittest shared algorithms against each other, e.g. > > LogP calculation, SMILES, or whatever. > > It would be an interesting exercise. I'm not convinced that it would > be trivial to get it right. There's a lot of devil in the details of > things like aromaticity handling and general sanitization problems > (the RDKit is *very* picky about molecules being "clean"). Well, as you can imagine, there are several levels of information in a chemical structure. I was initially thinking of just sharing coordinates, and allowing each program to work the rest out from there. Do you have bond perception? Well, anyway, we will sort this out later. Thanks for all the answers, Noel