Hi Geoff, On 9/14/07, Geoffrey Hutchison <ge...@geoffhutchison.net> wrote: > Hi Greg and company! I think we talked at some point about YAHhMOP > during my postdoc at Cornell.
yes! I knew your name was familiar beyond seeing it associated with OpenBabel. That's it. > Browsing through the thread, I see your comment that RDKit stuff > isn't nearly as optimized or "battle-tested" as Daylight (or > presumably Open Babel). I didn't include OpenBabel there because I honestly don't know enough about it to be able to realistically assess its performance or robustness. > You also seem worried that if the project will have more users, > you'll spend lots of time answering questions. > > From my perspective, neither of these have been problems with Open > Babel. Of course at this point, we also have more users and > developers, so the burden of support is spread over more people. > (Noel, for example, has been very active, as you've probably > noticed. :-) This is something that's nice to hear. I'd be happy to have a popular open-source project that works as it's supposed to (contributions from the community in terms of either code, examples, documentation, help for other users, etc.) but I know one needs to be very lucky to have that happen. > What I'm curious about is the question of collaboration/merging > efforts. I haven't had enough time to sit down and pour through your > code, but it looks like much of RDKit is complementary to Open Babel. > That is, what we do well (arbitrary generic data, file formats, > "battle-tested," etc.) is not something already in RDKit. We've > worked out installation/building on Mac, Linux, Windows, etc. and > automatic Python, Ruby, etc. interfaces using SWIG. We do have a > force field framework, and it has at least partial implementations of > MM2, MMFF94, and Ghemical (i.e., Tripos-5.2). > > I also think we have a nice framework for adding additional features > like force fields, fingerprints, file formats. It's all plugins that > can be dynamically loaded. > > OTOH, we've been discussing an effort for an "Open Babel 3.0" where > we break backwards compatibility and clean up some of the core code. > This would obviously be a fairly significant undertaking. Many of the > features and changes requested are along the lines of RDKit's codebase. > > Fortunately, the weekend is coming up. Do you think that: > a) There's some complementary overlap between RDKit and Open Babel > b) Collaboration and/or merging might be good for both projects? > (e.g., we'd certainly help improve the documentation, etc.) There's a lot here to discuss and think about. I am certainly in favor of collaboration and cooperation, but talking about integration is scary. :-) Let's definitely talk though. > Obviously, the combined project would have some GPL bits and some BSD > bits. To be completely up front, the GPL bit bothers me and presents a problem for any tight integration. We're already stuck with some "GPL contamination" for the GUI components of the RDKit due to our use of Qt, but I have tried to keep that as localized as I possibly can. Out of curiosity: is the GPL use in OpenBabel due to historical reasons (OB is derived from the old OELib, right?) or philosophical? > Is this just a crazy idea? I don't think so. I'm sure that we can find *something* productive and useful to do so that the two toolkits aren't competing/completely disjoint. :-) -greg
