honest question: what if your science isn't maths/physics/data? I'm a chemist and from what i can see there's @#$@# all out there in FOSS land.
So here are some generalizations.
While in school, I noticed that the physics students were far more interested than the chemistry students, in math and computer stuff. Maybe we were computer science wannabees, or maybe we guessed (correctly in my case) that proficiency with computers would make us more employable. This was true in both undergrad and grad school.
And there's a long tradition of physicists stealing ideas from math and computation for solving physics problems. When I was in school, computation was considered to be a specialized branch of chemistry, but was at the forefront of physics.
Another difference is that the physics students were generally more interested in making our own tools. The current "maker" and "hacker" trends are old hat for small-lab experimental physicists.
Chemistry has always been a bigger field than physics, which I suspect has attracted more interest in making commercial equipment and software. I've noticed in an industrial setting, that managers are often looking for closed solutions that can't be modified by the user, either for regulatory reasons or adversarial labor-management attitudes. The industry wants your boss to think that letting you make your own tools is either dangerous, or a waste of your time.
In contrast, even in industry, physicists still have to make our own tools. And management already knows that we're freaks. ;-)
So the absence of FOSS tools for chemistry doesn't shock me.
It's interesting to consider in this context that workers owning the means of production is what links the GPL with Marxism.
http://openbabel.org/wiki/Main_Page
which has some python bindings built in. I set some of this up for myself during my PhD but it was occasionally kind of a pain sometimes to get it to work. Also at the time I was a bit of a noob so there's that :).
It has some nice features for handling chemical structures, I used it mostly for translating one format into another and computing fingerprints, but I think more can be done.
In general I'd agree with @analog31, biology has some good OSS tools, physics has some good OSS tools, but you get to the bridging discipline of chemistry and you find very few. My theory re. organic chemistry and biochemistry applications: it's way more profitable to be closed source. In contrast to the other two fields (gross generalization I know, but somewhat true) there's a very large market for commercial software in Pharma. If someone is willing to pay top dollar, especially an industry that is paranoid about IP and therefore tends to (rightly or wrongly) prefer closed, proprietary solutions, then that's where software will end up.