Dear ALL,
When compile the program with scons, I don't see any Makefile which says that which source files make the fixbb binary program. What should I do to see this kind of information? I want to see which files are involved with the fixbb design program. Thank you!
Post Situation:
Scons is an alternative to make, and doesn't use Makefiles at all. (BTW, our scons build system is rather scary - I wouldn't recommend digging through it unless you absolutely have to.)
In general, the applications themselves are in rosetta_source/src/apps/public - for example, fixbb is located at rosetta_source/src/apps/public/design/fixbb.cc That's a rather small wrapper around the Rosetta libraries, though, which are found mostly in rosetta_source/src/protocols (higher level things), and rosetta_source/src/core (lower level things), with some minor things in the other directories of rosetta_source/src/
We try to make the layout of the code self-evident. The namespaces should match up with the directory structure, and major classes should get eponymous named .cc and .hh files, so if you find a class or function, there's usually strong hints as to where the implementation is located.
Thank you! I got it.
If you're interested in how the fixbb algorithm works, have a look in rosetta_source/src/core/pack. pack_rotamers.cc contains the entry point into "the packer." In the pack_rotamers function, rotamers are constructed, their pair energies evaluated and stored in tables, and then the rotamer assignment is optimized using a Monte Carlo with simulated annealing protocol. Code for these steps is in src/core/pack/rotamer_set/RotamerSet_.cc (rotamer building), src/core/scoring/ (energy calculation), and src/core/pack/annealer/FixbbSimAnnealer.cc (simulated annealing).