Merge pull request #3659 from RosettaCommons/JackMaguire/HBondState_part1
This PR is just the result of a bunch of sed commands to change AtomLevelHBondGraph to HBondGraph and MCHBNetInteractionGraph to HBondGraphInitializerIG (now that it's used in more than just MC HBNet). I also sprinkled in a few make_shared's but there's nothing exciting.
Thanks to Andy for the review!
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #3677 from RosettaCommons/vmullig/peptoid_rotamer_issue
Small mistake in MakeRotLib function return value
A function that should have been returning a Size was returning a Real. This probably wasn't causing problems, but I found it while searching for another bug, and I might as well fix it.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #3671 from RosettaCommons/jkleman/fix_domain_assembly_bug1_squash
bug fix in mp_domain_assembly and additional integration test for it
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #3670 from RosettaCommons/JackMaguire/Inlining
My benchmarks show that inlining ResidueType::atom, Residue::atom_type_index, Residue::atomic_charge, and Residue::xyz give an average speedup of 10% (using FastDesign with linmem_ig). These simple functions are called in the innermost loops of Rosetta but have previously been defined in their respective .cc files.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #3639 from RosettaCommons/vmullig/generate_mainchain_potential_2
Add an application to generate mainchain potentials for noncanonicals (attempt 2)
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #3658 from RosettaCommons/JackMaguire/MCHBNetSymmFix
Shane Caldwell recently showed me a case where MC HBNet was unable to handle a symmetric pose because of the existence of an additional pure-virtual chain. With this PR, MC HBNet now has bounds-checking to make sure that it does not interact with chains that are not considered subunits.
Thanks to Scott for the review.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #3617 from RosettaCommons/roccomoretti/update_submodule
Add a script to update compilation-needed submodules
Now that we're relying on submodules more heavily for things (especially that we're no longer prohibiting submodules for things necessary for compilation) we should have something which will automatically update needed submodules as part of the compilation process. This PR implements such a script, modelling it off of update_options.sh and the like.
To keep things clean, only the submodules needed for compilation are updated. The script has facilities to update a (currently empty) set of submodules needed for all compilation, as well as doing updates on an extras-dependent basis. -- Right now, only the extras=zeromq build has a non-trivial implementation. Other extras builds and the common case are no-ops. (Though things are implemented such that they can be added easily.)
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #3664 from RosettaCommons/vmullig/skip_makerotlib_logging
The MakeRotLib logfiles take up a huge amount of space. Adding an option to skip writing them.
The option is false by default.
Tasks:
- [x] Add the option and have it do something.
- [x] Beauty.
- [x] Documentation.
The make_rot_lib integration test is expected to show one additional line of output in its output log.
notify author
notify list [rosetta-logs@googlegroups.com]