Merge pull request #1552 from RosettaCommons/roccomoretti/integration_test_mode
Adjust integration.py to allow for other modes in demos tests.
e.g. release_debug
Merge pull request #1533 from RosettaCommons/rfalford12/extend-mpdock-rscript-interface
Extend the MPDock parse_my_tag function
Add options to MPDock's parse_my_tag to set alternate low & high resolution score functions from the RosettaScripts interface
Merge pull request #1513 from RosettaCommons/rhiju/reconcile_bps_input_pdb_farna
Rhiju/reconcile bps input pdb farna
+ this was needed to model eterna switches in 3D
+ changed behavior of bps_moves ("base_pair_step moves") to not move residues inherited from input PDBs. Makes SRP modeling cases (e.g. in integration test) worse, but more consistent with other conventions that we've used for, e.g., stepwise.
Merge pull request #1465 from RosettaCommons/amelie-stein/ddG_with_ligands
On behalf of Amelie, merge in some fixes to the ddg_monomer applicaition to allow it to work with non-amino acid residues.
Merge pull request #1400 from RosettaCommons/vmullig/cycpep_predict_tweaks
Adding try/catch block to individual calls to SimpleCycpepPredictApplication in the MPI version, so that individual job failures don't bring down everything. There's an ultra-rare failure occurring one time in 100,000, so it only shows up in my production jobs (in which I usually have to mute all output, so I can't even see what's failing). It's REALLY irritating. I don't know how to track down and fix it, so I have to make sure that I can recover from whatever the error is when it happens.
Merge pull request #1358 from RosettaCommons/vmullig/design_cycpep_app
Add filtering for oversaturated hydrogen bond acceptors to simple_cycpep_predict app.
This allows the simple_cycpep_predict app to automatically throw away sampled conformations in which more than the allowed number of hydrogen bonds are being formed to a hydrogen bond acceptor. It pains me to split that infinitive.
Merge pull request #1323 from RosettaCommons/tlinsky/random_residue_selector_rg
Replace instance of std::random_shuffle with Rosetta's random_permutation
Merge pull request #1306 from RosettaCommons/roccomoretti/external_build_flags2
Compile & Link flags settings for external libraries
Per a request by Andrew, update the new external build scheme to allow you to specify external-library specific compiler and linker flags.
Just add them to the appropriate section of the *.external.settings file. (Should work with both scons and CMake, although mixed C/C++ libraries under CMake only get a single set of flags.)
Merge pull request #1256 from RosettaCommons/tlinsky/rotamer_boltzmann_residue_selector
Add residue selector option to RotamerBoltzCalculator
Integration test change expected for new integration test symm_rotamer_boltzmann