Removing unused variable. Fixing the build.

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[update of SandwichFeatures] - refactored SandwichFeatures by introducing WriteToFileFromSandwichFeatures.cc - streamlined all inclusions - better comments - should not change any integration tests other than (expected) features and features_database_schema (if any)

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fix to RDAT.cc to compile on linux!

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Introduces RDAT file format for RNA chemical mapping into Rosetta as well as an app that should reach wide use, rna_predict_chemical_map. First connection of Rosetta 3D modeling to chemical mapping measurements that are widespread in RNA biochemistry, are exploding in throughput, and that are being put on a quantitative footing by our and other labs. This is a merge from rhiju/dms_score before closeout of that branch. No changes in integration tests except a couple that were failing already, and a couple that always seem to change on my mac (match_1n9l & flex_pep_dock).

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Merging changes in my pilot app with the trunk

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fixing build

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adding mover ResetBaseelineMover to reset the baselines of Operator and CompoundFilter movers. See wiki for details

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Adding support for FA constraints in DockingProtocol. The assemble_domains_jd2 test has a trajectory change due to constraints not being enabled in docking without the cst_file flag set.

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Maybe this will fix residue_types.txt

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Shoot, residue_types.txt got left out. No longer.

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Homocysteine (NC C26) can now form disulfides. Modification to Conformation and to disulfide scoring allows NC C26, homocysteine, to form a disulfide residue type (HCD, by analogy to CYD) and be scored as appropriate. (It retains the C26 rotamer library.) Integration test log file changes expected merely due to changes in Conformation log output

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adding flag omega to MinMover that defaults to true. If set to false, don't minimize the omega bb torsion. No test changes expected (except log changes where RosettaScripts use MinMover).

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Fix one bug in currently broken pyrosetta build.

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Myriad bug fixes and API improvements for Environment system. New (and improved) unit tests, construction of general LoopCM for managing dof-greedy loop modeling code, FragmentsMovers are now created as a tag inside the Environment in RosettaScripts. No (new) unit test breakages; no (new) integration test failures.

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Adding Talaris2014 weight set Adding a weight set and a flag -talaris2014 that incorporates two small changes to the score function: All the terms are scaled upwards by 25% so that fa_atr has a weight of 1.0. The hydrogen bond terms are scaled downwards by 20%, which benchmarking revealed to improve decoy discrimination, sequence recovery, and rotamer recovery.

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OK. I see what happened. I tried to reindent the MembranePotential.cc file because it's all kinds of poorly indented, but in so doing, I uncommented some code that doesn't work. I'm commenting out that code again.

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