Merge pull request #1303 from RosettaCommons/rhiju/farna_no_frags_across_cutpoint in FARNA, do not apply fragments across cutpoints in poses... + changes in rna_denovo tests expected. + other changes (glycan_clash_check & code_template_tests_src) appear to be broken/erratic in other pull requests to master.

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Merge pull request #1300 from RosettaCommons/jadolfbr/update_code_templates Make mover code_template use .fwd header for pose Fix my mover headers that have Pose.hh instead of Pose.fwd.hh

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Merge pull request #1302 from RosettaCommons/vmullig/parisa_bug2 Add unit tests for cyclic geometry with multiple chains and disulfides This pull request adds unit tests for cyclic geometry with multiple chains and disulfides. Circular permutations should score identically. Merging without testing (though I ran the unit tests locally to make sure that they don't fail).

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Merge pull request #1277 from RosettaCommons/vmullig/parisa_bug Trying to fix a bug identified by Parisa Cyclic geometry with multiple chains seems not to be calculating mainchain torsions at the breakpoint properly. This was due to an overly-lax check for cutpoints that wasn't actually looking for a cutpoint variant. This has been corrected now; some integration tests involving unconventional connections will show trajectory changes. Others show cosmetic changes due to certain DOFs not being found.

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Merge pull request #1299 from RosettaCommons/vmullig/fract_delta Add support for fractional penalty ranges to AACompositionEnergy Requested by @basantab. This will allow users to apply penalties that vary based on the fractional, rather than absolute, amino acid composition. (For example, rather than saying, "I want 7 alanines, and here are my penalties for 5, 6, 8, or 9 alanines," the user could say, "I want 7% alanine, and here are my penalties for 5%, 6%, 8%, or 9% alanine.") Tasks: Add FRACT_DELTA_START and FRACT_DELTA_END statement parsing to .comp files. Check that the user has either used DELTA_START/DELTA_END or FRACT_DELTA_START/FRACT_DELTA_END (but not both). Revise interpretation of PENALTIES lines if FRACT_DELTAs are used. Add logic to apply penalties based on fractional penalty values. Make change in note below: FRACT_DELTA_START and FRACT_DELTA_END should represent deviations from desired, not absolute values. Add logic to interpolate (linearly, since first and second derivatives don't matter here). Add logic to extrapolate (linearly and quadratically) for BEFORE_FUNCTION and AFTER_FUNCTION. Update added functions -- they need to take into account the penalty value spacing when fitting the linear and quadratic functions. Unit tests. Integration test. Documentation. Beauty.

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Merge pull request #1298 from RosettaCommons/dimaio/min_fixes Two small updates/bugfixes for minimization: 1) adding a minimizer 'lbfgs' that uses the lbfgs minimizer with Brent line search. Updating rtmin to use this as it is more efficient in energy function optimization tests. 2) fixing a bug where polymer bonded energy container was not properly scoring symm poses when the scoring subunit was not the first.

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Merge pull request #1296 from RosettaCommons/antibody Updating antibody app

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Merge pull request #1294 from RosettaCommons/vmullig/makebundle_fix Minor fix to MakeBundle Appending additional elements to a parametrically-generated pose wasn't working because there was no PDBInfo object in the pose to reset.

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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

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Merge pull request #1285 from RosettaCommons/vmullig/rosetta_bluegene Tweaks to try to get the Blue Gene build working again

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Merge pull request #1292 from RosettaCommons/everyday847/hbs_geometry Fixing HBS geometry and unifying setup functions

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Merge pull request #1291 from RosettaCommons/vmullig/horrible_error_msg Fixing a horrible error message. "ERROR: num" is largely non-informative, but for the limited information that Andy claims can be gleaned from it.

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Merge pull request #1290 from RosettaCommons/vmullig/shush_tests Shushing output of some unit tests Andrew wants the verbosity cut on some unit tests, so I'm taking those that I wrote. @aleaverfay: how much verbosity is acceptable? Do you want no output at all from a functioning unit test? I usually like there to be something in the log to let me know that the test ran and what it tested... Tasks: reduce verbosity of the following unit tests: - test/protocols/helical_bundle/params_data_storage.cxxtest.hh - test/core/io/pose_to_sfr/PoseToStructFileRepConverter.cxxtest.hh - test/core/scoring/aa_composition_energy/AACompositionEnergy.cxxtest.hh This also fixes the RestrictOperations unit test (thanks to @smlewis).

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fix key_name for an antibody task op to have it available via RS.

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Merge pull request #1272 from RosettaCommons/georgkuenze/AddShowInfoToPCSCode * Add a new show_additional_info() function to EnergyMethod and PCSEnergy classes * show_additional_info() prints out PCS tensor parameters and comparison of calc. vs exp. PCS values * Add an additional boolean variable verbose to show_additional_info() to control the amount of printed information * Add a new show_additional() function to the ScoreFunction class that can call show_additional_info() for all EnergyMethod objects * Add a call of ScoreFunction::show_additional() to the checkpointed_cycle_block of the FragmentSampler protocol

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Merge pull request #1283 from RosettaCommons/hahnbeom/normalmode_update Hahnbeom/normalmode update

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