commit 5e610c88cc274889eff7cd68d3d964f188ddc6f1 Merge: a0044a0 e7b6f3c Date: Mon May 2 09:04:38 2016 -0500 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.) commit a0044a002c51ad2389a690f9d5a675786bf10abb Merge: 643561b b0507b4 Date: Mon May 2 09:08:37 2016 -0400 Unit tests should produce output only when they fail.The first commit in this pull request makes it possible to trap on debug_assert failures. It also makes it possible to trap an expected exception in unit tests coming from utility_exit WITHOUT noise being piped through std::cerr. Many commits here preface the calling of functions that are expected to fail with calls to utility_exit_with_message(...) with a call to The remaining unit tests replace usage of TS_TRACE with sending output to basic::Tracer objects (that can be muted). Unit tests should produce output only when they fail. The first commit in this pull request makes it possible to trap on debug_assert failures. Specifically, it adds a function "throw_on_next_debug_assert_failure" so that instead of printing the backtrace to std::cerr and triggering a trap in assert( fail ), instead the debug_assert macro will throw an exception, which can be caught in a unit test without making any noise. The second or third commit also makes it possible to trap an expected exception in unit tests coming from utility_exit WITHOUT noise being piped through std::cerr. Many commits here preface the calling of functions that are expected to fail with calls to utility_exit_with_message(...) with a call to throw_on_next_assertion_failure so that they too avoid a message ending up printed. Several unit test changes replace usage of TS_TRACE with sending output to basic::Tracer objects (that can be muted). A small number of source changes print output to Tracers instead of to cout. These changes are responsible for the cosmetic integration test changes. Thank you Rocco, Vikram, and Steven for pitching in. @roccomoretti @vmullig @smlewis Please do not print directly to cout. Please do not use TS_TRACE. From here on out, if you see a message while running the unit tests, that means that something bad has happened. (It would be nice in the future to have test/run.py print very little -- it currently tells you about all the tests that it has launched, which is verbose for my tastes. Perhaps it could do that nifty thing where it overwrites the last line of a terminal the way ninja does?) commit 643561b2ec6cb7662f0c9a38f81db0c1b5b94d9e Merge: c38eb29 5b9a1fa Date: Sun May 1 18:28:16 2016 -0700 Merge pull request #1307 from RosettaCommons/hahnbeom/normalmode_update2 add support for restraining hbonding residues on solving normalmode t… commit c38eb29beae09aa0fbda8e6f00c0aee986afdfca Merge: 4ae2cbc bb6d31a Date: Sat Apr 30 16:10:26 2016 -0700 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. commit 4ae2cbc8cc6578d3860622be63b62748eb986b14 Merge: e53d6ba f8cd527 Date: Fri Apr 29 22:41:31 2016 -0700 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 commit e53d6ba33ca3e133beee84942400bf6e3c25ab5c Merge: b5c0931 b9370e4 Date: Fri Apr 29 22:39:27 2016 -0700 Merge pull request #1304 from RosettaCommons/jadolfbr/fix_glycan_clash_check Fix unstable Glycan Clash Check test commit b5c09310785c55d3a0780283c5ab875a8cfc00be Merge: 8c2b3b5 1e5c9d8 Date: Fri Apr 29 00:49:17 2016 -0700 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). commit 8c2b3b54f0aa8d21ab5031a420b96771a8c54a2b Merge: 6f7dba7 2afcad9 Date: Thu Apr 28 23:57:23 2016 -0700 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. commit 6f7dba72ced4538b33a693ca10e0832093601b5b Merge: 0168292 c03774a Date: Thu Apr 28 16:08:50 2016 -0700 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. commit 01682924436e29f074032241a50d1b2a50b279b7 Merge: 4423ffa 9c181f3 Date: Wed Apr 27 10:11:28 2016 -0700 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. commit 4423ffa60324ef31015e9a05c424d975e786af22 Merge: dcbe8d8 be06823 Date: Mon Apr 25 21:23:26 2016 -0600 Merge pull request #1296 from RosettaCommons/antibody Updating antibody app commit dcbe8d8ca938bc6f2916c4e399b2aac6e0791c1a Merge: 37bac29 32dde1f Date: Mon Apr 25 00:52:57 2016 -0700 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.