Merge pull request #1679 from RosettaCommons/everyday847/cache_rna_scoreterms Use extended interface for RNA_FA_Elec

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Merge pull request #1680 from RosettaCommons/vmullig/brian_sequence_bug Fixing inverted PDBInfo check in Sequence.cc Brian Koepnick and Jeff Flatten of the Foldit team found a bug in Sequence.cc: the existence of a PDBInfo object is checked before the object is accessed, but the check is inverted. That is, the object is accessed ONLY if it doesn't exist, which makes no sense. This fixes that. Thanks to these two for finding this. @bkoepnick @jflat06

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Merge pull request #1676 from RosettaCommons/tjbrunette/remodel_helical_repeat_test_fix bug fix for remodel_helical_repeat unit test

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Merge pull request #1345 from RosettaCommons/roccomoretti/clang_SA Clang Static Analysis -- is a go!

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Merge pull request #1663 from RosettaCommons/tlinsky/remove_csts_excn Add option to RemoveConstraints mover whether or not to throw excn

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Merge pull request #1677 from RosettaCommons/sergey/binder Adding bindings for operators -= and +=

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Merge pull request #1675 from RosettaCommons/bazzoli/pwsho-reparam Flags for pwSHO reparameterization

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Merge pull request #1671 from RosettaCommons/vmullig/simple_cycpep_predict_features Adding needed features to simple_cycpep_predict application Tasks: - Add options for torsion/angle/length space relaxation with: - Flexible bond angles. - Flexible bond angles and bond lengths. - Add option for full Cartesian-space relaxation. - Have the above options actually trigger appropriate rounds of relaxation. - Bond angles. - Bond angles + bond lengths. - Cartesian-space relaxation. - Integration tests for the above. - Add output of number of cis-peptide bonds. - Plus unit test for sorting by cis-peptide bond count. - Add hard energy cutoff for output. - Add to one integration test. - Turn cis-pro sampling on by default. (Do this last, after confirming that above changes do not change existing behaviour of integration tests.) - Disable cis-pro sampling explicitly in existing integration tests that did not sample cis-pro before. - Documentation. - Beauty.

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Reverting build breakage

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added option to thermal_sampler to sample varying bb angles, compiles successfully

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Merge pull request #1670 from RosettaCommons/jadolfbr/ab_h3_valgrind Jadolfbr/ab h3 valgrind Fix antibody_H3 valgrind issue for camelid antibodies. Note that the valgrind test was done here: http://benchmark.graylab.jhu.edu/revision?id=4809&branch= Integration tests are cosmetic

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Fixing Rosetta build on Stampede

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Merge pull request #1669 from RosettaCommons/vmullig/simple_cycpep_predict_features_firstmerge Splitting pull request for simple_cycpep_predict Since there will be some integration test changes, I want to merge this first part before the second part. Tasks: - Add options for torsion/angle/length space relaxation with: - Flexible bond angles. - Flexible bond angles and bond lengths. - Add option for full Cartesian-space relaxation. - Have the above options actually trigger appropriate rounds of relaxation. - Bond angles. - Bond angles + bond lengths. - Cartesian-space relaxation. - Integration tests for the above. - Documentation. - Beauty.

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Merge pull request #1659 from RosettaCommons/tjbrunette/repeat_fusion Tjbrunette/repeat fusion adds code for repeat fusion, code for calculating energy using Will's motifs, and a way to very accurately fix short loops ideally, and code that was necessary to propagate hemes. Will try to do smaller merges from here on out.

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Fix erraser_minimize integration tests on Macs. GNU and MacOS sed are stupidly incompatible.

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Merge pull request #1639 from RosettaCommons/everyday847/thermal_sampler_mover The ThermalSamplingMover now exists for all your thermal sampling needs, as does the ThermalMinimizer as a stepwise plug-in.

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