Merge pull request #1446 from RosettaCommons/bfrenz/denovo_density_point_selection Bfrenz/denovo density point selection

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Merge pull request #1448 from RosettaCommons/xingjiepan/LoopBuilder_bug_fix Remove the idealize_loop() function in LoopBuilder::do_apply()

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Merge pull request #1452 from RosettaCommons/Cyrus/mergetarget Cyrus/mergetarget Included in this PR: PR Cyrus 35: add comment clarifying pilot_apps.src.settings.release (there was some list traffic here) PR Cyrus 31: global replace old UNC address with gmail address in doxygen tags (smlewi@unc->gmail) PR Cyrus 33: Tweaks SSPredictionFilter (actually PsiPredInterface) to automatically allow for a second type of name mangling from a different version of runpsipred PR Cyrus 32: Smlewis cyrus/beta nov15 score catcher: Catches the problem where you pass a beta weights file without the accompanying required flag to activate the params overrides. (exit from ScoreFunctionFactory in the (in)appropriate circumstance). Also PR Cyrus 29, which got caught in a time vortex, and was merge -X theirs overwritten because Rhiju was forced to duplicate the code itself instead of taking it from its original crossfork PR.

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Merge pull request #1449 from RosettaCommons/vmullig/small_genkic_tweak Adding option to the GeneralizedKIC mover ("dont_fail_if_no_solution_found=true") to NOT set mover status to failure if no solution is found. (The default is false, which means that the mover WILL exit with failure status if no solution is found, aborting a trajectory. There are some cases in which one might not want this, though.) Tasks: - Add option, setter function, and parsing in parse_my_tag(). - Have it control mover status. - Update documentation. - Beauty.

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Merge pull request #1433 from RosettaCommons/everyday847/n3_adenine_prot Adenosine protonation variants

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Merge pull request #1447 from RosettaCommons/bazzoli/ignore_waters_by_default Ignore waters by default.

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Merge pull request #1450 from RosettaCommons/sergey/binder Adding bindings for ObjexxFCL

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Merge pull request #1441 from RosettaCommons/tlinsky/symmetry Add simple unit test and doxygen for core::pose::symmetry::symmetrize_fold_tree

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Merge pull request #1443 from RosettaCommons/dimaio/multichain_hybrid_bugfixes A bug in my previous checkin with multichain hybridize

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Merge pull request #1431 from RosettaCommons/tlinsky/helix_pair_filter Update and clean up HelixPairingFilter, add unit test

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Removing unneeded include to fix release’s

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Merge pull request #1439 from RosettaCommons/tlinsky/delete_region_pdb Make DeleteRegion parse_my_tag congruent with documentation

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Merge pull request #1442 from RosettaCommons/rhiju/rna_denovo_setup + hotfix to FARNA integration test that includes VRT residue + also removing some unnecessary verbiage from rna_denovo_setup + restoring rna_puzzl5_P15P3P8... test which used virtual residue & rigid body docking of all segments. + tests look OK

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Merge pull request #1436 from RosettaCommons/dimaio/multichain_hybrid_bugfixes Fix a few bugs in hybridize with multichain poses. - Run a bit faster when DetailedControls are enabled by skipping unnecessary calcs. - Move some output to Trace level. hybridize/mr_protocols integration test changes expected.

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Merge pull request #1437 from RosettaCommons/rhiju/rna_denovo_setup fix getcwd() compile bug in ubuntu. standard tests look OK (except profile, not yet complete), and separately ran ubuntu builds

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PyRosetta, decreasing runtime of Workshop5test.py test

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