Updating user.settings.template with os.environ line.

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Merge pull request #1626 from RosettaCommons/vmullig/modvartypeselector Switch the ModifyVariantTypeMover to use ResidueSelectors instead of TaskOperations Tasks: - Remove TaskOperation code. - Add setters and getters for ResidueSelector. - Add ResidueSelector XML parsing. - Modify apply() function. - Fix segfault. - Turns out that CTERM_AMIDATION has not been added to the VariantTypes list. - It also turns out that the patch file has a number of other problems. Fixed now. - Integration test. - Documentation. - Beauty.

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Merge pull request #1624 from RosettaCommons/everyday847/CA_rmsd_analogues RMSD for ribonucleoproteins

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Merge pull request #1619 from RosettaCommons/sergey/binder Adding bindings generation for overriding functions that return reference to primitive types or std::string

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Merge pull request #1612 from RosettaCommons/Cyrus/mergetarget From Steven Lewis: These are mostly small changes, the code I meant to push today is waiting on RosettaCommons #1601. Cyrus PR 46: Smlewis/cyrus/score mover tweak: I read ScoreMover fairly closely to write a documentation page for it, and fixed some issues with the code / comments while I was at it. Cyrus PR 47: smlewis/cyrus/fix copyright headers: fixing copyright headers in new files post Rocco’s fixes. (This is most of the changes in protocols) -> % python ~/ROSETTA/Rosetta/tools/Check_header_guards_and_copyright.py src/protocols/ | grep "^/Users/smlewis" | sed "s/://" > find_header_these This grabs the files that need header fixes cat find_header_these| while read line do sed -i bak "s/UW TechTransfer,email:license@u.washington.edu./CoMotion, email: license@uw.edu./" $line done Cyrus PR 52: smlewis/cyrus/fix_IA_ctor Fixes issues with ignoring user-set options in XML for InterfaceAnalyzer

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Merge pull request #1616 from RosettaCommons/dougrenfrew/embrace_emplace Enabling new C++11 std::vector functions in utility::vectorL/0/1

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Merge pull request #1561 from RosettaCommons/everyday847/gradually_idealize RNA idealization app

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Merge pull request #1622 from RosettaCommons/vmullig/fix_inttests Removing timing information from erraser_minimize integration test to stop the test from failing.

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Merge pull request #1602 from RosettaCommons/kylebarlow/general_dev BackrubProtocol refactoring and parse_my_tag * Refactoring BackrubProtocol to not access global option data as it applies * This allowed me to add a new parse_my_tag option to BackrubProtocol. This BackrubProtocol mover is less complicated to use in Rosetta Scripts, as it represents the composition of movers that makes up the full backrub protocol as it is applied in the command line backrub application.

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Merge pull request #1601 from RosettaCommons/kylebarlow/coupled_moves Allow coupled_moves to act on multiple ligands * New option: coupled_moves::number_ligands * Better behavior when the ligand_mode option is set to false; no longer also need to set the ligand_prob option to 0.0 to tell the code there is no ligand coupled_moves integration test changes expected

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Merge pull request #1605 from RosettaCommons/vmullig/bgfix3 I think this fixes compilation on Blue Gene

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Merge pull request #1604 from RosettaCommons/roccomoretti/fix_cxx11_dep Fix some issues with modern compilers. The C++11 update revealed some issues with modern compilers, mainly with deprecated constructs. This pull request should fix many of them. In particular, it fixes issues with gcc 6.2.0, clang 3.9.0, and ICC 14.0 on my Linux machine. This doesn't necessarily fix all issues: most notably Vikram is still experiencing issues on the Baker Lab machines. But those issues there can be addressed in a future pull request. (The fixes here are not contingent on fixing ICC 16.0.)

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Merge pull request #1614 from RosettaCommons/aleaverfay/add_srlz_funcs_for_lrecs Adding serialization routines for two long-range energy containers: ConstraintEnergyContainer DisulfideMatchingEnergyContainer

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Merge pull request #1615 from RosettaCommons/xingjiepan/fix_cppcheck_error_in_graph Fix the cppcheck errors in utility/graph/UpperEdgeGraph.hh

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Fixing line endings.

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Merge pull request #1610 from RosettaCommons/vmullig/rosettascripts_template_script Have RosettaScripts print a template script whenever the input script is omitted Tasks: - Remove the -print_template_script option. - Update the output message. - Update logic to decide whether to print output message (now, whenever -parser:protocol flag is omitted). - Update documentation. - Beauty.

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