Added two options: 1) "rsd_wdw_to_refine" to control the size of residue-window to refine and 2) "score_threshold" to control the score cutoff of error predictors (rama and geometry)

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Very small parameter change in localrelax. Extremely minor change so committing directly.

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Merge pull request #994 from RosettaCommons/xtal_min_fix Updates/bugfixes to crystal refinement code

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Merge pull request #967 from RosettaCommons/tlinsky/tomponents Updates/bugfixes to denovo design classes

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Merge pull request #981 from RosettaCommons/tlinsky/geometryfilter_selector Add residue selector option to geometry filter, also fix uninitialized variables

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Merge pull request #970 from RosettaCommons/tlinsky/checkcore_filter Add option to CoreResiduesPerElement filter to specify core threshold

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Merge pull request #977 from RosettaCommons/rhiju/stepwise_fixes_for_kalli Rhiju/stepwise fixes for kalli + tests that change are expected... + cppcheck failure occurs in master and seems to date back to @aleaverfay commit.

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Add -fno-omit-frame-pointer to release_debug build. Optimizations typically enable -fomit-frame-pointer, which makes things like tracebacks in debugging less relyable. If you have symbols enabled, you probably want that traceback information, so let's reenable it for the release_debug builds.

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Merge pull request #978 from RosettaCommons/JWLabonte/sugars/rotamers Carbohydrates: packing fixes/improvements This merge will correct a major issue with packing residues that are glycosylated -- namely, that should never have been happening to begin with. This merge will also prevent packing of virtual atoms on carbohydrate residues, something that was a huge waste of time and memory. All unit tests pass. carbohydrates and vancomycin unit test changes expected.

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Merge pull request #991 from RosettaCommons/roccomoretti/cppcheck_bugfix Fixes to the cppcheck script for race conditions and other bugs. Also, some fixes I had kicking around for some of the historical issues.

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Merge pull request #835 from RosettaCommons/roccomoretti/external_build A scheme for building non-header only external libraries. Basically, you just add your external library to the main/source/external/ directory, make a conventionally formatted *.external.settings file in the same directory, and then enable the external library by adding it to the main/source/project.settings file. Scons and CMake should take care of the rest (including turning off warnings for the external library). If you have complex compilation requirements, that's also supported somewhat, but you have to muck around with custom Sconscript.external.* files, and hand convert for CMake. Currently no libraries are set up to use this scheme, but may be included later.

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Merge pull request #987 from RosettaCommons/vmullig/smallmover_resselector Adding a ResidueSelector input to BackboneMover. For @gbhardwaj. Tasks: - Add a ResidueSelectorCOP to the private member data. - Add setters. - Add parsing. - Add logic in apply() function. - Update documentation. - Integration test.

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Merge pull request #990 from RosettaCommons/rhiju/cutpoint_closed_preserve_suite_torsions preservation of suite torsions at new cutpoint closed in stepwise 'internal moves' only tests that change are the 'usual' ones susceptible to numerical instability. cppcheck test is broken, but it has been broken in master for a bit.

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Merge pull request #985 from RosettaCommons/roccomoretti/user_database Implement Jonathan Sheehan's suggestion of caching the Dunbrack library in the user's home directory. Behavior in the standard case should be the same - the Dunbrack binary is read/written to the database directory. The big change is that when that directory is not writable, then the binary will be cached under the user's home directory. (This should be transparent for PyRosetta users.) Priority of locations for binary search (if any of these locations is not set or cannot be written to, it will move on to the next one.): * Directory specified with -in::path::database_cache_dir option * Directory specified with ROSETTA3_DBCACHE environment variable * The same database directory from which the ASCII files were/would be read * A .rosetta/database/ directory in the user's home directory, determined from the first non-empty setting of * The XDG_CONFIG_HOME environment variable * The HOME environment variable * The home directory specified in the POSIX password structure information. If none of these are writable, then it will skip database file writing. People who are working with multiple versions of the Dunbrack library may need to be slightly careful, as the location where the binary is read/written to may be different from where you expect. Use the validate_database application to check the cached binary, if you're seeing funky results.

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Merge pull request #982 from RosettaCommons/rfalford12/finish_removing_conf_from_memInfo Rfalford12/finish removing conf from mem info Andrew's manual serialization pull request modifies membrane info such that Conformation& is no longer a data member. I'm just finishing this up by changing the arguments to some constructors to make this more clear (also makes my next pull request cleaner)

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Adding an "residues_to_include" option to the CartesianSampler mover eg. residues_to_include="1-1612" lets CartesianSampler know these are residues to refine. Unlike the option "residues=" which can only be used under "user"mode, "residues_to_include" can designate any residues in all the residue-selection modes (eg. auto, density, rama). This option can be useful for users to specify additional residues while using automatic error predictors to select residues to refine.

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