Merge pull request #962 from RosettaCommons/roccomoretti/cifparse Add CIFPARSE-OBJ mmCIF parsing library to Rosetta This commit is part of the ChemicalXRW mmCIF is the new awesome. This commit doesn't actually add any mmCIF support to Rosetta, but it adds libraries (from the RCSB) to external/ which allow us to build such a beast. (Licensing has been cleared for inclusion with Rosetta through the lawyers at UW.) See source/test/core/io/mmcif_IO.cxxtest.hh for a very basic example of reading a CIF file and extracting the contents.

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Merge pull request #1040 from RosettaCommons/tlinsky/backbonemover_cleanup Cleanups to BackboneMover -- also add support for scorefunction Integration test change expected for smallmover_resselector. This is because the option name is now residue_selector for consistency across movers.

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Increasing profile test _failure_threshold_execution_time_pct_ to reduce number of false-positive failures

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Merge pull request #1050 from RosettaCommons/vmullig/basename Add storage and retrieval of base ResidueType name to ResidueType class Having to fiddle with strings all of the time to get the base ResidueType name is inefficient. This pull request introduces a cost of a little bit of memory to save some clock cycles. You can now set/get the base name for a ResidueType using ResidueType::base_name(). This pull request also moves all ResidueProperties access into Residue.cc from Residue.hh to speed recompilation when ResidueProperties are added (we now only include ResidueProperties.fwd.hh from Residue.hh). I also noticed that the name1_ private member variable (a char) was not initialized, so I added an initializer. The carbohydrates integration test shows cosmetic changes because it now reports the base name in addition to the patched name (expected changes). Very slightly more memory is allocated for the ResidueTypes in the ResidueTypeSet, now, as well, since they store an additional string, but this is very tiny compared to Rosetta's overall memory footprint.

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Merge pull request #1051 from RosettaCommons/vmullig/carbohydrate_issue Fixing an issue with the CarbohydratePoseIOTests, which were randomly failing for me. I tracked it down to the use of the atoi() function in core::io::carbohydrates::sugar_modifications_from_suffix(). The atoi() function expects a pointer to the first element of a null-terminated char array, but was being passed the address of a single char. As such, it was progressively reading from that memory location. In most cases, it would interpret the next byte as something other than a number, and would therefore only return the number associated with the input char. Sometimes, though, the next byte would correspond to the ASCII for a number, which would result in misinterpretation of the char passed in (e.g. 68 or 687 for '6', or whatnot). The solution was to implement a simple utility function to convert a single-byte char to the integer that it represents. All integration test changes seen are the switching behaviour seen in the unstable ones.

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Merge pull request #1043 from RosettaCommons/tlinsky/rotamerboltz_skip_report Add skip_report option to RotamerBoltzmannWeightFilter

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Merge pull request #1052 from RosettaCommons/dimaio/nblist_autoupdate_Hatr_bugfix Fix a few bugs for beta_nov15 minimization with non-default fa_maxdis and with nblist_autoupdate.

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Merge pull request #1042 from RosettaCommons/antibody Merging antibody grafting

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Merge pull request #1035 from RosettaCommons/tlinsky/disulfidize_fix Fix bug in disulfidize when keeping input disulfides

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Merge pull request #1034 from RosettaCommons/tlinsky/ssprediction_structuredata Add ability from SSPrediction filter to search for StructureData

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Merge pull request #1037 from RosettaCommons/vmullig/details_not_detailed Correcting Doxygen tags - Fix all instances of "///@" (should be "/// @"). - Fix all instances of "/// @detailed" (should be "/// @details") Branch not tested since only comments are affected. No test changes expected.

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Merge pull request #1032 from RosettaCommons/kylebarlow/alascan Allow first chain to be moved in interface ddG mover

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Merge pull request #1033 from RosettaCommons/vmullig/fix_thread_issue Issue in our threadsafety code fixed Jeff Flatten of the Foldit team identified an error in our thread safety code. The URL in the comment matches the corrected version, not the original. @aleaverfay, @roccomoretti, could you double-check this? @jflat06, @scoopergit Only those integration tests that are showing instabilities are failing.

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Updating the Xcode template to account for the removal of all source files from protocols_f.5

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Merge pull request #968 from RosettaCommons/sjbertolani/pyrosetta_tmalign Adding a function signature to TMaligns alignment2atommap method that works in Pyrosetta, there was a pass-by-reference that Python can't handle. Also, Split the TMalign.hh into cc and hh files, Added Unit test for basic TMalign function, Changed a number of function signatures to take values by reference (from cppcheck), remove unnecessary \#includes

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Merge pull request #996 from RosettaCommons/JWLabonte/sugars/modifications Carbohydrates: fixing bug where Hs on NAc groups were not placed in the plane of the amide All unit tests pass. carbohydrates integration test changes expected; anything else is a broken test -- I only changed a single carbohydrate .params file.

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