Warnings Removal: silencing one error type specifically for GCC 4.4

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Fix uninitialized variable issue reported by Tim Issues found with gcc 4.6

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Refactoring SampleApplier.cc to remove construction of Pose object during static initializations

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Better error checking re: membrane spanfiles

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Fixing an error with newly added flags for auto-detection of metals. The problem was related to invalid 'legals' options within options_rosetta.py Fixing the Xcode project to work with the recent upgrade of boost. Specifically, set BOOST_ERROR_CODE_HEADER_ONLY and BOOST_SYSTEM_NO_DEPRECATED flags, which are now part of the default build

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Fix initialization issues Fix uninitialized variable issue in GasteigerAtomTyper Fix -Wmaybe-uninitialized issue with numeric/xyzVector.hh Turn off -Wno-uninitialized in cmake and scons builds. Rosetta compiles with cmake & scons, gcc & clang, at least on my machine.

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attempt 6 to fix Mac PyRosetta

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attempt 5 to fix Mac PyRosetta

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attempt 4

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attempt 3

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trying to fix Mac PyRosetta

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removing warning only caught by Mac PyRosetta build

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Change to GLY.params: glycine is not an L-amino acid. Duh. This is a minor change to the database. Therefore: --Integration tests were not run. --Unit tests were not run.

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Updating properties and BACKBONE_AA of BPY.params. Minor change to database; unit and integration tests not re-run.

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Merging vmullig/ncaas into master to get my changes to NCAAs. --Add 4,5-dihydroxyisoleucine (a component of alpha-amanitin) to the l-ncaas part of the database. --Change is_D_aa() function in core/chemical/AA.cc to is_canonical_D_aa() --Removed some code duplication in Ramachandran.cc. --Added BACKBONE_AA lines to params files. This can be used to tell Rosetta that the rama and p_aa_pp scoring functions should treat a particular noncanonical amino acid like a designated canonical amino acid. (For example, in the 4,5-dihydroxyisoleucine params file, we have "BACKBONE_AA ILE"). --Added ALPHA_AA, BETA_AA, L_AA, and D_AA properties for alpha, beta, L-alpha, and D-alpha amino acids, respectively. --Updates D-proline with shadow atoms so that it scores and minimizes identically to (i.e. like the mirror image of) L-proline. --Fixes one more dependency problem in core/pose/util.cc, which should hopefully fix any remaining build problems not fixed by my last tweak to master. These changes have not yet been described on the Gollum Wiki, but will soon. TODO: --Update BPY.params. Unit test status: Pass Integration test status: ZERO changed tests!

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Attempt at fixing Mac Clang build that I broke with my previous changes to metalloprotein handling. --I think I had bad dependencies -- something from core.3 depending on something from core.4. I've moved all the metalloproteins utilities to core/util/metalloproteins_util.cc, which is in core.4. --I have no idea why the build was working under Linux, though (with both gcc or Clang). Unit test status: Pass Integration test status: Not Run --I don't have access to a Mac with Clang right now, so I'm relying on the test server to tell me whether this works. Everything compiles fine on my Linux PC with gcc, though everything did before, too.

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