Miscellaneous updates and bugfixes for density/xray/symmetry code. Make quiet option for symmdef file generation quieter. Missed some Py_DECREF calls in phenix interface code. Removing numeric deriv checks in model-map error code.

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[minor update of SandwichFeatures] - write resfile automatically (NOTAACFHWY for loop residues and surface heading strand residues) - default value of CB_b_factor_cutoff_for_electrostatic_interactions = 10,000 instead of 60 which is mentioned in http://spdbv.vital-it.ch/TheMolecularLevel/SPVTut/text/STut09aTN.html in order to count all possible electrostatic interactions [integration tests comment] - should not change other than features and features_database_schema (if any)

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Add per-residue controls to hybridize protocol

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Temporary #ifdef to fig bug with Rosetta crystal refinement. This will be removed once boost has been updated.

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Carbohydrates: adding missing file for Lewisx to i. test system

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Fix -jd2:ntrials behavior According to all the documentation, the -ntrials value should be reset for each nstruct. That is, if you FAIL_RETRY on every attempt, a setting of -nstruct 6 -jd2:ntrials 5 should run through 30 attempts for each input structure. Previously, the ntrials was shared between all nstructs for all input structures, so a -nstruct 6 -jd2:ntrials 5 with a constant FAIL_RETRY would do just 10 attempts, 5 for *_0001, and 1 each for *_0002 through *_0006. This commit changes it to the intended behavior.

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Updating unit tests script so it add used command-line's in to the logs

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Attempt to fix performance build. The performance build uses gcc 4.1, which isn't all that C++11 aware. This means things like std::map.at(), which work fine for recent gccs, don't work on the performance build.

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Adding a new pilot app (symmetric grafting)

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Reducing timeout value for integration.debug tests to 17 minutes

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Fix some remaining warnings under gcc 4.8 On my machine with gcc 4.8 only 5 warnings remain, regarding either RNA enums or aa_mpr, all of which I believe are being addressed by others. Also, tweaks to the cmake warnings-as-errors setup, again to better match scons builds.

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Fix unused-local-typedefs warnings GCC 4.8 added a class of warnings for in-function typedefs which are defined but never used. This commit clears them up, cleaning up compile output for those of us using GCC 4.8.

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Fix debug mode scaffold_matcher integration test. Protocol was attempting to add backbone stub constraints across polymeric bonds which weren't polymeric. Add checks which will keep this from happening. scaffold_matcher integration test changes expected, as it was previously using uninitilized memory for backbone stubs.

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Cmake build fixes. Turn off enum-compare-as-error (like scons builds). Also, remove -w from release build, as that inhibits the warnings-as-errors settings.

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Try to fix performance build by removing std::map.at()

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Attempt to fix header only build.

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