CircularPermutation bugfixes

• Summary

Rings: fixing broken integration test The rings integration test had been silently broken since @rhiju set the max `ResidueType` limit.

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Benchmark scripts, adding integration.release_debug test.

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Skipping non-protein residues in CircularPermutation and SSMotif Finders

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CircularPermutation can now align only binding surface residues

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Adding a unit test for the -in:auto_setup_metals flag.

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Merge pull request #57 from RosettaCommons/dougrenfrew/fix_aeh Dougrenfrew/fix aeh

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fix tookit main GUI tracer function name

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update toolkit doxygen file to reflect any directory running of SetPyRosettaEnvironment script

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fix tracer function name change in toolkit to reflect C++

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fix PYROSETTA_DATABASE environment variable not being set properly in SetPyRosettaEnvironment

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SSMotifFinder more useful output

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Removing some debugging output from surface docking that I foolishly left in after it was pointed out to me at Rosettacon.

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Change PDB_Info to PDBInfo in unit test include - which was part of the branch changes and the master merge did not change it back

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add pdb file missing from previous commit.

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fix bug in CCDEndsGraftMover and remove all.hh files Fix a bug in CCDEndsGraftMover where the wrong loop was being used for modeling through incorrect setting of insert_length with the refactoring. Add more testing within the grafting unit tests so this never happens again. Replace 2j88 unit test PDB with pre-loaded one from Rosetta to increase load speed. Add option in AnchoredGraftMovers to idealize the insert which defaults false - keep idealization on for AnchoredPDBCreator. Remove most all.hh files. Integration test changes expected in antibody_designer app.

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