Fixing some build errors on Cygwin platform

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Adding missing namespace specification to boost function_template

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Fixing Clang build

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Another couple bugfixes to cryst dock. Working for all spacegroups now.

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Another bugfix for cryst_design. All spacegroups but F4132 working.

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Minor fixes to Splice.cc Can handle multiple seqeunces when adding seqeunce constraint to pose Expect Integration changes to splice_out, splice_in and splice_seq_const

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Fix handling of ligands when using DSSP with SSPrediction filter

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New Integration test for LayerDesign Task Includes a ligand and a short pack-only run.

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Merging my copy of the master

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LayerDesign fix to allow ligand-containing pdbs to run Original layerdesign didn't work on ligands. Our old fix added "L" to the ddsp secstruct string for each ligand molecule. Rocco's recent, better, fix, puts a " " for each ligand, which broke our old, hacky and un-integration-tested fix. This commit gits rid of the hacky fix and works with Rocco's fix. All Unit tests pass and integration tests pass. We should still make a LayerDesign integration test.

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Adding git-branch prefix to observer emails

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Fix Performance benchmark Adjusting performance benchmark to account for metal ion changes Vikram recently checked in. Interesting note: if a non-polymeric residue exists by name in the PDB, but doesn't have any appropriately named atoms, it will be built, but fill missing coordinates will never succeed. Better error checking of this is probably necessary.

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Porting integration tests observers from svn_users.py to <test>/observers files

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Benchmark scripts. Refactoring how exclude files are handled in regression tests (i.e. store them but do not compare). Adding example observers files.

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PyRosetta. Fixing build script error when running on Python-2.6.

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Revert "Revert "Fix issues with Gasteiger atom typing"" This reverts commit b1603f390f31c154481f5b0a4fc58c208c1cc2a6, restoring cab6655af046ce82e656c1c35b9fda7c7cc9fa33 I could not get the test server changes to recapitulate locally -- more tellingly, the reversion did not see the inverse of the observed test changes. Moreover, it looks like other commits from the same time period also showed similar test changes, indicating an issue with the tests. I don't see any test changes locally with this commit, aside from the added unit tests, and the standard numeric instabilities.

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