Re-adding index.html which is required for doxygen daemon

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Fixed code in protocols/pockets to enable debug building.

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Added missing SingResCnlCrea code in app constel to repo.

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Merged master and JK-lab branch (protocols/pocket, devel/constel) to reflect recent changes in master (warnings as errors, SasaCalculator to SasaCalculatorLegacy, getScoreFunction() to get_score_function() ...

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Merge pull request #79 from RosettaCommons/PyRosetta Updating PyRosetta unit test script, adding option for parallel run

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Fixed bug where PocketGrid mishandled glycine as a target residue.

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Merge remote branch 'origin/master'

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Bug fix in splice to allow splice out of H3. Splice out integration test should change. Bug fix in splice to allow splice out of H3. Splice out integration test should change.

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Corrected problem related to splicing out longer tail segments, and added lambda specific PSSMs and profilematch files for splice out. So far the AbDesign and AbPredict protocol has not worked with lambda light chains. Here I'm adding PSSMs and profileMatch info to enable this. At the same time I'm also fixing a bug in LoopLengthChange which did not allow appending of more than one residue to tail segments when used with splice.cc.

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Corrected problem with spliceing out specifically longer tail segments. This also meant changing LoopLengthChangeMover Integration test changes expected to Splice integration test

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RMSD Functions: adding ability to calculate RMSDs for non-peptide heavy atoms only This will allow me to calculate RMSDs for oligosaccharide ligands. no test changes

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Eliminating a piece of global data from the shape complementarity code that was producing null pointer errors in multithreaded code.

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Fixed problem with splicing out tail segment in Splice mover Will not cause integration tests changes

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In Splice mover I added to superimpose function a feature that automatically aligns the source antibody to the template antibody In CutChainMover I removed verbose tracer msgs In splice_seq_constraints integration test I updated the xml and flags files to the latets version of Splice mover All splice integration tests are expected to change

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Adding configuration file for benchmark script. Updating PyRosetta unit test script so it now use boost_python_library config option.

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Adding configuration file for benchmark script. Updating PyRosetta unit test script so it now use boost_python_library config option.

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