Now fixing clang build.

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Fixing gcc build (wasn't an error on my machine). Also fixing NetChargeFilter to test build.

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expansion_rounds default set to 12

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expansion_rounds as a new option

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MultiplePoseMover additions: task operations import support, Filter pose selector, filter status passing from sub-protocol. Merge from luki-mbi/rosetta_scripts. Unit test status: All Pass Intergration test status: All Pass

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Updates to pilot app.

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NetCharge filter now accepts task operations. Designable residues in the task operations are used to select the residues over which to count the net charge. no test changes expected. see wiki for details.

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remove unimplemented copy constructor to fix pyrosetta build

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Remove autogenerated options files which were (re)added to the repository.

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Merge with head.

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fix more warnings that only showed up on gcc build

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Fixed a small bug in the boinc app.

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fix another warning, remove options files that were re-added

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fix a warning that broke the build

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Add AntibodyFeatures reporter and R scripts, update InterfaceFeatures and R scripts, update AntibodyInfo and cdr clusters NEWS: ==Antibody== - closest North-Dunbrack CDR cluster now prints in AntibodyInfo show method - have Antibody metrics Sasa calculations use SasaCalculator2 (which means default radii is now correctly reduce like InterfaceAnalyzerMover) - add check for peptide bond C-N lengths in AntibodyInfo to check for missing cdr density or poorly closed loops. This check is default true and can be turned off using the option -antibody:check_cdr_chainbreaks false. - add optional AntibodyInfo check for wonky peptide bond geometries in cdrs. This check is default false and can be enabled using the option -antibody:check_cdr_pep_bond_geom true. The function that is called has been added to loops/util and checks the deviations from the dunbrack/karplus Conformation Dependent Library values within some user-controlled cutoff value. ==Features== - Add AntibodyFeatures reporter + many R scripts for analysis - Update InterfaceFeatures reporter (add a few more columns), reorganize R scripts and add a few more ==Bugs== -debug missing enums of some rare cdr clusters -debug some antibody metrics via testing with thousands of antibodies ---------------------------------------- Unit test status: Pass Integration test status: Antibody integration tests will change - both cosmetically and any reporting Sasa metrics *SnugDock integration test updated to not check CN peptide bond. There is a 2.56 A C-N bond at 31 H.

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TaskAwareCsts is now able to constrain residues to a particular residue of choice rather than to the first residue in the constrained segment. In multi-chain poses it makes sense to put the anchor positions at the source and sink of the minimized jump degree of freedom. This way minimization along the jump dof is not affected by the chain constraints; only bb minimization is affected. See wiki for details. No test changes expected.

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