Revert "Adding two complex glycnas necessary for HIV as non-canoical amino acids" This reverts commit f2b476e2ed0f508fd2a770ec6b809c8e9d246f68.

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Adding two complex glycnas necessary for HIV as non-canoical amino acids

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fixed a bug in the base_name option in eval_natie run

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Fixed bug to LayerDesign when parsing CombinedTasks

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added the -compact flag to output only the transformation matrix

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updated random_rotate flag name

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updates on 050514 for cryst_design.cc. Removed some tracer outputs.

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merging orielg/fpd_multichain_receptor to master modified: source/src/protocols/flexpep_docking/FlexPepDockingFlags.cc modified: source/src/protocols/flexpep_docking/FlexPepDockingFlags.hh modified: source/src/protocols/flexpep_docking/FlexPepDockingProtocol.cc

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fixing build

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Movers should report statistics to Pose rather than Job. Updating ddG and MotifGraftMover.

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Make clang PyRosetta happy.

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Bugfix to pilot app

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Adding uncached / lazy generation MultiplePoseMover mode. In the uncached mode (enabled by default) poses are pulled from previous mover, selected and processed on demand, without caching all input and output poses. This should allow operations on larger sets without blowing up the memory requirements. Certain selectors (TopNByProperty, Cluster) require a full set of poses to perform their selection. When these selectors are used, cached mode is automatically enabled and all input poses are cached first as before. The caching behaviour can also be controlled with the "cached" parameter in the XML script. Unit Tests: All Pass Integration Tests: No changes (vs. 85c6b69)

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Small bugfix to crystal docking

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Output data added to a pose with setPoseExtraScores() to PDB and score files. Use this function if you'd like the additional scores from your movers, filters, etc. to be output by the JD2 to files. Extra scores and strings are kept in the DataCache types ARBITRARY_FLOAT_DATA and ARBITRARY_STRING_DATA. RosettaScripts filters and pose selectors now report their computed values to the pose using setPoseExtraScores() rather than to the job, since a job can operate on many poses if the used mover implements get_additional_output(). Unit Test Status: All Pass Integration Test Status: 16 test changes (vs. fe265a4df6): Additional data in output PDB/score/silent files in tests: density_refine density_refine_symm docking_ensemble Enzrevert_xml filter_termini_near_interface hotspot_graft KIC_refine KIC_vicinity kinematic_looprelax loop_modeling next_generation_KIC place_simultaneously rs_loophash score12_docking score_only_silence torsion_restricted_sampling

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Always add a suffix tag to the decoy name when a mover generates multiple poses. The tag is used in PDB file names, and within score and silent files. As most movers currently generate only one pose, this only affects LoopHash and the MutiplePoseMover and MultipleOutputWrapper. Also change the tag for intermediate poses back to a prefix in the decoy name. Unit Test Status: All Pass Integration Test Status: Changes to file names and decoy names in score files in: AnchoredDesign antibody_designer broker_membrane dna_interface_design docking_prepack jd2test rs_loophash surface_docking

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