Merge pull request #2410 from RosettaCommons/sergey/binder Explicitly adding ‘basic’ dir into PyRosetta bindings list, this should fix problem with PyRosetta option access functions. Adding unit test for option functions.

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Merge pull request #2409 from RosettaCommons/benchmark Adding extra constraint to Condor HPC driver so profile/performance jobs will only be routed to particular nodes. This should solve instability issues that we observed lately.

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Merge pull request #2399 from RosettaCommons/jadolfbr/nbr_selector_unit_tests Add additional NBRhoodResSelector unit test for code-level and multi-distance access.

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changed default fragment value in ES xml to what it should be

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Update reorder_chains.py Now with support for gzipped files (input and output). Just give the script filename ending with .pdb.gz and it (the script) will do the rest.

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Create reorder_chains.py Ever need to reorder the chains in a PDB file? Use this here script for that. Example usage: You ran RosettaAntibody (and got some awesome models), but they are heavy chain then light chain. Now you want to run SnugDock, and that requires the light chain to come first. Do this: `python reorder_chains.py -i mdl_0001.pdb -o mdl_0001.reordered.pdb -c L H`

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Merge pull request #2407 from RosettaCommons/vmullig/cycpep_integration_tests Add integration tests for the small cyclic peptide design pipeline that we want to publish, so that the pipeline continues to be usable in the future.

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Beautifying master.

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Merge pull request #2404 from RosettaCommons/bazzoli/add_interface_energy_app Adds public app analysis/interface_energy.

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Merge pull request #2390 from RosettaCommons/everyday847/full_model_jq Make jd3 versions of common RNA applications

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Merge pull request #2400 from RosettaCommons/bfrenz/maintain_sugar_names Bfrenz/maintain sugar names

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Merge pull request #2395 from RosettaCommons/roccomoretti/jd2ectomy Laying the groundwork for a jd2-ectomy A number of people have made use of the JD2 system when writing their Movers, etc. -- that is, they're not implementing something that has a direct dependence on JD2, but use various convenience functions in JD2 which allows you get various job-running data (e.g. output name) This has worked for the past decade or so, but now that JD3 is staring us in the face, it would be good to move such code off of a strict JD2-dependency. This PR goes through and, as much as reasonably possible, attempts to remove the direct dependence on JD2 Jobs, JobDistributors, JobOutputters, etc. from everywhere that's not intimately tied to the JD2 system. The form this takes in the current PR is that a number of utility functions have been added to src/protocols/jd2/util.hh, so instead of doing something like protocols::jd2::JobDistributor::get_instance()->current_job()->input_tag() you can do protocols::jd2::current_input_tag(). While the implementation of protocols::jd2::current_input_tag() still has the same reliance on the JD2 system, it serves as a single point which can be generalized when we come up with a JD2-independent system for passing around the input tag. (It should also be easier to mode it to a different namespace.)

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Merge pull request #2396 from RosettaCommons/roccomoretti/fix_talaris_warning Fix issue where 'pre_talaris_2013_standard' was being classified as a talaris scorefunction.

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Merge pull request #2383 from RosettaCommons/bfrenz/auto_glycan_with_links_records Bfrenz/auto glycan with links records

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Merge pull request #2397 from RosettaCommons/vmullig/fix_link_issue Fixing a minor issue with using simple_cycpep_predict with native PDB files containing LINK records Requested by @gbhardwaj . When provided with a native structure with a LINK record specifying cyclic geometry, simple_cycpep_predict would attempt to set up cyclic geometry anew, first stripping off terminal types. When the terminal types were absent, it would crash. This fixes that.

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Merge pull request #2073 from RosettaCommons/bfrenz/FixDensScaling This code fixes the issue where the order in which you called protocols effected the density scoring values do the the initialize fast scoring first time function using the pose to setup the density scoring. Hopefully the effect is minor but density weights may need to change as a result. Especially if your protocol operated using a centroid model as input to rosetta.

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