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Revisions №59556

branch: master 「№59556」
Commited by: Jared Adolf-Bryfogle
GitHub commit link: 「c2597b2e5432f089」 「№2348」
Difference from previous tested commit:  code diff
Commit date: 2017-06-24 18:28:07

Merge pull request #2348 from RosettaCommons/jadolfbr/rs_jd3 RosettaScripts - JD3 Port and PyRosetta Support Overview ====== This PR brings RosettaScripts into the modern era of JD3 and PyRosetta. The implementation is version 1 - with support for different protocols and script_vars being passed to the job_definition file. This should enable fairly robust benchmarking of protocols through RosettaScripts. Thanks to @aleaverfay for his guidance, debugging, and code added to the branch! PyRosetta support is here through a slew of new functions in RosettaScriptsParser to easily take an XML/Pose and return a ParsedProtocol. @basantab ``` ///@brief /// Main, Basic XML to Mover Function. /// ParsedProtocolOP generate_mover_and_apply_to_pose(core::pose::Pose & pose, std::string const & xml_fname); ``` This PR also removes the JD2 integrated code in the RosettaScriptsParser and removes the 'Parser' class as it was unused. An example JD3 job_definition file for RosettaScripts: ``` <JobDefinitionFile> <Job nstruct="2"> <Input> <PDB filename="five_glycans.pdb"/> </Input> <Output> <PDB filename_pattern="default_$"/> </Output> <Options> <parser__protocol value="glycan_relax.xml"/> <parser__script_vars value="cartmin=0"/> </Options> </Job> <Job nstruct="1"> <Input> <PDB filename="five_glycans.pdb"/> </Input> <Output> <PDB filename_pattern="cartmin_$"/> </Output> <Options> <parser__protocol value="glycan_relax.xml"/> <parser__script_vars value="cartmin=1"/> </Options> </Job> <Job nstruct="1"> <Input> <PDB filename="pareto_4JAN_CH103_GP120_renum_0001.pdb"/> </Input> <Output> <PDB filename_pattern="glycosylated_$"/> </Output> <Options> <parser__protocol value="glycosylate.xml"/> <parser__script_vars value="positions=463G,460G glycosylation=man5 cartmin=1"/> </Options> </Job> </JobDefinitionFile> ``` Command to run this: ``` rosetta_scripts_jd3.macosclangrelease -include_sugars -write_pdb_link_records -in:file:job_definition_file jd3_rs_definition.xml ``` Other Changes ========== - Add Overwrite support to JD3 (Thanks @aleaverfay ) - Fix a few JD3 bugs ( @aleaverfay ) - Add support for prefix/suffix - Move ```protocols/jd2/parser``` to ```protocols/parser``` - Add Integration test - @vmullig Port -info and -output_schema options to the JD3 implementation, moved functions to rosetta_scripts/util.hh Integration tests: =========== All changes are cosmetic and have been gone over manually.