commit 15b290e9e51c486bfd77660159ef82887b05e17e Merge: 44ae9d8 102a5db Date: Mon May 16 12:09:29 2016 -0700 Merge pull request #1333 from RosettaCommons/tlinsky/cst_score_filter Add ConstraintScoreFilter to score constraints generated by ConstraintGenerators commit 44ae9d84d1f11c358c004e3a146c5accc17e5c47 Merge: 54a0a0a d68062a Date: Sat May 14 18:46:00 2016 -0700 Merge pull request #1339 from RosettaCommons/kkappel/farna_protein_vdw+swa_revival fixing cppcheck test failure that I created in pull request #1332 commit 54a0a0ad46c1b716856debdd5390872e35f46661 Merge: e395e6f f8626c3 Date: Fri May 13 15:06:37 2016 -0700 Merge pull request #1332 from RosettaCommons/kkappel/farna_protein_vdw+swa_revival add protein clash score for rna_denovo See comments for expected test failures. commit e395e6fc2f608de8472278fb1cea709a72aac768 Merge: d3643ba 2604aeb Date: Thu May 12 13:26:42 2016 -0700 Merge pull request #1310 from RosettaCommons/jadolfbr/antibodies/fix_cdr_instruct_caps small bug fix in ab design instructions Fixes an issue identified at the MeilerLab Workshop, where not all instruction lines were being capitalized properly, which lead to crashes for some options. This fixes it the way it should have been from the beginning. commit d3643ba81b72850b8925a454423b5e0c49f9cf09 Merge: 2647054 8ba7f8b Date: Thu May 12 13:25:26 2016 -0700 Merge pull request #1335 from RosettaCommons/jadolfbr/antibodies/ab_design_defaults Update options for antibody design Change a few RAbD options for current best-practices. Make outer_cycle_rounds from 150 to 100 to decrease overall run time vs nstruct. Use even_cluster_mc instead of general montecarlo and output the graft log into the pdb by default. commit 2647054bcbd16b888752bd0e90e36d1dcde19905 Merge: fb7d47d 090436a Date: Tue May 10 15:04:38 2016 -0700 Merge pull request #1330 from RosettaCommons/hahnbeom/ramaprepro_add_libraries Hahnbeom/ramaprepro add libraries commit fb7d47d7addbd1e1aee428ab15c46ae998cddbc1 Merge: 4c7f81a 33ea693 Date: Tue May 10 07:08:02 2016 -0700 Merge pull request #1321 from RosettaCommons/tlinsky/hb_cst_gen Update HydrogenBondConstriaintGenerator plus more vigorous unit test commit 4c7f81a37663c0ebaadfbae076f54ec532fa3a03 Merge: a30f06f 31c6322 Date: Tue May 10 08:52:37 2016 -0400 Merge pull request #1301 from RosettaCommons/aleaverfay/aleaverfay/standard_job_queen_jobdef_interface JD3 Standard Job Queen XSD Interface This branch completes the XML Schema integration into JD3 by working out an interface between the StandardJobQueen and her subclasses which allows for the specification of the XML Schema of the job-definition file. Per-job options may be specified on the command line, in a block at the top of a job-definition XML file, or in the block of a particular set of jobs in the job-definition file. The StandardJobQueen must be told about all of the options that could be specified -- she will hold std::list of OptionKeys -- and she initializes an OptionCollection which contains only the options that she has been told about. When a derived JobQueen wants to initialize a job, she should read from the OptionCollection the StandardJobQueen hands her. If she is calling a function that will read from the command line, then she should instead call a function that reads from an OptionCollection object. For example, the PackerTask now has an initialize_from_option_collection function that takes an OptionCollection const &. If you call the PackerTask's initialize_from_command_line() function, that will pass the global OptionCollection (that is, the basic::options::option global variable) in to the initialize_from_option_collection function. The PackerTask is responsible for listing all of the OptionKeys that are used to read from the input OptionCollection in its "list_read_options" method. Derived JobQueens that want to allow the user to initialize a PackerTask from the command line should call the PackerTask::list_read_options function to get that list of options and then to hand that list to the StandardJobQueen. E.g., in the FixbbJobQueen in src/apps/pilot/andrew/fixbb_jd3, there are these calls: FixbbJobQueen() { utility::options::OptionKeyList opts; core::scoring::list_read_options_in_get_score_function( opts ); core::pack::task::PackerTask::list_options_read( opts ); core::pack::task::operation::ReadResfile::list_options_read( opts ); add_options( opts ); add_option( basic::options::OptionKeys::minimize_sidechains ); add_option( basic::options::OptionKeys::min_pack ); add_option( basic::options::OptionKeys::off_rotamer_pack ); } As a result, the XML Schema for the fixbb_jd3 application lists all of the options that are read by get_score_function, the PackerTasks's initialize_from_command_line / initialize_from_option_collection, and the ReadResfile task operation. The StandardJobQueen asks the derived JobQueen to flesh out the subtags that can be defined in the and tags. To do so, the derived JobQueen will interact with the XMLSchemaDefinition and XMLSchemaComplexTypeGenerator classes. The FixbbJobQueen allows the user to define TaskOperations and ScoreFunctions using the canonical RosettaScripts interface, and then to use those TaskOperations and ScoreFunctions in initializing a PackRotamersMover. The elements of the JobDefinition file are optional, though, so the user can get a vanilla version of fixbb without using the rosetta-scripts like interface. The StandardJobQueen expects jobs to be defined by input Poses -- not all JobQueens will want this, of course, but JD2 expected this, so that's where we start with JD3. Input poses come from PoseInputters -- currently, there is only implemented a PDBPoseInputter. Within a job-definition file, each element must specify an subelement which itself will contain a single subelement listing a particular pose inputter -- e.g. a element specifying the PDBPoseInputter. If a PoseInputter specifies more than one Pose, then all of the input poses will be run through the protocol using the same per-job specification. E.g. an eventual SilentPoseInputter could be used to specify all the Poses in a silent file, or only a handful of them listed by their tags. The optional element can be specified to name the output poses, e.g. you might run 1ubq.pdb through two different protocols specified in the same job-definition file, but where you don't want them to overwrite one another -- so you would name the outputs from the first job block to "first_1ubq_foo_0001.pdb" and the outputs from the second job block to "second_1ubq_bar_0001.pdb"; this would be accomplished with and where the $ is replaced by the input-tag for the pose, and the nstruct index is appended to the end of the filename. commit a30f06f5e408a72059fd4f8cd9e551f734715875 Date: Mon May 9 18:21:44 2016 -0700 reverting my last commit. I thought I was in a branch. commit fc0e5a213305907a7182b1b014cdfbaf1d9b11d2 Date: Mon May 9 18:20:17 2016 -0700 add DihedralConstraintGenerator class using Toms code template.