|
Rosetta
|
Utilities for JD2, which are somewhat safe to use outside of the JD2 system itself. More...
#include <protocols/jd2/util.hh>#include <protocols/jd2/JobDistributor.hh>#include <protocols/jd2/MPIMultiCommJobDistributor.hh>#include <protocols/jd2/JobInputter.hh>#include <protocols/jd2/JobOutputter.hh>#include <protocols/jd2/Job.hh>#include <protocols/jd2/internal_util.hh>#include <core/pose/Pose.hh>#include <core/io/silent/SilentStruct.hh>#include <core/io/silent/SilentFileData.hh>#include <core/io/silent/SilentFileOptions.hh>#include <core/io/silent/SilentStructFactory.hh>#include <basic/Tracer.hh>#include <basic/options/option.hh>#include <basic/options/keys/out.OptionKeys.gen.hh>#include <basic/options/keys/in.OptionKeys.gen.hh>#include <core/chemical/ChemicalManager.hh>#include <protocols/moves/Mover.hh>#include <core/import_pose/import_pose.hh>#include <utility/vector1.hh>#include <utility/file/FileName.hh>#include <utility/io/izstream.hh>#include <utility/options/keys/OptionKeyList.hh>Namespaces | |
| protocols | |
| The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP. | |
| protocols::jd2 | |
Functions | |
| static basic::Tracer | protocols::jd2::TR ("protocols.jd2.util") |
| static basic::Tracer | protocols::jd2::tr_score ("protocols.jd2.score", basic::t_info, true) |
| bool | protocols::jd2::jd2_used () |
| is this application running with JD2? Useful for code that might not be running under JD2. More... | |
| std::string | protocols::jd2::current_input_tag () |
| What is the tag of the current input structure? More... | |
| core::Size | protocols::jd2::current_nstruct_index () |
| What 'nstruct' value are we currently processing? More... | |
| core::Size | protocols::jd2::max_nstruct_index () |
| What's the maximum nstruct we're processing? More... | |
| std::string | protocols::jd2::current_output_name () |
| gets used output name of pose ask jd for current-job —> ask jobOutputter for name of this job More... | |
| std::string | protocols::jd2::current_output_filename () |
| call the 'filename' accessor of the current job-distributor with the current job More... | |
| std::string | protocols::jd2::current_batch () |
| core::Size | protocols::jd2::current_batch_id () |
| core::Size | protocols::jd2::current_replica () |
| returns 0 if no replicas (i.e., multiple processes per job ) otherwise it returns the sub-rank of the process within the job starting at 1 More... | |
| core::pose::PoseCOP | protocols::jd2::get_current_jobs_starting_pose () |
| Get the starting structure for the current run. Will return a null pointer if that is not possible. More... | |
| void | protocols::jd2::output_intermediate_pose (core::pose::Pose const &pose, std::string const &stage_tag, int copy_count, bool score_only) |
| end parser interface, start Job Distributor interface///////////// More... | |
| void | protocols::jd2::add_string_to_current_job (std::string const &string_in) |
| add output string More... | |
| void | protocols::jd2::add_strings_to_current_job (std::list< std::string > const &strings) |
| add output strings More... | |
| void | protocols::jd2::add_string_string_pair_to_current_job (std::string const &string1, std::string const &string2) |
| add a string/string pair More... | |
| void | protocols::jd2::add_string_real_pair_to_current_job (std::string const &string_in, core::Real const real_in) |
| add a string/real pair More... | |
| std::list< std::string > | protocols::jd2::get_strings_from_current_job () |
| std::map< std::string, std::string > | protocols::jd2::get_string_string_pairs_from_current_job () |
| std::map< std::string, core::Real > | protocols::jd2::get_string_real_pairs_from_current_job () |
| void | protocols::jd2::add_current_job_data_to_ss (core::io::silent::SilentStructOP ss) |
| void | protocols::jd2::write_score_tracer (core::pose::Pose const &pose_in, std::string tracer_point) |
| utility::vector1< utility::file::FileName > | protocols::jd2::input_pdb_files_from_command_line () |
| Read the -s and -l flags to get a list of PDB files that should be read in and operated upon. More... | |
| void | protocols::jd2::set_native_in_mover (protocols::moves::Mover &mover) |
| Set the "native" for the Mover by reading from the global option collection. More... | |
| void | protocols::jd2::set_native_in_mover (protocols::moves::Mover &mover, utility::options::OptionCollection const &options) |
| Set the "native" for the Mover by reading from a possibly-local option collection. More... | |
| void | protocols::jd2::options_for_set_native_in_mover (utility::options::OptionKeyList &opts) |
| Companion function for set_native_in_mover that reports on the options that are read out of the (possibly-local) option collection. More... | |
Utilities for JD2, which are somewhat safe to use outside of the JD2 system itself.
For utilities internal to the jd2 system, see internal_util.hh
1.9.1