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Rosetta
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Classes | |
| class | BaseJobDistributor |
| Coordinates processing of jobs across multiple Rosetta processes. More... | |
| class | AtomTreeDiffJobDistributor |
| Distributor for use with atomtree_diff silent files. More... | |
| class | PlainPdbJobDistributor |
| Distributor for use with plain old PDB files. Use is strongly discouraged in production environments! More... | |
| class | PlainRawJobDistributor |
| Distributor for use with raw files. More... | |
| class | PlainSilentFileJobDistributor |
| Distributor for use with silent files. More... | |
| class | BasicJob |
| Each Job object describes a particular input to Rosetta. More... | |
Typedefs | |
| using | BaseJobDistributorOP = utility::pointer::shared_ptr< BaseJobDistributor > |
| typedef utility::pointer::shared_ptr< PlainSilentFileJobDistributor > | PlainSilentFileJobDistributorOP |
| typedef utility::pointer::shared_ptr< BasicJob > | BasicJobOP |
| typedef utility::pointer::shared_ptr< BasicJob const > | BasicJobCOP |
Functions | |
| static basic::Tracer | JobDistributorTracer ("protocols.jobdist.JobDistributors") |
| static basic::Tracer | jobs_tracer ("protocol.jobdist.jobs.hh") |
| static basic::Tracer | tr ("protocols.jobdist.not_universal_main") |
| bool | pose_matches_user_tag (core::pose::Pose &pose, utility::vector1< std::string > const &user_tags) |
| int | not_universal_main (protocols::moves::Mover &mover) |
| main function that applies a mover to a set of input poses and only does silent-file output. Similar in idea to universal_main, but without all of the code duplication for silent-files/PDB files. More... | |
| static basic::Tracer | TR ("protocols.jobdist.main") |
| utility::vector1< BasicJobOP > | load_s_and_l () |
| Reads inputs from -s/-l/-nstruct and writes atomtree_diff silent files. Supplied Mover is used to transform input structure into output structure. undefined - commenting out to make pyrosetta compile... More... | |
| std::string | get_output_tag (core::pose::Pose const &pose) |
| Helper function to safely get current output tag that's cached in Pose. More... | |
| std::map< std::string, core::Real > | get_score_map (core::pose::Pose const &pose) |
| Helper function to safely get score_map that's cached in Pose. More... | |
| void | register_options_universal_main () |
| Handles loading and writing of silent files and or PDB files - superseeds the bottom two functions. More... | |
| int | universal_main (protocols::moves::Mover &mover, float thinout_factor) |
| int | main_plain_mover (protocols::moves::Mover &mover, bool random_permutation=true) |
| Reads inputs from -s/-l/-nstruct and writes (possibly gzipped) PDB files. Supplied Mover is used to transform input structure into output structure. More... | |
| int | main_plain_pdb_mover (protocols::moves::Mover &mover, core::scoring::ScoreFunctionOP scorefxn) |
| Reads inputs from -s/-l/-nstruct and writes (possibly gzipped) PDB files. Supplied Mover is used to transform input structure into output structure. More... | |
| int | main_atom_tree_diff_mover (protocols::moves::Mover &mover, core::scoring::ScoreFunctionOP scorefxn) |
| typedef utility::pointer::shared_ptr< BaseJobDistributor > protocols::jobdist::BaseJobDistributorOP |
| typedef utility::pointer::shared_ptr< BasicJob const > protocols::jobdist::BasicJobCOP |
| typedef utility::pointer::shared_ptr< BasicJob > protocols::jobdist::BasicJobOP |
| typedef utility::pointer::shared_ptr< PlainSilentFileJobDistributor > protocols::jobdist::PlainSilentFileJobDistributorOP |
| std::string protocols::jobdist::get_output_tag | ( | core::pose::Pose const & | pose | ) |
Helper function to safely get current output tag that's cached in Pose.
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG.
| std::map< std::string, core::Real > protocols::jobdist::get_score_map | ( | core::pose::Pose const & | pose | ) |
Helper function to safely get score_map that's cached in Pose.
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::SCORE_MAP.
Referenced by main_plain_mover().
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Referenced by protocols::jobdist::BaseJobDistributor::find_available_job(), protocols::jobdist::PlainRawJobDistributor::is_finished(), protocols::jobdist::BaseJobDistributor::next_job(), protocols::jobdist::PlainRawJobDistributor::PlainRawJobDistributor(), protocols::jobdist::BaseJobDistributor::shutdown(), and protocols::jobdist::PlainSilentFileJobDistributor::startup().
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| utility::vector1< BasicJobOP > protocols::jobdist::load_s_and_l | ( | ) |
Reads inputs from -s/-l/-nstruct and writes atomtree_diff silent files. Supplied Mover is used to transform input structure into output structure. undefined - commenting out to make pyrosetta compile...
Makes BasicJob objects from command line flags -s, -l, and -nstruct.
References protocols::jd2::input_pdb_files_from_command_line(), and protocols::mean_field::max().
Referenced by main_atom_tree_diff_mover(), main_plain_mover(), main_plain_pdb_mover(), and universal_main().
| int protocols::jobdist::main_atom_tree_diff_mover | ( | protocols::moves::Mover & | mover, |
| core::scoring::ScoreFunctionOP | scorefxn | ||
| ) |
Example of how to use the job distributor with silent files. If this function doesn't meet your needs as is, please COPY it into your own main method rather than modifying it in place! The goal is to keep this one as a simple-as-possible EXAMPLE for others, although it will suffice for many protocols as-is.
References protocols::moves::Mover::apply(), protocols::jobdist::AtomTreeDiffJobDistributor::dump_pose(), core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG, load_s_and_l(), core::import_pose::atom_tree_diffs::map_of_weighted_scores(), protocols::jobdist::BaseJobDistributor::next_job(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), core::scoring::rg, protocols::jobdist::AtomTreeDiffJobDistributor::shutdown(), protocols::jobdist::BaseJobDistributor::startup(), and TR().
| int protocols::jobdist::main_plain_mover | ( | protocols::moves::Mover & | mover, |
| bool | random_permutation | ||
| ) |
Reads inputs from -s/-l/-nstruct and writes (possibly gzipped) PDB files. Supplied Mover is used to transform input structure into output structure.
Example of how to use the job distributor that will write either a pdb or a raw_data (silent) file depending on an input flag Because PDBs are so big and inefficient, this function is NOT RECOMMENDED for use in production environements. If this function doesn't meet your needs as is, please COPY it into your own main method rather than modifying it in place! The goal is to keep this one as a simple-as-possible EXAMPLE for others, although it will suffice for many protocols as-is.
References protocols::moves::Mover::apply(), core::import_pose::centroid_pose_from_pdb(), get_score_map(), core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG, load_s_and_l(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), core::scoring::rg, protocols::moves::Mover::set_input_pose(), protocols::moves::Mover::set_native_pose(), and TR().
| int protocols::jobdist::main_plain_pdb_mover | ( | protocols::moves::Mover & | mover, |
| core::scoring::ScoreFunctionOP | scorefxn | ||
| ) |
Reads inputs from -s/-l/-nstruct and writes (possibly gzipped) PDB files. Supplied Mover is used to transform input structure into output structure.
Example of how to use the job distributor with plain old PDB files. Because PDBs are so big and inefficient, this function is NOT RECOMMENDED for use in production environements. If this function doesn't meet your needs as is, please COPY it into your own main method rather than modifying it in place! The goal is to keep this one as a simple-as-possible EXAMPLE for others, although it will suffice for many protocols as-is.
References protocols::moves::Mover::apply(), core::scoring::CA_rmsd(), core::import_pose::centroid_pose_from_pdb(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG, load_s_and_l(), core::scoring::native_CA_rmsd(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), core::scoring::rg, core::pose::setPoseExtraScore(), and TR().
| int protocols::jobdist::not_universal_main | ( | protocols::moves::Mover & | mover | ) |
main function that applies a mover to a set of input poses and only does silent-file output. Similar in idea to universal_main, but without all of the code duplication for silent-files/PDB files.
References protocols::viewer::add_conformation_viewer(), core::scoring::angle_constraint, protocols::moves::Mover::apply(), core::scoring::atom_pair_constraint, core::scoring::CA_gdtmm(), core::scoring::CA_maxsub(), core::scoring::CA_rmsd(), core::pose::clearPoseExtraScores(), core::pose::Pose::conformation(), core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, core::scoring::dunbrack_constraint, core::import_pose::pose_stream::MetaPoseInputStream::fill_pose(), core::scoring::get_score_function(), core::import_pose::pose_stream::MetaPoseInputStream::has_another_pose(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), pose_matches_user_tag(), core::import_pose::pose_stream::streams_from_cmd_line(), tr(), and core::io::silent::SilentFileData::write_silent_struct().
| bool protocols::jobdist::pose_matches_user_tag | ( | core::pose::Pose & | pose, |
| utility::vector1< std::string > const & | user_tags | ||
| ) |
References core::sequence::end, core::pose::get_comment(), and tr().
Referenced by not_universal_main().
| void protocols::jobdist::register_options_universal_main | ( | ) |
Handles loading and writing of silent files and or PDB files - superseeds the bottom two functions.
Universal IO handler for score, relax and cluster (and hopefully more) executables Handles reading/writing of Silent OR PDB files.
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Referenced by main_atom_tree_diff_mover(), main_plain_mover(), main_plain_pdb_mover(), and universal_main().
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Referenced by not_universal_main(), and pose_matches_user_tag().
| int protocols::jobdist::universal_main | ( | protocols::moves::Mover & | mover, |
| float | thinout_factor | ||
| ) |
References core::scoring::constraints::add_constraints_from_cmdline_to_pose(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_pose(), protocols::moves::Mover::apply(), protocols::idealize::IdealizeMover::apply(), core::io::silent::SilentFileData::begin(), core::scoring::CA_rmsd(), core::import_pose::centroid_pose_from_pdb(), core::chemical::CENTROID_t, core::io::silent::SilentFileData::end(), core::sequence::end, core::chemical::FA_STANDARD, protocols::idealize::IdealizeMover::fast(), protocols::abinitio::filename(), core::scoring::MembraneTopology::initialize(), core::pose::Pose::is_fullatom(), core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG, load_s_and_l(), protocols::mean_field::max(), core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY, core::scoring::native_CA_rmsd(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), core::io::silent::SilentFileData::read_file(), core::scoring::rg, protocols::moves::Mover::set_current_tag(), protocols::moves::Mover::set_native_pose(), core::pose::setPoseExtraScore(), core::util::switch_to_residue_type_set(), TR(), and core::io::silent::SilentFileData::write_silent_struct().
1.9.1