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Rosetta 3.5
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Rosetta 3.5
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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 | |
| typedef utility::pointer::owning_ptr < BaseJobDistributor > | BaseJobDistributorOP |
| typedef utility::pointer::owning_ptr < PlainSilentFileJobDistributor > | PlainSilentFileJobDistributorOP |
| typedef utility::pointer::owning_ptr < BasicJob > | BasicJobOP |
| typedef utility::pointer::owning_ptr < BasicJob const > | BasicJobCOP |
Functions | |
| 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... | |
| basic::Tracer | TR ("protocols.jobdist.main") |
| static numeric::random::RandomGenerator | RG (32342524) |
| 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) |
Variables | |
| basic::Tracer | JobDistributorTracer |
Definition at line 26 of file JobDistributors.fwd.hh.
| typedef utility::pointer::owning_ptr< BasicJob const > protocols::jobdist::BasicJobCOP |
Definition at line 26 of file Jobs.fwd.hh.
Definition at line 24 of file Jobs.fwd.hh.
| typedef utility::pointer::owning_ptr< PlainSilentFileJobDistributor > protocols::jobdist::PlainSilentFileJobDistributorOP |
Definition at line 29 of file JobDistributors.fwd.hh.
| 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.
Definition at line 159 of file standard_mains.cc.
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.
Definition at line 171 of file standard_mains.cc.
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::SCORE_MAP.
Referenced by main_plain_mover().
| basic::Tracer protocols::jobdist::JobDistributorTracer | ( | "protocols.jobdist.JobDistributors" | ) |
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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.
Definition at line 99 of file standard_mains.cc.
References protocols::swa::rna::file_exists(), and protocols::abinitio::filename().
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.
Definition at line 904 of file standard_mains.cc.
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::pose_from_pdb(), 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.
Definition at line 686 of file standard_mains.cc.
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::pose_from_pdb(), 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.
Definition at line 791 of file standard_mains.cc.
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::pose_from_pdb(), RG(), core::pose::setPoseExtraScores(), 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.
Definition at line 94 of file not_universal_main.cc.
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::scoring::coordinate_constraint, core::scoring::dihedral_constraint, core::scoring::dunbrack_constraint, core::io::silent::SilentStructFactory::get_instance(), core::chemical::ChemicalManager::get_instance(), core::io::silent::SilentStructFactory::get_silent_struct_out(), core::scoring::getScoreFunction(), core::import_pose::pose_from_pdb(), pose_matches_user_tag(), core::chemical::ChemicalManager::residue_type_set(), core::import_pose::pose_stream::streams_from_cmd_line(), and tr().
| bool protocols::jobdist::pose_matches_user_tag | ( | core::pose::Pose & | pose, |
| utility::vector1< std::string > const & | user_tags | ||
| ) |
Definition at line 57 of file not_universal_main.cc.
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.
Definition at line 188 of file standard_mains.cc.
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Referenced by universal_main().
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Referenced by not_universal_main(), and pose_matches_user_tag().
| basic::Tracer protocols::jobdist::TR | ( | "protocols.jobdist.main" | ) |
Referenced by main_atom_tree_diff_mover(), main_plain_mover(), main_plain_pdb_mover(), and universal_main().
| int protocols::jobdist::universal_main | ( | protocols::moves::Mover & | mover, |
| float | thinout_factor | ||
| ) |
Definition at line 208 of file standard_mains.cc.
References protocols::evaluation::EvaluatorFactory::add_all_evaluators(), core::scoring::constraints::add_constraints_from_cmdline_to_pose(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_pose(), protocols::idealize::IdealizeMover::apply(), protocols::moves::Mover::apply(), core::io::silent::SilentFileData::begin(), core::scoring::CA_rmsd(), core::chemical::CENTROID, core::import_pose::centroid_pose_from_pdb(), core::sequence::end, core::io::silent::SilentFileData::end(), protocols::idealize::IdealizeMover::fast(), protocols::swa::rna::file_exists(), protocols::abinitio::filename(), core::io::silent::SilentStructFactory::get_instance(), protocols::evaluation::EvaluatorFactory::get_instance(), core::chemical::ChemicalManager::get_instance(), core::io::silent::SilentStructFactory::get_silent_struct_out(), core::scoring::MembraneTopology::initialize(), core::pose::Pose::is_fullatom(), core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG, load_s_and_l(), core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY, core::scoring::native_CA_rmsd(), core::import_pose::pose_from_pdb(), core::io::silent::SilentFileData::read_file(), core::chemical::ChemicalManager::residue_type_set(), RG(), protocols::moves::Mover::set_current_tag(), protocols::moves::Mover::set_native_pose(), core::pose::setPoseExtraScores(), core::util::switch_to_residue_type_set(), TR(), and core::io::silent::SilentFileData::write_silent_struct().
| basic::Tracer protocols::jobdist::JobDistributorTracer |
1.8.4