Classes
class	AtomTreeDiffJobDistributor
	Distributor for use with atomtree_diff silent files. More...

class	BaseJobDistributor
	Coordinates processing of jobs across multiple Rosetta processes. More...

class	BasicJob
	Each Job object describes a particular input to Rosetta. 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...

Typedefs
typedef utility::pointer::shared_ptr < BaseJobDistributor >	BaseJobDistributorOP

typedef utility::pointer::shared_ptr < PlainSilentFileJobDistributor >	PlainSilentFileJobDistributorOP

typedef utility::pointer::shared_ptr < BasicJob >	BasicJobOP

typedef utility::pointer::shared_ptr < BasicJob const >	BasicJobCOP

Functions
static THREAD_LOCAL basic::Tracer	JobDistributorTracer ("protocols.jobdist.JobDistributors")

static THREAD_LOCAL basic::Tracer	jobs_tracer ("protocol.jobdist.jobs.hh")

static THREAD_LOCAL 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 THREAD_LOCAL 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 Documentation

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

Function Documentation

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().

static THREAD_LOCAL basic::Tracer protocols::jobdist::JobDistributorTracer ( "protocols.jobdist.JobDistributors" )

static

static THREAD_LOCAL basic::Tracer protocols::jobdist::jobs_tracer ( "protocol.jobdist.jobs.hh" )

static

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().

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::scoring::coordinate_constraint, core::scoring::dihedral_constraint, core::scoring::dunbrack_constraint, core::scoring::get_score_function(), 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.

static THREAD_LOCAL basic::Tracer protocols::jobdist::tr ( "protocols.jobdist.not_universal_main" )

static

Referenced by not_universal_main(), and pose_matches_user_tag().

static THREAD_LOCAL basic::Tracer protocols::jobdist::TR ( "protocols.jobdist.main" )

static

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
	)

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, protocols::jobdist::PlainSilentFileJobDistributor::dump_silent(), core::sequence::end, core::io::silent::SilentFileData::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(), 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().

Classes

Typedefs

Functions

Typedef Documentation

Function Documentation