Rosetta Protocols  2014.35
Classes | Typedefs | Functions | Variables
protocols::jobdist Namespace Reference

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::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

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...
 
utility::vector1< BasicJobOPload_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::Realget_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 ("protocols.jobdist.JobDistributors")
 
static basic::Tracer jobs_tracer ("protocol.jobdist.jobs.hh")
 
static basic::Tracer tr ("protocols.jobdist.not_universal_main")
 
basic::Tracer TR ("protocols.jobdist.main")
 
static
numeric::random::RandomGenerator 
RG (32342524)
 

Typedef Documentation

Function Documentation

std::string protocols::jobdist::get_output_tag ( core::pose::Pose const &  pose)
std::map< std::string, core::Real > protocols::jobdist::get_score_map ( core::pose::Pose const &  pose)
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 utility::file::file_exists(), filename(), getline(), in::file::l, in::file::list, in::file::native, out::nstruct, nstruct, option, basic::options::option, in::file::s, user, and utility_exit_with_message.

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 
)
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(), in::file::centroid_input, core::import_pose::centroid_pose_from_pdb(), core::pose::Pose::data(), utility::pointer::owning_ptr< T >::get(), get_score_map(), core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG, load_s_and_l(), out::nooutput, basic::options::option, option, core::import_pose::pose_from_pdb(), numeric::random::random_permutation(), out::file::raw, numeric::random::RG, basic::datacache::BasicDataCache::set(), protocols::moves::Mover::set_input_pose(), protocols::moves::Mover::set_native_pose(), out::file::silent, run::timer, TR, user, and basic::Warning().

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(), in::file::centroid_input, core::import_pose::centroid_pose_from_pdb(), core::pose::Pose::data(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG, load_s_and_l(), in::file::native, core::scoring::native_CA_rmsd(), out::nooutput, basic::options::option, option, core::import_pose::pose_from_pdb(), numeric::random::random_permutation(), repeat, run::repeat, numeric::random::RG, basic::datacache::BasicDataCache::set(), core::pose::setPoseExtraScore(), out::file::silent, TR, user, and basic::Warning().

int protocols::jobdist::not_universal_main ( protocols::moves::Mover mover)
bool protocols::jobdist::pose_matches_user_tag ( core::pose::Pose pose,
utility::vector1< std::string > const &  user_tags 
)

References end, 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.

References utility::options::OptionCollection::add_relevant(), in::file::centroid_input, in::file::fullatom, in::file::l, in::file::native, out::nooutput, out::nstruct, option, out::prefix, run::repeat, in::file::s, out::file::scorefile, out::file::silent, in::file::silent, in::file::silent_list, in::file::silent_struct_type, and in::file::tags.

int protocols::jobdist::universal_main ( protocols::moves::Mover mover,
float  thinout_factor 
)

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, in::file::centroid_input, core::import_pose::centroid_pose_from_pdb(), core::pose::Pose::data(), end, core::io::silent::SilentFileData::end(), protocols::idealize::IdealizeMover::fast(), utility::file::file_exists(), filename(), core::io::silent::SilentStruct::fill_struct(), in::file::fullatom, core::chemical::ChemicalManager::get_instance(), core::io::silent::SilentStructFactory::get_instance(), protocols::evaluation::EvaluatorFactory::get_instance(), basic::datacache::BasicDataCache::get_ptr(), core::io::silent::SilentStructFactory::get_silent_struct_out(), getline(), core::scoring::MembraneTopology::initialize(), core::pose::Pose::is_fullatom(), core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG, in::file::l, load_s_and_l(), core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY, in::file::native, core::scoring::native_CA_rmsd(), out::nooutput, out::nstruct, nstruct, option, basic::options::option, core::import_pose::pose_from_pdb(), out::prefix, core::io::silent::SilentFileData::read_file(), run::repeat, repeat, core::chemical::ChemicalManager::residue_type_set(), in::file::residue_type_set, out::file::residue_type_set, RG, in::file::s, out::file::scorefile, basic::datacache::BasicDataCache::set(), protocols::moves::Mover::set_current_tag(), protocols::moves::Mover::set_native_pose(), setPoseExtraScore(), core::pose::setPoseExtraScore(), out::file::silent, in::file::silent, in::file::silent_list, in::file::spanfile, spanfile, ss, core::util::switch_to_residue_type_set(), tag, in::file::tags, TR, numeric::random::RandomGenerator::uniform(), user, user_tag, in::file::user_tags, utility_exit_with_message, basic::Warning(), and core::io::silent::SilentFileData::write_silent_struct().

Variable Documentation

basic::Tracer protocols::jobdist::JobDistributorTracer
basic::Tracer protocols::jobdist::jobs_tracer("protocol.jobdist.jobs.hh")
static
numeric::random::RandomGenerator protocols::jobdist::RG(32342524)
static

Referenced by universal_main().

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