Rosetta 3.4
Public Types | Public Member Functions | Protected Types | Protected Member Functions
protocols::jobdist::PlainPdbJobDistributor Class Reference

Distributor for use with plain old PDB files. Use is strongly discouraged in production environments! More...

#include <JobDistributors.hh>

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List of all members.

Public Types

typedef BaseJobDistributor parent

Public Member Functions

 PlainPdbJobDistributor (JobVector jobs, std::string outfile_name="none")
virtual ~PlainPdbJobDistributor ()
virtual void startup ()
 Allows setting of inprogress.
virtual std::string get_output_filename (std::string const &tag)
 Translates an output tag name to an output PDB file name.
virtual void dump_pose_and_map (std::string const &tag, core::pose::Pose &pose)
 Writes pose and basic score data to a standard PDB file.
virtual void temp_file (std::string const &tag)
 Opens a temp file (.in_progress)
void score_map (std::map< std::string, core::Real > &score_map_in)
 Virtual function for score_map that is needed for main_plain_mover sets the score_map.

Protected Types

typedef utility::vector1
< BasicJobOP
JobVector

Protected Member Functions

virtual bool is_finished (BasicJobOP const &job, int struct_n)
 Is the given nstruct number of the given input job already finished by the local process? To be implemented by subclasses.
virtual void dump_scores (utility::io::ozstream &out, std::string const &tag, core::pose::Pose &pose)
 Writes score data to PDB file in YAML format.

Detailed Description

Distributor for use with plain old PDB files. Use is strongly discouraged in production environments!

This class is deliberately designed for each process to write its own PDB files in its own directory; it checks for pre-existing files only for use by stopped and re-started jobs, NOT for coordinating between processes. (To coordinate, it would have to "touch" the non-existant file in next_job() before starting to process it, but see AtomtreeDiffJobDistributor for an explanation of why coordinating processes via the filesystem is a bad idea.)


Member Typedef Documentation


Constructor & Destructor Documentation

protocols::jobdist::PlainPdbJobDistributor::PlainPdbJobDistributor ( JobVector  jobs,
std::string  outfile_name = "none" 
)
protocols::jobdist::PlainPdbJobDistributor::~PlainPdbJobDistributor ( ) [virtual]

Member Function Documentation

void protocols::jobdist::PlainPdbJobDistributor::dump_pose_and_map ( std::string const &  tag,
core::pose::Pose pose 
) [virtual]
void protocols::jobdist::PlainPdbJobDistributor::dump_scores ( utility::io::ozstream &  out,
std::string const &  tag,
core::pose::Pose pose 
) [protected, virtual]

Writes score data to PDB file in YAML format.

In order for this to work as expected, the Pose's cached energies must match up with the (current) conformation. A good time to do this is at the end of your protocol's apply() method: scorefxn( pose ); scorefxn.accumulate_residue_total_energies( pose );

References core::pose::Pose::energies(), core::scoring::n_score_types, core::conformation::Residue::name(), core::scoring::name_from_score_type(), core::pose::Pose::residue(), core::scoring::Energies::residue_total_energies(), core::scoring::Energies::total_energies(), core::pose::Pose::total_residue(), and core::scoring::Energies::weights().

Referenced by dump_pose_and_map().

std::string protocols::jobdist::PlainPdbJobDistributor::get_output_filename ( std::string const &  tag) [virtual]

Translates an output tag name to an output PDB file name.

References protocols::wum::mpi_rank().

bool protocols::jobdist::PlainPdbJobDistributor::is_finished ( BasicJobOP const &  job,
int  struct_n 
) [protected, virtual]

Is the given nstruct number of the given input job already finished by the local process? To be implemented by subclasses.

Implements protocols::jobdist::BaseJobDistributor.

References protocols::swa::rna::file_exists(), protocols::jobdist::BaseJobDistributor::get_output_filename(), and protocols::jobdist::BaseJobDistributor::ignorefinished().

void protocols::jobdist::PlainPdbJobDistributor::score_map ( std::map< std::string, core::Real > &  ) [inline, virtual]

Virtual function for score_map that is needed for main_plain_mover sets the score_map.

Needed if a score_map is to be output by the derived class

Reimplemented from protocols::jobdist::BaseJobDistributor.

void protocols::jobdist::PlainPdbJobDistributor::startup ( ) [virtual]

Allows setting of inprogress.

Over riding baseclass to enable inprogress file.

Reimplemented from protocols::jobdist::BaseJobDistributor.

References protocols::jobdist::BaseJobDistributor::enable_inprogress().

void protocols::jobdist::PlainPdbJobDistributor::temp_file ( std::string const &  tag) [virtual]

Opens a temp file (.in_progress)

Reimplemented from protocols::jobdist::BaseJobDistributor.

References protocols::jobdist::BaseJobDistributor::get_output_filename().


The documentation for this class was generated from the following files:
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