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

#include <JobDistributors.hh>

Inheritance diagram for protocols::jobdist::PlainPdbJobDistributor:

Public Types
typedef BaseJobDistributor	parent

Public Member Functions
	PlainPdbJobDistributor (JobVector jobs, std::string outfile_name="none")

	~PlainPdbJobDistributor () override

void	startup () override
	Allows setting of inprogress. More...

virtual std::string	get_output_filename (std::string const &tag)
	Translates an output tag name to an output PDB file name. More...

void	dump_pose_and_map (std::string const &tag, core::pose::Pose &pose) override
	Writes pose and basic score data to a standard PDB file. More...

void	temp_file (std::string const &tag) override
	Opens a temp file (.in_progress) More...

void	score_map (std::map< std::string, core::Real > &score_map_in) override
	Virtual function for score_map that is needed for main_plain_mover sets the score_map. More...

virtual std::string	get_output_filename ()

Public Member Functions inherited from protocols::jobdist::BaseJobDistributor
	BaseJobDistributor (JobVector const &jobs)

	BaseJobDistributor (BaseJobDistributor const &)

	~BaseJobDistributor () override

bool	next_job (BasicJobOP &job, int &struct_n)
	If true, sets the next Job and nstruct number to be processed. Deliberately not virtual: should not be overriden. Uses the "find_available_job" method, which is common to both MPI and standard protocols, but used in slightly different manners. More...

virtual void	shutdown ()
	Must be called by client after last call to next_job(). If overriden by a subclass, it MUST call the superclass implementation. More...

virtual void	begin_critical_section ()
	Signal that if at all possible, we would like to not be killed while in the critical section. If overriden by a subclass, it MUST call the superclass implementation. More...

virtual void	end_critical_section ()
	Signal that if at all possible, we would like to not be killed while in the critical section. If overriden by a subclass, it MUST call the superclass implementation. More...

void	disable_ignorefinished ()

void	enable_ignorefinished ()

void	disable_output ()

void	enable_output ()

void	disable_inprogress ()

void	enable_inprogress ()

bool	ignorefinished () const

bool	nooutput () const

bool	inprogress () const

void	set_proc_id (core::Size proc_id, core::Size nproc)

virtual std::string	get_current_output_tag ()
	get output_tag for current job's current nstruct More...

Protected Types
typedef utility::vector1< BasicJobOP >	JobVector

Protected Types inherited from protocols::jobdist::BaseJobDistributor
typedef utility::vector1< BasicJobOP >	JobVector

Protected Member Functions
bool	is_finished (BasicJobOP const &job, int struct_n) override
	Is the given nstruct number of the given input job already finished by the local process? To be implemented by subclasses. More...

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. More...

Protected Member Functions inherited from protocols::jobdist::BaseJobDistributor
virtual void	checkpoint_read ()
	Restore state from checkpoint file, if it exists. More...

virtual void	checkpoint_write ()
	Save state to checkpoint file, overwriting previous. More...

virtual void	checkpoint_clear ()
	Remove checkpoint file (at end of batch) More...

int	current_nstruct ()
	accessor for current_nstruct_ More...

BasicJobOP	current_job ()
	accessor for current_job owning pointer More...

int	get_next_random_range (int low, int high)

Private Attributes
bool	scorefile_

utility::file::FileName	scorefile_name_

std::map< std::string, core::Real >	score_map_

Additional Inherited Members
Protected Attributes inherited from protocols::jobdist::BaseJobDistributor
bool	ignorefinished_
	ignore already done jobs - redo everything ! More...

bool	nooutput_
	do not write files - useful such things as statistics or rescoring ! More...

bool	inprogress_
	write .in_progress files for multiple processor runs More...

int	start_time_
	starttime More...

int	random_counter_
	RandomStore - needed for. More...

utility::vector1< core::Real >	random_store_

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

◆ JobVector

typedef utility::vector1< BasicJobOP > protocols::jobdist::PlainPdbJobDistributor::JobVector

protected

◆ parent

typedef BaseJobDistributor protocols::jobdist::PlainPdbJobDistributor::parent

Constructor & Destructor Documentation

◆ PlainPdbJobDistributor()

protocols::jobdist::PlainPdbJobDistributor::PlainPdbJobDistributor	(	JobVector	jobs,
		std::string	outfile_name = `"none"`
	)

References scorefile_, and scorefile_name_.

◆ ~PlainPdbJobDistributor()

protocols::jobdist::PlainPdbJobDistributor::~PlainPdbJobDistributor ( )

overridedefault

Member Function Documentation

◆ dump_pose_and_map()

void protocols::jobdist::PlainPdbJobDistributor::dump_pose_and_map	(	std::string const &	tag,
		core::pose::Pose &	pose
	)

overridevirtual

Writes pose and basic score data to a standard PDB file.

Reimplemented from protocols::jobdist::BaseJobDistributor.

References protocols::jobdist::BaseJobDistributor::begin_critical_section(), core::io::pdb::dump_pdb(), dump_scores(), protocols::jobdist::BaseJobDistributor::end_critical_section(), get_output_filename(), protocols::jobdist::BaseJobDistributor::nooutput(), core::conformation::membrane::out, score_map_, scorefile_, scorefile_name_, and core::io::raw_data::ScoreFileData::write_pose().

◆ dump_scores()

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

protectedvirtual

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::conformation::membrane::out, core::pose::Pose::residue(), core::scoring::Energies::residue_total_energies(), protocols::hybridization::score, core::pose::Pose::size(), core::scoring::Energies::total_energies(), and core::scoring::Energies::weights().