Class used to generate and load in edge files for use with SEWING protocols. More...

#include <EdgeMapGenerator.hh>

Inheritance diagram for protocols::sewing::hashing::EdgeMapGenerator:

Public Member Functions
	EdgeMapGenerator ()

	EdgeMapGenerator (std::string model_file_name, core::Size boxes_per_dimension, core::Size min_hash_score, core::Size max_clash_score, std::string edge_file_name, bool hash_opposite_termini)

	EdgeMapGenerator (EdgeMapGenerator const &other)

	EdgeMapGenerator (std::string edge_file_name)

	~EdgeMapGenerator () override

EdgeMapGeneratorOP	clone ()

bool	edge_exists (data_storage::SmartSegmentCOP seg1, data_storage::SmartSegmentCOP seg2, HasherOP hasher)
	Check whether two SewSegments can form an edge. More...

void	write_edges_for_segment (core::Size current_n_segment, HasherOP hasher, std::ostream &output_file, utility::vector1< core::Size > const &c_segs)
	Method called by each individual processor to write to its edge file. More...

std::pair< utility::vector1 < core::Size > , utility::vector1< core::Size > >	get_terminal_segments ()
	Generate vectors of IDs of N-terminal and C-terminal segments. More...

void	append_to_edge_map (core::Size base_seg_id)
	Used to add a given segment's n-most and c-most terminal segments to EdgeMap. More...

void	generate_edge_file ()
	Main method of this class that is responsible for dividing work between nodes and iterating over models. More...

void	initialize_from_options ()
	Get values of command-line options. More...

void	set_private_data (std::string model_file_name, core::Size boxes_per_dimension, core::Size min_hash_score, core::Size max_clash_score, bool hash_opposite_termini)
	Shared setup of private data members. More...

EdgeMapOP	edge_map () const

core::Size	version () const

std::string	edge_file_name () const

HasherSettings	hasher_settings () const

std::map< core::Size, data_storage::SmartSegmentOP > &	pdb_segments ()

std::map< core::Size, data_storage::SmartSegmentOP > const	const_pdb_segments () const

SegmentVectorCOP	segment_vector () const

bool	is_edge_file_loaded () const

void	version (core::Size ver)

void	edge_file_name (std::string name)

void	segment_vector (SegmentVectorCOP segvector)

void	hasher_settings (HasherSettings &hs)

void	pdb_segments (std::map< core::Size, data_storage::SmartSegmentOP > &)

void	load_edge_file (std::string edge_file_name)
	Main function for reading edge files (sets values of other member variables) More...

void	read_edge_file ()
	Alternate function to read edge file when name is already known. More...

EdgeMap::iterator	get_edges (core::Size)
	function returns a set of segments that the provided segment can connect to. More...

Private Attributes
HasherSettings	hasher_settings_

core::Size	version_ =0

EdgeMapOP	edges_ = utility::pointer::make_shared< EdgeMap >()

SegmentVectorCOP	segment_vector_

std::string	edge_file_name_

bool	is_edge_file_loaded_

std::map< core::Size, data_storage::SmartSegmentOP >	pdb_segments_

Detailed Description

Class used to generate and load in edge files for use with SEWING protocols.

Constructor & Destructor Documentation

protocols::sewing::hashing::EdgeMapGenerator::EdgeMapGenerator ( )

References pdb_segments_.

protocols::sewing::hashing::EdgeMapGenerator::EdgeMapGenerator	(	std::string	model_file_name,
		core::Size	boxes_per_dimension,
		core::Size	min_hash_score,
		core::Size	max_clash_score,
		std::string	edge_file_name,
		bool	hash_opposite_termini
	)

References pdb_segments_, and set_private_data().

protocols::sewing::hashing::EdgeMapGenerator::EdgeMapGenerator ( EdgeMapGenerator const & other )

protocols::sewing::hashing::EdgeMapGenerator::EdgeMapGenerator ( std::string edge_file_name )

References pdb_segments_.

protocols::sewing::hashing::EdgeMapGenerator::~EdgeMapGenerator ( )

override

Member Function Documentation

void protocols::sewing::hashing::EdgeMapGenerator::append_to_edge_map ( core::Size base_seg_id )

Used to add a given segment's n-most and c-most terminal segments to EdgeMap.

This function is intended to be used with AppendAssemblyMover ( and possibly with some later applications) to add a set of connected segments (formerly known as a model) to an existing EdgeMap

References edge_exists(), protocols::sewing::data_storage::SmartSegment::get_c_most_segment(), protocols::sewing::data_storage::SmartSegment::get_n_most_segment(), get_terminal_segments(), hasher_settings_, pdb_segments_, and segment_vector_.

EdgeMapGeneratorOP protocols::sewing::hashing::EdgeMapGenerator::clone ( )

std::map< core::Size, data_storage::SmartSegmentOP > const protocols::sewing::hashing::EdgeMapGenerator::const_pdb_segments ( ) const

References pdb_segments_.

bool protocols::sewing::hashing::EdgeMapGenerator::edge_exists	(	data_storage::SmartSegmentCOP	seg1,
		data_storage::SmartSegmentCOP	seg2,
		HasherOP	hasher
	)

Check whether two SewSegments can form an edge.

References protocols::TR().

Referenced by append_to_edge_map(), and write_edges_for_segment().

std::string protocols::sewing::hashing::EdgeMapGenerator::edge_file_name ( ) const

References edge_file_name_.

Referenced by load_edge_file().

void protocols::sewing::hashing::EdgeMapGenerator::edge_file_name ( std::string name )

References edge_file_name_.

EdgeMapOP protocols::sewing::hashing::EdgeMapGenerator::edge_map ( ) const

References edges_.

void protocols::sewing::hashing::EdgeMapGenerator::generate_edge_file ( )

Main method of this class that is responsible for dividing work between nodes and iterating over models.

This function handles the distribution of labor for edge file generation. The actual calls to the hasher & writing to the file (really everything directly dealing with SEWING elements) happens elsewhere.

References protocols::sewing::hashing::HasherSettings::boxes_per_dimension, edge_file_name_, get_terminal_segments(), protocols::sewing::hashing::HasherSettings::hash_between_termini, hasher_settings_, protocols::sewing::hashing::HasherSettings::max_clash_score, protocols::sewing::hashing::HasherSettings::min_hash_score, protocols::wum::mpi_rank(), pdb_segments_, segment_vector_, core::id::to_string(), protocols::TR(), version_, and write_edges_for_segment().

EdgeMap::iterator protocols::sewing::hashing::EdgeMapGenerator::get_edges ( core::Size sew_segment )

function returns a set of segments that the provided segment can connect to.

References edges_.

std::pair< utility::vector1< core::Size >, utility::vector1< core::Size > > protocols::sewing::hashing::EdgeMapGenerator::get_terminal_segments ( )

Generate vectors of IDs of N-terminal and C-terminal segments.

References pdb_segments_, and segment_vector_.

Referenced by append_to_edge_map(), and generate_edge_file().

HasherSettings protocols::sewing::hashing::EdgeMapGenerator::hasher_settings ( ) const

References hasher_settings_.

void protocols::sewing::hashing::EdgeMapGenerator::hasher_settings ( HasherSettings & hs )

References hasher_settings_.

void protocols::sewing::hashing::EdgeMapGenerator::initialize_from_options ( )

Get values of command-line options.

References edge_file_name_, and set_private_data().

bool protocols::sewing::hashing::EdgeMapGenerator::is_edge_file_loaded ( ) const

References is_edge_file_loaded_.

void protocols::sewing::hashing::EdgeMapGenerator::load_edge_file ( std::string edge_file_name )

Main function for reading edge files (sets values of other member variables)

References edge_file_name(), edge_file_name_, and read_edge_file().

std::map< core::Size, data_storage::SmartSegmentOP > & protocols::sewing::hashing::EdgeMapGenerator::pdb_segments ( )

References pdb_segments_.

void protocols::sewing::hashing::EdgeMapGenerator::pdb_segments ( std::map< core::Size, data_storage::SmartSegmentOP > & pdbsegs )

References pdb_segments_.

void protocols::sewing::hashing::EdgeMapGenerator::read_edge_file ( )

Alternate function to read edge file when name is already known.

References edge_file_name_, hasher_settings_, is_edge_file_loaded_, and version_.

Referenced by load_edge_file().

SegmentVectorCOP protocols::sewing::hashing::EdgeMapGenerator::segment_vector ( ) const

References segment_vector_.

void protocols::sewing::hashing::EdgeMapGenerator::segment_vector ( SegmentVectorCOP segvector )

References segment_vector_.

void protocols::sewing::hashing::EdgeMapGenerator::set_private_data	(	std::string	model_file_name,
		core::Size	boxes_per_dimension,
		core::Size	min_hash_score,
		core::Size	max_clash_score,
		bool	hash_opposite_termini
	)

Shared setup of private data members.

References hasher_settings_, protocols::sewing::hashing::ModelFileReader::read_model_file(), segment_vector_, protocols::TR(), and version_.

Referenced by EdgeMapGenerator(), and initialize_from_options().

core::Size protocols::sewing::hashing::EdgeMapGenerator::version ( ) const

References version_.

void protocols::sewing::hashing::EdgeMapGenerator::version ( core::Size ver )

References version_.

void protocols::sewing::hashing::EdgeMapGenerator::write_edges_for_segment	(	core::Size	current_n_segment,
		HasherOP	hasher,
		std::ostream &	output_file,
		utility::vector1< core::Size > const &	c_segs
	)