Given a model file, edge file ,and one or more input structures, generates alignment files for use with AppendAssemblyMover. More...

#include <BasisMapGenerator.hh>

Public Member Functions
	BasisMapGenerator ()

	BasisMapGenerator (BasisMapGenerator const &src)

	BasisMapGenerator (EdgeMapGeneratorOP edge_file_reader, SegmentVectorCOP segments)

	BasisMapGenerator (EdgeMapGeneratorOP edge_file_reader, std::string model_file_name, std::string alignment_file_name)

	BasisMapGenerator (EdgeMapGeneratorOP edge_file_reader, std::string model_file_name)

	BasisMapGenerator (std::string model_file_name, std::string edge_file_name, utility::vector1< core::Size > match_segments, utility::vector1< core::Size > pose_segment_starts, utility::vector1< core::Size > pose_segment_ends, core::Size recursive_depth)

virtual	~BasisMapGenerator ()

void	initialize_from_options ()

void	set_private_data (std::string model_file_name, std::string edge_file_name, utility::vector1< core::Size > match_segments, utility::vector1< core::Size >pose_segment_starts, utility::vector1< core::Size > pose_segment_ends, core::Size recursive_depth)

void	write_alignments_to_file (std::string file_name) const

void	edge_file_from_options ()

void	model_file_from_options ()

void	alignment_settings_from_options ()

void	set_model_file (std::string model_file_name)

void	set_edge_file (std::string edge_file)

void	set_edge_file_reader (EdgeMapGeneratorOP edge_file_reader)

void	set_alignment_settings (utility::vector1< core::Size > match_segments, utility::vector1< core::Size > pose_segment_starts, utility::vector1< core::Size > pose_segment_ends, core::Size recursive_depth)

core::Size	version () const

HasherSettings	hasher_settings () const

SegmentVectorCOP	segment_vector () const

EdgeMapGeneratorOP	edge_file_reader () const

AlignmentSettings	alignment_settings () const

AlignmentGeneratorOP	alignment_generator () const

BasisMapOP	basis_map () const

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

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

BasisMap::iterator	get_alignments (data_storage::SmartSegmentOP query_segment)

void	delete_segment_basis_pairs (core::Size)

void	version (core::Size ver)

void	segment_vector (SegmentVectorCOP segvec)

void	hasher_settings (HasherSettings &hs)

void	alignment_generator (AlignmentGeneratorOP ag)

void	alignment_settings (AlignmentSettings &as)

void	basis_map (BasisMapOP bm)

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

BasisMapGeneratorOP	clone () const
	required in the context of the parser/scripting scheme More...

void	recurse_over_segments (core::Size current_depth, std::set< data_storage::SmartSegmentCOP > segments_to_check)

void	read_alignments_from_file (std::string file_name)

data_storage::BasisPair	get_basis_pair_for_segment (core::Size segment_id)
	Given a segmentID, return a randomly chosen basis pair from the BasisMap for this segment. More...

std::pair< bool, data_storage::BasisPair >	get_basis_pair_for_local_segments (data_storage::SmartSegmentCOP seg1, data_storage::SmartSegmentCOP seg2, bool first_is_N)
	This function wraps several of the functions below to retrieve a basis pair for local (possibly chimaeric) input segments. More...

std::pair< std::pair < core::Size, core::Size > , std::pair< core::Size, core::Size > >	get_basis_res_bounds (data_storage::SmartSegmentCOP seg1, data_storage::SmartSegmentCOP seg2, bool first_is_N)
	Given two (possibly chimaeric) segments, return ranges of valid basis residues for each. More...

data_storage::BasisPair	get_basis_pair_for_segment_pair (core::Size seg1, core::Size seg2, bool first_is_N)
	Given two (original, non-chimaeric) segments, return a possible basis pair for those two segments. More...

std::pair< bool, bool >	segs_can_chimerize (data_storage::SmartSegmentCOP seg1, data_storage::SmartSegmentCOP seg2, bool first_is_N)
	Checks that a pair of segments (including chimaerae!) can chimerize. More...

bool	basis_pair_is_valid (data_storage::BasisPair basis_pair, bool first_is_N)
	Checks that the given basis pair exists in the BasisMap after calling recurse_over_segments on seg1. More...

Private Attributes
HasherSettings	hasher_settings_

core::Size	version_

SegmentVectorCOP	segment_vector_

EdgeMapGeneratorOP	edge_file_reader_

AlignmentSettings	alignment_settings_

BasisMapOP	basis_map_

AlignmentGeneratorOP	alignment_generator_

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

Detailed Description

Given a model file, edge file ,and one or more input structures, generates alignment files for use with AppendAssemblyMover.

Constructor & Destructor Documentation

protocols::sewing::hashing::BasisMapGenerator::BasisMapGenerator ( )

protocols::sewing::hashing::BasisMapGenerator::BasisMapGenerator ( BasisMapGenerator const & src )

References alignment_generator(), alignment_generator_, alignment_settings(), alignment_settings_, basis_map(), basis_map_, const_pdb_segments(), edge_file_reader(), edge_file_reader_, hasher_settings(), hasher_settings_, pdb_segments_, segment_vector(), segment_vector_, version(), and version_.

protocols::sewing::hashing::BasisMapGenerator::BasisMapGenerator	(	EdgeMapGeneratorOP	edge_file_reader,
		SegmentVectorCOP	segments
	)

References alignment_settings_, basis_map_, protocols::sewing::hashing::AlignmentSettings::recursive_depth_, segment_vector_, set_edge_file_reader(), and version_.

protocols::sewing::hashing::BasisMapGenerator::BasisMapGenerator	(	EdgeMapGeneratorOP	edge_file_reader,
		std::string	model_file_name,
		std::string	alignment_file_name
	)

References alignment_settings_, basis_map_, read_alignments_from_file(), protocols::sewing::hashing::AlignmentSettings::recursive_depth_, set_edge_file_reader(), and set_model_file().

protocols::sewing::hashing::BasisMapGenerator::BasisMapGenerator	(	EdgeMapGeneratorOP	edge_file_reader,
		std::string	model_file_name
	)

References alignment_settings_, basis_map_, protocols::sewing::hashing::AlignmentSettings::recursive_depth_, set_edge_file_reader(), and set_model_file().

protocols::sewing::hashing::BasisMapGenerator::BasisMapGenerator	(	std::string	model_file_name,
		std::string	edge_file_name,
		utility::vector1< core::Size >	match_segments,
		utility::vector1< core::Size >	pose_segment_starts,
		utility::vector1< core::Size >	pose_segment_ends,
		core::Size	recursive_depth
	)

References set_private_data().

protocols::sewing::hashing::BasisMapGenerator::~BasisMapGenerator ( )

virtual

Member Function Documentation

AlignmentGeneratorOP protocols::sewing::hashing::BasisMapGenerator::alignment_generator ( ) const

References alignment_generator_.

Referenced by BasisMapGenerator().

void protocols::sewing::hashing::BasisMapGenerator::alignment_generator ( AlignmentGeneratorOP ag )

References alignment_generator_.

AlignmentSettings protocols::sewing::hashing::BasisMapGenerator::alignment_settings ( ) const

References alignment_settings_.

Referenced by BasisMapGenerator().

void protocols::sewing::hashing::BasisMapGenerator::alignment_settings ( AlignmentSettings & as )

References alignment_settings_.

void protocols::sewing::hashing::BasisMapGenerator::alignment_settings_from_options ( )

References set_alignment_settings().

Referenced by initialize_from_options().

utility::pointer::shared_ptr< BasisMap > protocols::sewing::hashing::BasisMapGenerator::basis_map ( ) const

References basis_map_.

Referenced by BasisMapGenerator().

void protocols::sewing::hashing::BasisMapGenerator::basis_map ( BasisMapOP bm )

bool protocols::sewing::hashing::BasisMapGenerator::basis_pair_is_valid	(	data_storage::BasisPair	basis_pair,
		bool	first_is_N
	)

Checks that the given basis pair exists in the BasisMap after calling recurse_over_segments on seg1.

Must be called for original segment IDs (no chimaerae or segment duplicates)

References basis_map_, pdb_segments_, recurse_over_segments(), and segment_vector_.

BasisMapGeneratorOP protocols::sewing::hashing::BasisMapGenerator::clone ( ) const

required in the context of the parser/scripting scheme

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

References pdb_segments_.

Referenced by BasisMapGenerator().

void protocols::sewing::hashing::BasisMapGenerator::delete_segment_basis_pairs ( core::Size segment_to_delete )

References basis_map_.

void protocols::sewing::hashing::BasisMapGenerator::edge_file_from_options ( )

References set_edge_file().

Referenced by initialize_from_options().

EdgeMapGeneratorOP protocols::sewing::hashing::BasisMapGenerator::edge_file_reader ( ) const

References edge_file_reader_.

Referenced by BasisMapGenerator(), set_edge_file(), and set_edge_file_reader().

BasisMap::iterator protocols::sewing::hashing::BasisMapGenerator::get_alignments ( data_storage::SmartSegmentOP query_segment )

References basis_map_, and recurse_over_segments().

std::pair< bool, data_storage::BasisPair > protocols::sewing::hashing::BasisMapGenerator::get_basis_pair_for_local_segments	(	data_storage::SmartSegmentCOP	seg1,
		data_storage::SmartSegmentCOP	seg2,
		bool	first_is_N
	)

This function wraps several of the functions below to retrieve a basis pair for local (possibly chimaeric) input segments.

This function first calls segs_can_chimerize to determine whether the segments can ever chimerize It then retrieves the basis residue bounds for the two segmnets If seg1 (or seg2) is chimaeric, it gets the appropriate parent to use for finding a basis pair. It also handles all conversions between parent and chimaeric residue numbering It has 1000 chances to choose a valid basis pair for the chimaera that fits within the residue bounds If it hasn't found something by then, it just gives up

References get_basis_pair_for_segment_pair(), get_basis_res_bounds(), and segs_can_chimerize().

data_storage::BasisPair protocols::sewing::hashing::BasisMapGenerator::get_basis_pair_for_segment ( core::Size segment_id )

Given a segmentID, return a randomly chosen basis pair from the BasisMap for this segment.

References basis_map_, get_basis_pair_for_segment_pair(), pdb_segments_, recurse_over_segments(), core::scoring::rg, and segment_vector_.

data_storage::BasisPair protocols::sewing::hashing::BasisMapGenerator::get_basis_pair_for_segment_pair	(	core::Size	seg1,
		core::Size	seg2,
		bool	first_is_N
	)

Given two (original, non-chimaeric) segments, return a possible basis pair for those two segments.

Does not take chimaeric basis residue bounds into account; currently we handle those by first checking if the chimaeric segment can chimerize with the partner and then call this repeatedly until we get something that works

References basis_map_, pdb_segments_, recurse_over_segments(), core::scoring::rg, and segment_vector_.

Referenced by get_basis_pair_for_local_segments(), and get_basis_pair_for_segment().

std::pair< std::pair< core::Size, core::Size >, std::pair< core::Size, core::Size > > protocols::sewing::hashing::BasisMapGenerator::get_basis_res_bounds	(	data_storage::SmartSegmentCOP	seg1,
		data_storage::SmartSegmentCOP	seg2,
		bool	first_is_N
	)

Given two (possibly chimaeric) segments, return ranges of valid basis residues for each.

Accounds for both chimaeric basis residues and vital residues. Returns pairs (resnum ranges) in the same order that the segments were provided.

References hasher_settings(), protocols::mean_field::max(), protocols::mean_field::min(), protocols::sewing::hashing::HasherSettings::min_hash_score, and protocols::TR().

Referenced by get_basis_pair_for_local_segments(), and segs_can_chimerize().

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

References hasher_settings_.

Referenced by BasisMapGenerator(), get_basis_res_bounds(), and segs_can_chimerize().

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

References hasher_settings_.

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

References alignment_settings_from_options(), edge_file_from_options(), and model_file_from_options().

void protocols::sewing::hashing::BasisMapGenerator::model_file_from_options ( )

References set_model_file().

Referenced by initialize_from_options().

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

References pdb_segments_.

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

References pdb_segments_.

void protocols::sewing::hashing::BasisMapGenerator::read_alignments_from_file ( std::string file_name )

References alignment_settings_, and version_.

Referenced by BasisMapGenerator().

void protocols::sewing::hashing::BasisMapGenerator::recurse_over_segments	(	core::Size	current_depth,
		std::set< data_storage::SmartSegmentCOP >	segments_to_check
	)

References alignment_generator_, alignment_settings_, basis_map_, edge_file_reader_, protocols::sewing::data_storage::SmartSegment::get_c_most_segment(), pdb_segments_, protocols::sewing::hashing::AlignmentSettings::recursive_depth_, and segment_vector_.

Referenced by basis_pair_is_valid(), get_alignments(), get_basis_pair_for_segment(), and get_basis_pair_for_segment_pair().

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

References segment_vector_.

Referenced by BasisMapGenerator().

void protocols::sewing::hashing::BasisMapGenerator::segment_vector ( SegmentVectorCOP segvec )

References segment_vector_, and version_.

std::pair< bool, bool > protocols::sewing::hashing::BasisMapGenerator::segs_can_chimerize	(	data_storage::SmartSegmentCOP	seg1,
		data_storage::SmartSegmentCOP	seg2,
		bool	first_is_N
	)

Checks that a pair of segments (including chimaerae!) can chimerize.

First bool indicates whether seg1 can ever be chimerized with ANYTHING; second indicates if it can chimerize with seg2 specifically. Calls get_basis_res_bounds to handle chimaera( only checks on the correct terminal-side of the old basis res for chimaerae

References get_basis_res_bounds(), hasher_settings(), protocols::sewing::hashing::HasherSettings::min_hash_score, and protocols::TR().

Referenced by get_basis_pair_for_local_segments().

void protocols::sewing::hashing::BasisMapGenerator::set_alignment_settings	(	utility::vector1< core::Size >	match_segments,
		utility::vector1< core::Size >	pose_segment_starts,
		utility::vector1< core::Size >	pose_segment_ends,
		core::Size	recursive_depth
	)

References alignment_settings_.

Referenced by alignment_settings_from_options(), and set_private_data().

void protocols::sewing::hashing::BasisMapGenerator::set_edge_file ( std::string edge_file )

References edge_file_reader(), segment_vector_, and set_edge_file_reader().

Referenced by edge_file_from_options(), and set_private_data().

void protocols::sewing::hashing::BasisMapGenerator::set_edge_file_reader ( EdgeMapGeneratorOP edge_file_reader )

References alignment_generator_, edge_file_reader(), edge_file_reader_, hasher_settings_, pdb_segments_, segment_vector_, and version_.

Referenced by BasisMapGenerator(), and set_edge_file().

void protocols::sewing::hashing::BasisMapGenerator::set_model_file ( std::string model_file_name )

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

Referenced by BasisMapGenerator(), model_file_from_options(), and set_private_data().

void protocols::sewing::hashing::BasisMapGenerator::set_private_data	(	std::string	model_file_name,
		std::string	edge_file_name,
		utility::vector1< core::Size >	match_segments,
		utility::vector1< core::Size >	pose_segment_starts,
		utility::vector1< core::Size >	pose_segment_ends,
		core::Size	recursive_depth
	)