Class responsible for reading database Numbering Scheme definitions and their transforms from the database. More...

#include <AntibodyNumberingParser.hh>

Inheritance diagram for protocols::antibody::AntibodyNumberingParser:

Public Member Functions
	AntibodyNumberingParser (AntibodyEnumManagerCOP enum_manager)
	Default constructor. We pass the enum manager which is constructed in AbInfo so we only should have one instance of it. Its not a singleton, so instead of global data, we are careful where and when we pass it around. More...

	~AntibodyNumberingParser () override

AntibodyNumbering	get_antibody_numbering (AntibodyNumberingSchemeEnum const numbering_scheme, CDRDefinitionEnum const cdr_definition)
	Read numbering file and return AntibodyNumbering structure. More...

Private Member Functions
void	read_cdr_definition_file (std::string const &file_path, AntibodyNumbering &numbering)

void	read_numbering_scheme_file (std::string const &file_path, AntibodyNumbering &numbering)

void	read_cdr_definition_numbering_line (utility::vector1< std::string > const &lineSP, AntibodyNumbering &numbering) const
	Reads lines defining start/end of each CDR and the relative transforms to the numbering schemes defined by the TRANSFORM line. More...

void	read_cdr_definition_transform_line (utility::vector1< std::string > const &lineSP, AntibodyNumbering &numbering)
	Reads line corresponding to TRANSFORM, which lists columns for which the transform to another numbering scheme is defined. More...

void	read_scheme_numbering_line (utility::vector1< std::string > const &lineSP, AntibodyNumbering &numbering) const

void	read_scheme_defines_line (utility::vector1< std::string > const &lineSP)

void	check_path (std::string const &numbering_file_path) const
	Check to make sure the path to the numbering scheme file is good. More...

AntibodyNumberingSchemeEnum	get_numbering_scheme_used_for_cdr_definition (CDRDefinitionEnum) const

PDBLandmarkOP	get_equivalent_landmark (AntibodyNumbering &numbering, const AntibodyNumberingSchemeEnum scheme, PDBLandmark &landmark_to_match) const
	Gets equivalent landmark from that defined in landmark_to_match. More...

void	debug_print (AntibodyNumbering &numbering)

Private Attributes
AntibodyEnumManagerCOP	enum_manager_

std::string	numbering_database_directory_

std::string	scheme_file_

std::string	cdr_definition_file_

utility::vector1 < CDRDefinitionEnum >	cdr_definitions_defined_

utility::vector1 < AntibodyNumberingSchemeEnum >	cdr_definitions_defined_using_

utility::vector1 < AntibodyNumberingSchemeEnum >	schemes_defined_

Detailed Description

Class responsible for reading database Numbering Scheme definitions and their transforms from the database.

Constructor & Destructor Documentation

protocols::antibody::AntibodyNumberingParser::AntibodyNumberingParser ( AntibodyEnumManagerCOP enum_manager )

Default constructor. We pass the enum manager which is constructed in AbInfo so we only should have one instance of it. Its not a singleton, so instead of global data, we are careful where and when we pass it around.

protocols::antibody::AntibodyNumberingParser::~AntibodyNumberingParser ( )

overridedefault

Member Function Documentation

void protocols::antibody::AntibodyNumberingParser::check_path ( std::string const & numbering_file_path ) const

private

Check to make sure the path to the numbering scheme file is good.

References core::conformation::membrane::in.

Referenced by read_cdr_definition_file(), and read_numbering_scheme_file().

void protocols::antibody::AntibodyNumberingParser::debug_print ( AntibodyNumbering & numbering )

private

References protocols::antibody::AntibodyNumbering::cdr_definition, protocols::antibody::AntibodyNumbering::cdr_definition_transform, protocols::antibody::cdr_start, protocols::antibody::Chothia, enum_manager_, protocols::antibody::North, protocols::antibody::AntibodyNumbering::numbering_scheme, and protocols::antibody::TR().

AntibodyNumbering protocols::antibody::AntibodyNumberingParser::get_antibody_numbering	(	AntibodyNumberingSchemeEnum const	numbering_scheme,
		CDRDefinitionEnum const	cdr_definition
	)

Read numbering file and return AntibodyNumbering structure.

References protocols::antibody::AntibodyNumbering::cdr_definition, cdr_definition_file_, cdr_definitions_defined_, cdr_definitions_defined_using_, numbering_database_directory_, protocols::antibody::AntibodyNumbering::numbering_scheme, read_cdr_definition_file(), read_numbering_scheme_file(), scheme_file_, and schemes_defined_.

PDBLandmarkOP protocols::antibody::AntibodyNumberingParser::get_equivalent_landmark	(	AntibodyNumbering &	numbering,
		const AntibodyNumberingSchemeEnum	scheme,
		PDBLandmark &	landmark_to_match
	)		const

private

Gets equivalent landmark from that defined in landmark_to_match.

. Ex. landmark_to_match defines a CDR start point in Chothia_scheme. Our numbering must be in Kabat. What is the PDBLandmark for the same residue?

References protocols::antibody::AntibodyNumbering::numbering_scheme, protocols::antibody::PDBLandmark::numbering_scheme(), and protocols::antibody::AntibodyNumbering::numbering_scheme_transform.

Referenced by read_cdr_definition_numbering_line().

AntibodyNumberingSchemeEnum protocols::antibody::AntibodyNumberingParser::get_numbering_scheme_used_for_cdr_definition ( CDRDefinitionEnum ) const

private

void protocols::antibody::AntibodyNumberingParser::read_cdr_definition_file	(	std::string const &	file_path,
		AntibodyNumbering &	numbering
	)

private

References protocols::antibody::AntibodyNumbering::cdr_numbering, protocols::antibody::CDRLandmarkEnum_total, check_path(), enum_manager_, read_cdr_definition_numbering_line(), read_cdr_definition_transform_line(), and protocols::antibody::TR().

Referenced by get_antibody_numbering().

void protocols::antibody::AntibodyNumberingParser::read_cdr_definition_numbering_line	(	utility::vector1< std::string > const &	lineSP,
		AntibodyNumbering &	numbering
	)		const

private

Reads lines defining start/end of each CDR and the relative transforms to the numbering schemes defined by the TRANSFORM line.

References protocols::antibody::AntibodyNumbering::cdr_definition, protocols::antibody::AntibodyNumbering::cdr_definition_transform, cdr_definitions_defined_, cdr_definitions_defined_using_, protocols::antibody::AntibodyNumbering::cdr_numbering, enum_manager_, get_equivalent_landmark(), and protocols::antibody::AntibodyNumbering::numbering_scheme.

Referenced by read_cdr_definition_file().

void protocols::antibody::AntibodyNumberingParser::read_cdr_definition_transform_line	(	utility::vector1< std::string > const &	lineSP,
		AntibodyNumbering &	numbering
	)

private

Reads line corresponding to TRANSFORM, which lists columns for which the transform to another numbering scheme is defined.

References protocols::antibody::AntibodyNumbering::cdr_definition_transform, cdr_definitions_defined_, cdr_definitions_defined_using_, protocols::antibody::CDRLandmarkEnum_total, and enum_manager_.

Referenced by read_cdr_definition_file().

void protocols::antibody::AntibodyNumberingParser::read_numbering_scheme_file	(	std::string const &	file_path,
		AntibodyNumbering &	numbering
	)

private

References check_path(), protocols::antibody::AntibodyNumbering::numbering_scheme_transform, read_scheme_defines_line(), read_scheme_numbering_line(), schemes_defined_, and protocols::antibody::TR().

Referenced by get_antibody_numbering().

void protocols::antibody::AntibodyNumberingParser::read_scheme_defines_line ( utility::vector1< std::string > const & lineSP )

private

References enum_manager_, and schemes_defined_.

Referenced by read_numbering_scheme_file().

void protocols::antibody::AntibodyNumberingParser::read_scheme_numbering_line	(	utility::vector1< std::string > const &	lineSP,
		AntibodyNumbering &	numbering
	)		const