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

#include <AntibodyNumberingParser.hh>

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...

virtual	~AntibodyNumberingParser ()

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

void	read_scheme_defines_line (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_

vector1< CDRDefinitionEnum >	cdr_definitions_defined_

vector1 < AntibodyNumberingSchemeEnum >	cdr_definitions_defined_using_

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 ( )

virtual

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 utility_exit_with_message.

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, 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, basic::database::full_name(), and protocols::antibody::AntibodyNumbering::numbering_scheme.

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(), protocols::antibody::AntibodyNumbering::numbering_scheme_transform, and utility_exit_with_message.

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, getline(), PyAssert, utility::startswith(), utility::string_split_multi_delim(), protocols::antibody::TR, and utility::trim().

void protocols::antibody::AntibodyNumberingParser::read_cdr_definition_numbering_line	(	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, protocols::antibody::AntibodyNumbering::cdr_numbering, chain, protocols::antibody::AntibodyNumbering::numbering_scheme, utility::string_split(), and utility_exit_with_message.

void protocols::antibody::AntibodyNumberingParser::read_cdr_definition_transform_line	(	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 cdr_definition, protocols::antibody::AntibodyNumbering::cdr_definition_transform, protocols::antibody::CDRLandmarkEnum_total, utility::string_split(), and utility_exit_with_message.

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

private

References getline(), protocols::antibody::AntibodyNumbering::numbering_scheme_transform, PyAssert, utility::startswith(), utility::string_split_multi_delim(), protocols::antibody::TR, utility::trim(), and utility_exit_with_message.

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

private

References utility_exit_with_message.

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

private

References chain, protocols::antibody::AntibodyNumbering::numbering_scheme_transform, utility::string_split(), and utility_exit_with_message.

Member Data Documentation

std::string protocols::antibody::AntibodyNumberingParser::cdr_definition_file_

private

vector1< CDRDefinitionEnum > protocols::antibody::AntibodyNumberingParser::cdr_definitions_defined_

private

vector1< AntibodyNumberingSchemeEnum > protocols::antibody::AntibodyNumberingParser::cdr_definitions_defined_using_

private

AntibodyEnumManagerCOP protocols::antibody::AntibodyNumberingParser::enum_manager_

private

std::string protocols::antibody::AntibodyNumberingParser::numbering_database_directory_

private

std::string protocols::antibody::AntibodyNumberingParser::scheme_file_

private

vector1< AntibodyNumberingSchemeEnum > protocols::antibody::AntibodyNumberingParser::schemes_defined_

private

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

src/protocols/antibody/AntibodyNumberingParser.hh
src/protocols/antibody/AntibodyNumberingParser.cc

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation