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protocols::antibody::AntibodyNumberingParser Class Reference

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

#include <AntibodyNumberingParser.hh>

Inheritance diagram for protocols::antibody::AntibodyNumberingParser:
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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
AntibodyNumbering protocols::antibody::AntibodyNumberingParser::get_antibody_numbering ( AntibodyNumberingSchemeEnum const  numbering_scheme,
CDRDefinitionEnum const  cdr_definition 
)
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
void protocols::antibody::AntibodyNumberingParser::read_cdr_definition_numbering_line ( utility::vector1< std::string > const &  lineSP,
AntibodyNumbering numbering 
) const
private
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
void protocols::antibody::AntibodyNumberingParser::read_scheme_defines_line ( utility::vector1< std::string > const &  lineSP)
private
void protocols::antibody::AntibodyNumberingParser::read_scheme_numbering_line ( utility::vector1< std::string > const &  lineSP,
AntibodyNumbering numbering 
) const
private

Member Data Documentation

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

Referenced by get_antibody_numbering().

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

Referenced by get_antibody_numbering().

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

Referenced by get_antibody_numbering().

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

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