protocols::antibody::CDRSetOptionsParser Class Reference

Parses CDRSetOptions for a single CDR at a time from a simple instruction file. More...

#include <CDRSetOptionsParser.hh>

Inheritance diagram for protocols::antibody::CDRSetOptionsParser:

Public Member Functions
	CDRSetOptionsParser ()
	~CDRSetOptionsParser () override
	CDRSetOptionsParser (CDRSetOptionsParser const &src)
CDRSetOptionsParserOP	clone () const
CDRSetOptionsOP	parse_options (CDRNameEnum cdr, std::string const &filename)
CDRSetOptionsOP	parse_default_and_user_options (CDRNameEnum cdr, std::string const &filename)
	Parse default instructions (mainly used for AbDesign) then parse user file. More...
utility::vector1< CDRSetOptionsOP >	parse_options (std::string const &filename)
utility::vector1< CDRSetOptionsOP >	parse_default_and_user_options (std::string const &filename)

Private Member Functions
void	check_path ()
	Tries to find the path in either database, relative, or absolute, sets it. More...
void	check_line_len (const utility::vector1< std::string > &lineSP, const core::Size len_check) const
void	parse_cdr_option (std::string const &mode, utility::vector1< std::string > const &lineSP)
void	parse_cdr_set_option (std::string const &adjective, utility::vector1< std::string > const &lineSP)
void	set_cdr_set_exclude_options (std::string const &type, utility::vector1< std::string > const &lineSP)
void	clear_cdr_set_exclude_options (std::string const &type)
void	set_cdr_set_include_options (std::string const &type, utility::vector1< std::string > const &lineSP)
void	clear_cdr_set_include_options (std::string const &type)
void	set_cdr_set_mintype_options (std::string const &mintype)
void	set_cdr_set_general_option (std::string const &option)

Private Attributes
std::string	instructions_path_
CDRSetOptionsOP	cdr_options_
AntibodyEnumManagerCOP	ab_manager_
clusters::CDRClusterEnumManagerCOP	cluster_manager_
bool	default_and_user_

Detailed Description

Parses CDRSetOptions for a single CDR at a time from a simple instruction file.

Constructor & Destructor Documentation

protocols::antibody::CDRSetOptionsParser::CDRSetOptionsParser

(

)

References ab_manager_, and cluster_manager_.

protocols::antibody::CDRSetOptionsParser::~CDRSetOptionsParser ( )

overridedefault

protocols::antibody::CDRSetOptionsParser::CDRSetOptionsParser

(

CDRSetOptionsParser const &

src

)

References ab_manager_, cdr_options_, and cluster_manager_.

Member Function Documentation

void protocols::antibody::CDRSetOptionsParser::check_line_len ( const utility::vector1< std::string > &  lineSP, const core::Size  len_check  ) const

private

References core::id::to_string().

Referenced by parse_cdr_option(), parse_cdr_set_option(), and parse_options().

void protocols::antibody::CDRSetOptionsParser::check_path ( )

private

Tries to find the path in either database, relative, or absolute, sets it.

References core::conformation::membrane::in, and instructions_path_.

Referenced by parse_options().

void protocols::antibody::CDRSetOptionsParser::clear_cdr_set_exclude_options ( std::string const &  type )

private

References cdr_options_.

Referenced by set_cdr_set_exclude_options().

void protocols::antibody::CDRSetOptionsParser::clear_cdr_set_include_options ( std::string const &  type )

private

References cdr_options_.

Referenced by set_cdr_set_include_options().

CDRSetOptionsParserOP protocols::antibody::CDRSetOptionsParser::clone

(

)

const

void protocols::antibody::CDRSetOptionsParser::parse_cdr_option ( std::string const &  mode, utility::vector1< std::string > const &  lineSP  )

private

References check_line_len(), and parse_cdr_set_option().

Referenced by parse_options().

void protocols::antibody::CDRSetOptionsParser::parse_cdr_set_option ( std::string const &  adjective, utility::vector1< std::string > const &  lineSP  )

private

References cdr_options_, check_line_len(), set_cdr_set_exclude_options(), set_cdr_set_general_option(), and set_cdr_set_include_options().

Referenced by parse_cdr_option().

CDRSetOptionsOP protocols::antibody::CDRSetOptionsParser::parse_default_and_user_options	(	CDRNameEnum	cdr,
		std::string const &	filename
	)

Parse default instructions (mainly used for AbDesign) then parse user file.

References cdr_options_, default_and_user_, parse_options(), and protocols::hybridization::path.

Referenced by protocols::antibody::design::get_cdr_set_options(), and parse_default_and_user_options().

utility::vector1< CDRSetOptionsOP > protocols::antibody::CDRSetOptionsParser::parse_default_and_user_options

(

std::string const &

filename

)

References protocols::antibody::CDRNameEnum_proto_total, and parse_default_and_user_options().

CDRSetOptionsOP protocols::antibody::CDRSetOptionsParser::parse_options	(	CDRNameEnum	cdr,
		std::string const &	filename
	)

References ab_manager_, cdr_options_, check_line_len(), check_path(), default_and_user_, protocols::antibody::h4, instructions_path_, protocols::antibody::l4, parse_cdr_option(), and protocols::hybridization::path.

Referenced by protocols::antibody::design::get_cdr_set_options(), parse_default_and_user_options(), and parse_options().

utility::vector1< CDRSetOptionsOP > protocols::antibody::CDRSetOptionsParser::parse_options

(

std::string const &

filename

)

References protocols::antibody::CDRNameEnum_proto_total, and parse_options().

void protocols::antibody::CDRSetOptionsParser::set_cdr_set_exclude_options ( std::string const &  type, utility::vector1< std::string > const &  lineSP  )

private

References cdr_options_, clear_cdr_set_exclude_options(), and cluster_manager_.

Referenced by parse_cdr_set_option().

void protocols::antibody::CDRSetOptionsParser::set_cdr_set_general_option ( std::string const &  option )

private

References cdr_options_.

Referenced by parse_cdr_set_option().

void protocols::antibody::CDRSetOptionsParser::set_cdr_set_include_options ( std::string const &  type, utility::vector1< std::string > const &  lineSP  )

private

References cdr_options_, clear_cdr_set_include_options(), cluster_manager_, and protocols::antibody::TR().

Referenced by parse_cdr_set_option().

void protocols::antibody::CDRSetOptionsParser::set_cdr_set_mintype_options ( std::string const &  mintype )

private

Member Data Documentation

AntibodyEnumManagerCOP protocols::antibody::CDRSetOptionsParser::ab_manager_

private

Referenced by CDRSetOptionsParser(), and parse_options().

CDRSetOptionsOP protocols::antibody::CDRSetOptionsParser::cdr_options_

private

Referenced by CDRSetOptionsParser(), clear_cdr_set_exclude_options(), clear_cdr_set_include_options(), parse_cdr_set_option(), parse_default_and_user_options(), parse_options(), set_cdr_set_exclude_options(), set_cdr_set_general_option(), and set_cdr_set_include_options().

clusters::CDRClusterEnumManagerCOP protocols::antibody::CDRSetOptionsParser::cluster_manager_

private

Referenced by CDRSetOptionsParser(), set_cdr_set_exclude_options(), and set_cdr_set_include_options().

bool protocols::antibody::CDRSetOptionsParser::default_and_user_

private

Referenced by parse_default_and_user_options(), and parse_options().

std::string protocols::antibody::CDRSetOptionsParser::instructions_path_

private

Referenced by check_path(), and parse_options().

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

• src/protocols/antibody/database/CDRSetOptionsParser.hh
• src/protocols/antibody/database/CDRSetOptionsParser.cc