protocols::antibody::design::CDRGraftDesignOptionsParser Class Reference

#include <CDRGraftDesignOptions.hh>

Inheritance diagram for protocols::antibody::design::CDRGraftDesignOptionsParser:

Public Member Functions
	CDRGraftDesignOptionsParser ()
	~CDRGraftDesignOptionsParser () override
	CDRGraftDesignOptionsParser (CDRGraftDesignOptionsParser const &src)
CDRGraftDesignOptionsParserOP	clone () const
CDRGraftDesignOptionsOP	parse_options (CDRNameEnum cdr, std::string const &filename)
CDRGraftDesignOptionsOP	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 < CDRGraftDesignOptionsOP >	parse_options (std::string const &filename)
utility::vector1 < CDRGraftDesignOptionsOP >	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_graft_option (std::string const &adjective, utility::vector1< std::string > const &lineSP)
void	parse_cdr_general_option (utility::vector1< std::string > const &lineSP)
void	set_cdr_graft_mintype_options (std::string const &mintype)
void	set_cdr_graft_neighbor_mintype_options (utility::vector1< std::string > const &lineSP)
void	set_cdr_graft_general_option (std::string const &option)

Private Attributes
std::string	instructions_path_
AntibodyEnumManagerOP	ab_manager_
CDRGraftDesignOptionsOP	cdr_options_
bool	default_and_user_

Constructor & Destructor Documentation

protocols::antibody::design::CDRGraftDesignOptionsParser::CDRGraftDesignOptionsParser

(

)

References ab_manager_.

protocols::antibody::design::CDRGraftDesignOptionsParser::~CDRGraftDesignOptionsParser ( )

overridedefault

protocols::antibody::design::CDRGraftDesignOptionsParser::CDRGraftDesignOptionsParser

(

CDRGraftDesignOptionsParser const &

src

)

References ab_manager_, and cdr_options_.

Member Function Documentation

void protocols::antibody::design::CDRGraftDesignOptionsParser::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_general_option(), parse_cdr_graft_option(), parse_cdr_option(), and parse_options().

void protocols::antibody::design::CDRGraftDesignOptionsParser::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().

CDRGraftDesignOptionsParserOP protocols::antibody::design::CDRGraftDesignOptionsParser::clone

(

)

const

void protocols::antibody::design::CDRGraftDesignOptionsParser::parse_cdr_general_option ( utility::vector1< std::string > const &  lineSP )

private

References check_line_len(), and set_cdr_graft_general_option().

Referenced by parse_cdr_option().

void protocols::antibody::design::CDRGraftDesignOptionsParser::parse_cdr_graft_option ( std::string const &  adjective, utility::vector1< std::string > const &  lineSP  )

private

References cdr_options_, check_line_len(), set_cdr_graft_general_option(), set_cdr_graft_mintype_options(), and set_cdr_graft_neighbor_mintype_options().

Referenced by parse_cdr_option().

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

private

References cdr_options_, check_line_len(), parse_cdr_general_option(), and parse_cdr_graft_option().

Referenced by parse_options().

CDRGraftDesignOptionsOP protocols::antibody::design::CDRGraftDesignOptionsParser::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_graft_design_options(), and parse_default_and_user_options().

utility::vector1< CDRGraftDesignOptionsOP > protocols::antibody::design::CDRGraftDesignOptionsParser::parse_default_and_user_options

(

std::string const &

filename

)

References parse_default_and_user_options().

CDRGraftDesignOptionsOP protocols::antibody::design::CDRGraftDesignOptionsParser::parse_options	(	CDRNameEnum	cdr,
		std::string const &	filename
	)

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

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

utility::vector1< CDRGraftDesignOptionsOP > protocols::antibody::design::CDRGraftDesignOptionsParser::parse_options

(

std::string const &

filename

)

References parse_options().

void protocols::antibody::design::CDRGraftDesignOptionsParser::set_cdr_graft_general_option ( std::string const &  option )

private

References cdr_options_.

Referenced by parse_cdr_general_option(), and parse_cdr_graft_option().

void protocols::antibody::design::CDRGraftDesignOptionsParser::set_cdr_graft_mintype_options ( std::string const &  mintype )

private

References protocols::antibody::design::backrub_protocol, cdr_options_, protocols::antibody::design::dualspace, protocols::antibody::design::minimize, protocols::antibody::design::minimize_cartesian, protocols::antibody::design::no_min, protocols::antibody::design::relax, and protocols::antibody::design::repack.

Referenced by parse_cdr_graft_option().

void protocols::antibody::design::CDRGraftDesignOptionsParser::set_cdr_graft_neighbor_mintype_options ( utility::vector1< std::string > const &  lineSP )

private

References ab_manager_, and cdr_options_.

Referenced by parse_cdr_graft_option().

Member Data Documentation

AntibodyEnumManagerOP protocols::antibody::design::CDRGraftDesignOptionsParser::ab_manager_

private

Referenced by CDRGraftDesignOptionsParser(), parse_options(), and set_cdr_graft_neighbor_mintype_options().

CDRGraftDesignOptionsOP protocols::antibody::design::CDRGraftDesignOptionsParser::cdr_options_

private

Referenced by CDRGraftDesignOptionsParser(), parse_cdr_graft_option(), parse_cdr_option(), parse_default_and_user_options(), parse_options(), set_cdr_graft_general_option(), set_cdr_graft_mintype_options(), and set_cdr_graft_neighbor_mintype_options().

bool protocols::antibody::design::CDRGraftDesignOptionsParser::default_and_user_

private

Referenced by parse_default_and_user_options(), and parse_options().

std::string protocols::antibody::design::CDRGraftDesignOptionsParser::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/design/CDRGraftDesignOptions.hh
• src/protocols/antibody/design/CDRGraftDesignOptions.cc