protocols::antibody::design::CDRSeqDesignOptionsParser Class Reference

#include <CDRSeqDesignOptions.hh>

Inheritance diagram for protocols::antibody::design::CDRSeqDesignOptionsParser:

Public Member Functions
	CDRSeqDesignOptionsParser ()
	~CDRSeqDesignOptionsParser () override
	CDRSeqDesignOptionsParser (CDRSeqDesignOptionsParser const &src)
CDRSeqDesignOptionsParserOP	clone () const
CDRSeqDesignOptionsOP	parse_options (CDRNameEnum cdr, std::string const &filename)
CDRSeqDesignOptionsOP	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< CDRSeqDesignOptionsOP >	parse_options (std::string const &filename)
	ALL CDRs. More...
utility::vector1< CDRSeqDesignOptionsOP >	parse_default_and_user_options (std::string const &filename)

Private Member Functions
void	check_path ()
void	check_line_len (utility::vector1< std::string > const &lineSP, core::Size len_check) const
void	parse_cdr_option (std::string const &mode, utility::vector1< std::string > const &lineSP)
void	parse_cdr_design_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_design_primary_option (std::string const &option)
void	set_cdr_design_fallback_option (std::string const &option)
void	set_disallow_amino_acids (utility::vector1< std::string > const &lineSP)

Private Attributes
std::string	instructions_path_
AntibodyEnumManagerCOP	ab_manager_
AntibodyDesignEnumManagerCOP	design_enum_manager_
CDRSeqDesignOptionsOP	cdr_options_
bool	default_and_user_

Constructor & Destructor Documentation

CDRSeqDesignOptionsParser() [1/2]

protocols::antibody::design::CDRSeqDesignOptionsParser::CDRSeqDesignOptionsParser

(

)

References ab_manager_, and design_enum_manager_.

~CDRSeqDesignOptionsParser()

protocols::antibody::design::CDRSeqDesignOptionsParser::~CDRSeqDesignOptionsParser ( )

overridedefault

CDRSeqDesignOptionsParser() [2/2]

protocols::antibody::design::CDRSeqDesignOptionsParser::CDRSeqDesignOptionsParser

(

CDRSeqDesignOptionsParser const &

src

)

References ab_manager_, cdr_options_, and design_enum_manager_.

Member Function Documentation

check_line_len()

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

private

References core::id::to_string().

Referenced by parse_cdr_design_option(), parse_cdr_general_option(), parse_cdr_option(), and parse_options().

check_path()

void protocols::antibody::design::CDRSeqDesignOptionsParser::check_path ( )

private

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

Referenced by parse_options().

clone()

CDRSeqDesignOptionsParserOP protocols::antibody::design::CDRSeqDesignOptionsParser::clone

(

)

const

parse_cdr_design_option()

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

private

References cdr_options_, check_line_len(), set_cdr_design_fallback_option(), set_cdr_design_primary_option(), and set_disallow_amino_acids().

Referenced by parse_cdr_option().

parse_cdr_general_option()

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

private

References cdr_options_, and check_line_len().

Referenced by parse_cdr_option().

parse_cdr_option()

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

private

References check_line_len(), parse_cdr_design_option(), and parse_cdr_general_option().

Referenced by parse_options().

parse_default_and_user_options() [1/2]

CDRSeqDesignOptionsOP protocols::antibody::design::CDRSeqDesignOptionsParser::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_, protocols::abinitio::filename(), parse_options(), and protocols::hybridization::path.

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

parse_default_and_user_options() [2/2]

utility::vector1< CDRSeqDesignOptionsOP > protocols::antibody::design::CDRSeqDesignOptionsParser::parse_default_and_user_options

(

std::string const &

filename

)

References protocols::abinitio::filename(), and parse_default_and_user_options().

parse_options() [1/2]

CDRSeqDesignOptionsOP protocols::antibody::design::CDRSeqDesignOptionsParser::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_seq_design_options(), parse_default_and_user_options(), and parse_options().

parse_options() [2/2]

utility::vector1< CDRSeqDesignOptionsOP > protocols::antibody::design::CDRSeqDesignOptionsParser::parse_options

(

std::string const &

filename

)

ALL CDRs.

References protocols::abinitio::filename(), and parse_options().

set_cdr_design_fallback_option()

void protocols::antibody::design::CDRSeqDesignOptionsParser::set_cdr_design_fallback_option ( std::string const &  option )

private

References cdr_options_, design_enum_manager_, protocols::antibody::design::seq_design_profile_sets, protocols::antibody::design::seq_design_profile_sets_combined, and protocols::antibody::design::seq_design_profiles.

Referenced by parse_cdr_design_option().

set_cdr_design_primary_option()

void protocols::antibody::design::CDRSeqDesignOptionsParser::set_cdr_design_primary_option ( std::string const &  option )

private

References cdr_options_, design_enum_manager_, protocols::antibody::h4, protocols::antibody::l4, protocols::antibody::design::seq_design_profile_sets, protocols::antibody::design::seq_design_profile_sets_combined, and protocols::antibody::design::seq_design_profiles.

Referenced by parse_cdr_design_option().

set_disallow_amino_acids()

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

private

References core::chemical::aa_from_one_or_three(), and cdr_options_.

Referenced by parse_cdr_design_option().

Member Data Documentation

ab_manager_

AntibodyEnumManagerCOP protocols::antibody::design::CDRSeqDesignOptionsParser::ab_manager_

private

Referenced by CDRSeqDesignOptionsParser(), and parse_options().

cdr_options_

CDRSeqDesignOptionsOP protocols::antibody::design::CDRSeqDesignOptionsParser::cdr_options_

private

Referenced by CDRSeqDesignOptionsParser(), parse_cdr_design_option(), parse_cdr_general_option(), parse_default_and_user_options(), parse_options(), set_cdr_design_fallback_option(), set_cdr_design_primary_option(), and set_disallow_amino_acids().

default_and_user_

bool protocols::antibody::design::CDRSeqDesignOptionsParser::default_and_user_

private

Referenced by parse_default_and_user_options(), and parse_options().

design_enum_manager_

AntibodyDesignEnumManagerCOP protocols::antibody::design::CDRSeqDesignOptionsParser::design_enum_manager_

private

Referenced by CDRSeqDesignOptionsParser(), set_cdr_design_fallback_option(), and set_cdr_design_primary_option().

instructions_path_

std::string protocols::antibody::design::CDRSeqDesignOptionsParser::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/CDRSeqDesignOptions.hh
• src/protocols/antibody/design/CDRSeqDesignOptions.cc