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

#include <CDRSeqDesignOptions.hh>

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

protocols::antibody::design::CDRSeqDesignOptionsParser::CDRSeqDesignOptionsParser ( )
protocols::antibody::design::CDRSeqDesignOptionsParser::~CDRSeqDesignOptionsParser ( )
overridedefault
protocols::antibody::design::CDRSeqDesignOptionsParser::CDRSeqDesignOptionsParser ( CDRSeqDesignOptionsParser const &  src)

Member Function Documentation

void protocols::antibody::design::CDRSeqDesignOptionsParser::check_line_len ( utility::vector1< std::string > const &  lineSP,
core::Size  len_check 
) const
private
void protocols::antibody::design::CDRSeqDesignOptionsParser::check_path ( )
private
CDRSeqDesignOptionsParserOP protocols::antibody::design::CDRSeqDesignOptionsParser::clone ( ) const
void protocols::antibody::design::CDRSeqDesignOptionsParser::parse_cdr_design_option ( std::string const &  adjective,
utility::vector1< std::string > const &  lineSP 
)
private
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().

void protocols::antibody::design::CDRSeqDesignOptionsParser::parse_cdr_option ( std::string const &  mode,
utility::vector1< std::string > const &  lineSP 
)
private
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_, parse_options(), and protocols::hybridization::path.

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

utility::vector1< CDRSeqDesignOptionsOP > protocols::antibody::design::CDRSeqDesignOptionsParser::parse_default_and_user_options ( std::string const &  filename)
CDRSeqDesignOptionsOP protocols::antibody::design::CDRSeqDesignOptionsParser::parse_options ( CDRNameEnum  cdr,
std::string const &  filename 
)
utility::vector1< CDRSeqDesignOptionsOP > protocols::antibody::design::CDRSeqDesignOptionsParser::parse_options ( std::string const &  filename)

ALL CDRs.

References parse_options().

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

Member Data Documentation

AntibodyEnumManagerCOP protocols::antibody::design::CDRSeqDesignOptionsParser::ab_manager_
private
CDRSeqDesignOptionsOP protocols::antibody::design::CDRSeqDesignOptionsParser::cdr_options_
private
bool protocols::antibody::design::CDRSeqDesignOptionsParser::default_and_user_
private
AntibodyDesignEnumManagerCOP protocols::antibody::design::CDRSeqDesignOptionsParser::design_enum_manager_
private
std::string protocols::antibody::design::CDRSeqDesignOptionsParser::instructions_path_
private

Referenced by check_path(), and parse_options().


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