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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:
Inheritance graph
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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< CDRSetOptionsOPparse_options (std::string const &filename)
 
utility::vector1< CDRSetOptionsOPparse_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)

Member Function Documentation

void protocols::antibody::CDRSetOptionsParser::check_line_len ( const utility::vector1< std::string > &  lineSP,
const core::Size  len_check 
) const
private
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
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)
CDRSetOptionsOP protocols::antibody::CDRSetOptionsParser::parse_options ( CDRNameEnum  cdr,
std::string const &  filename 
)
utility::vector1< CDRSetOptionsOP > protocols::antibody::CDRSetOptionsParser::parse_options ( std::string const &  filename)
void protocols::antibody::CDRSetOptionsParser::set_cdr_set_exclude_options ( std::string const &  type,
utility::vector1< std::string > const &  lineSP 
)
private
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
void protocols::antibody::CDRSetOptionsParser::set_cdr_set_mintype_options ( std::string const &  mintype)
private

Member Data Documentation

AntibodyEnumManagerCOP protocols::antibody::CDRSetOptionsParser::ab_manager_
private
CDRSetOptionsOP protocols::antibody::CDRSetOptionsParser::cdr_options_
private
clusters::CDRClusterEnumManagerCOP protocols::antibody::CDRSetOptionsParser::cluster_manager_
private
bool protocols::antibody::CDRSetOptionsParser::default_and_user_
private
std::string protocols::antibody::CDRSetOptionsParser::instructions_path_
private

Referenced by check_path(), and parse_options().


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