#include <CDRGraftDesignOptions.hh>
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
◆ CDRGraftDesignOptionsParser() [1/2]
| protocols::antibody::design::CDRGraftDesignOptionsParser::CDRGraftDesignOptionsParser | ( | ) |
References ab_manager_.
◆ ~CDRGraftDesignOptionsParser()
|
overridedefault |
◆ CDRGraftDesignOptionsParser() [2/2]
| protocols::antibody::design::CDRGraftDesignOptionsParser::CDRGraftDesignOptionsParser | ( | CDRGraftDesignOptionsParser const & | src | ) |
References ab_manager_, and cdr_options_.
Member Function Documentation
◆ check_line_len()
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private |
References core::id::to_string().
Referenced by parse_cdr_general_option(), parse_cdr_graft_option(), parse_cdr_option(), and parse_options().
◆ check_path()
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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().
◆ clone()
| CDRGraftDesignOptionsParserOP protocols::antibody::design::CDRGraftDesignOptionsParser::clone | ( | ) | const |
◆ parse_cdr_general_option()
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private |
References check_line_len(), and set_cdr_graft_general_option().
Referenced by parse_cdr_option().
◆ parse_cdr_graft_option()
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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().
◆ parse_cdr_option()
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private |
References cdr_options_, check_line_len(), parse_cdr_general_option(), and parse_cdr_graft_option().
Referenced by parse_options().
◆ parse_default_and_user_options() [1/2]
| 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_, protocols::abinitio::filename(), parse_options(), and protocols::hybridization::path.
Referenced by protocols::antibody::design::get_graft_design_options(), and parse_default_and_user_options().
◆ parse_default_and_user_options() [2/2]
| utility::vector1< CDRGraftDesignOptionsOP > protocols::antibody::design::CDRGraftDesignOptionsParser::parse_default_and_user_options | ( | std::string const & | filename | ) |
References protocols::abinitio::filename(), and parse_default_and_user_options().
◆ parse_options() [1/2]
| 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().
◆ parse_options() [2/2]
| utility::vector1< CDRGraftDesignOptionsOP > protocols::antibody::design::CDRGraftDesignOptionsParser::parse_options | ( | std::string const & | filename | ) |
References protocols::abinitio::filename(), and parse_options().
◆ set_cdr_graft_general_option()
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private |
References cdr_options_.
Referenced by parse_cdr_general_option(), and parse_cdr_graft_option().
◆ set_cdr_graft_mintype_options()
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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().
◆ set_cdr_graft_neighbor_mintype_options()
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private |
References ab_manager_, and cdr_options_.
Referenced by parse_cdr_graft_option().
Member Data Documentation
◆ ab_manager_
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private |
Referenced by CDRGraftDesignOptionsParser(), parse_options(), and set_cdr_graft_neighbor_mintype_options().
◆ cdr_options_
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private |
◆ default_and_user_
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private |
Referenced by parse_default_and_user_options(), and parse_options().
◆ instructions_path_
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private |
Referenced by check_path(), and parse_options().
The documentation for this class was generated from the following files:
- src/protocols/antibody/design/CDRGraftDesignOptions.hh
- src/protocols/antibody/design/CDRGraftDesignOptions.cc
