| add(BooleanOptionKey const &key, std::string const &description) | utility::options::OptionCollection | inline |
| add(IntegerOptionKey const &key, std::string const &description) | utility::options::OptionCollection | inline |
| add(RealOptionKey const &key, std::string const &description) | utility::options::OptionCollection | inline |
| add(StringOptionKey const &key, std::string const &description) | utility::options::OptionCollection | inline |
| add(FileOptionKey const &key, std::string const &description) | utility::options::OptionCollection | inline |
| add(PathOptionKey const &key, std::string const &description) | utility::options::OptionCollection | inline |
| add(BooleanVectorOptionKey const &key, std::string const &description) | utility::options::OptionCollection | inline |
| add(IntegerVectorOptionKey const &key, std::string const &description) | utility::options::OptionCollection | inline |
| add(RealVectorOptionKey const &key, std::string const &description) | utility::options::OptionCollection | inline |
| add(ResidueChainVectorOptionKey const &key, std::string const &description) | utility::options::OptionCollection | inline |
| add(StringVectorOptionKey const &key, std::string const &description) | utility::options::OptionCollection | inline |
| add(FileVectorOptionKey const &key, std::string const &description) | utility::options::OptionCollection | inline |
| add(PathVectorOptionKey const &key, std::string const &description) | utility::options::OptionCollection | inline |
| add(BooleanOption const &opt) | utility::options::OptionCollection | inline |
| add(IntegerOption const &opt) | utility::options::OptionCollection | inline |
| add(RealOption const &opt) | utility::options::OptionCollection | inline |
| add(StringOption const &opt) | utility::options::OptionCollection | inline |
| add(FileOption const &opt) | utility::options::OptionCollection | inline |
| add(PathOption const &opt) | utility::options::OptionCollection | inline |
| add(AnyOption< T > const &opt) | utility::options::OptionCollection | inline |
| add(BooleanVectorOption const &opt) | utility::options::OptionCollection | inline |
| add(IntegerVectorOption const &opt) | utility::options::OptionCollection | inline |
| add(RealVectorOption const &opt) | utility::options::OptionCollection | inline |
| add(ResidueChainVectorOption const &opt) | utility::options::OptionCollection | inline |
| add(StringVectorOption const &opt) | utility::options::OptionCollection | inline |
| add(FileVectorOption const &opt) | utility::options::OptionCollection | inline |
| add(PathVectorOption const &opt) | utility::options::OptionCollection | inline |
| add(AnyVectorOption< T > const &opt) | utility::options::OptionCollection | inline |
| add_built_in_options() | utility::options::OptionCollection | |
| add_edits(std::set< std::string > &items) | utility::options::OptionCollection | static |
| add_relevant(const OptionKey &key) | utility::options::OptionCollection | inline |
| All typedef | utility::options::OptionCollection | private |
| all_ | utility::options::OptionCollection | private |
| any_vectors_ | utility::options::OptionCollection | private |
| Anys typedef | utility::options::OptionCollection | private |
| anys_ | utility::options::OptionCollection | private |
| AnyVectors typedef | utility::options::OptionCollection | private |
| argv_copy_ | utility::options::OptionCollection | private |
| boolean_vectors_ | utility::options::OptionCollection | private |
| Booleans typedef | utility::options::OptionCollection | private |
| booleans_ | utility::options::OptionCollection | private |
| BooleanVectors typedef | utility::options::OptionCollection | private |
| check_key(OptionKey const &key) | utility::options::OptionCollection | static |
| check_key(Option const &option) | utility::options::OptionCollection | static |
| check_specs() const | utility::options::OptionCollection | |
| check_values() const | utility::options::OptionCollection | |
| cleaned(std::string const &s) | utility::options::OptionCollection | static |
| clone() const | utility::options::OptionCollection | inline |
| file_vectors_ | utility::options::OptionCollection | private |
| Files typedef | utility::options::OptionCollection | private |
| files_ | utility::options::OptionCollection | private |
| FileVectors typedef | utility::options::OptionCollection | private |
| find_key_cl(std::string const &key_string, std::string const &cid, bool const top) | utility::options::OptionCollection | |
| find_key_file(std::string const &key_string, std::string const &cid, bool const top) | utility::options::OptionCollection | static |
| get_argv() const | utility::options::OptionCollection | |
| has(BooleanOptionKey const &key) const | utility::options::OptionCollection | inline |
| has(IntegerOptionKey const &key) const | utility::options::OptionCollection | inline |
| has(RealOptionKey const &key) const | utility::options::OptionCollection | inline |
| has(StringOptionKey const &key) const | utility::options::OptionCollection | inline |
| has(FileOptionKey const &key) const | utility::options::OptionCollection | inline |
| has(PathOptionKey const &key) const | utility::options::OptionCollection | inline |
| has(AnyOptionKey const &key) const | utility::options::OptionCollection | inline |
| has(BooleanVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| has(IntegerVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| has(RealVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| has(ResidueChainVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| has(StringVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| has(FileVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| has(PathVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| has(AnyVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| has(OptionKey const &key) const | utility::options::OptionCollection | inline |
| integer_vectors_ | utility::options::OptionCollection | private |
| Integers typedef | utility::options::OptionCollection | private |
| integers_ | utility::options::OptionCollection | private |
| IntegerVectors typedef | utility::options::OptionCollection | private |
| is_relevant(OptionKey const &key) | utility::options::OptionCollection | |
| load(const std::vector< std::string > &args, bool const free_args) | utility::options::OptionCollection | |
| load(int const argc, char *const argv[], bool const free_args=false) | utility::options::OptionCollection | |
| load(std::string executable_name, ValueStrings &arg_strings, bool const free_args) | utility::options::OptionCollection | |
| load_option_cl(std::string const &arg_string, ValueStrings &arg_strings, std::string const &pid) | utility::options::OptionCollection | private |
| load_option_file(std::string const &arg_string, ValueStrings &val_strings, std::string &cid, bool const cl_context=false) | utility::options::OptionCollection | private |
| load_option_from_file(std::string const &arg_string, ValueStrings &arg_strings, std::string const &pid) | utility::options::OptionCollection | private |
| load_options_from_file(std::string const &file_string, std::string const &cid="") | utility::options::OptionCollection | |
| load_options_from_file_exception(std::string const &file_string, std::string const &cid="") | utility::options::OptionCollection | |
| load_options_from_stream(std::istream &stream, std::string const &file_string="STREAM", std::string const &cid="", bool print_lines=false) | utility::options::OptionCollection | |
| lower_no_under(std::string const &instring) | utility::options::OptionCollection | static |
| merged(std::string const &s, std::string const &t) | utility::options::OptionCollection | static |
| n_part(std::string const &s) | utility::options::OptionCollection | static |
| n_part_prefix_match(std::string const &s, std::string const &t) | utility::options::OptionCollection | static |
| operator()(BooleanOptionKey const &key, bool check_restricted_access=true) const | utility::options::OptionCollection | inline |
| operator()(BooleanOptionKey const &key, bool check_restricted_access=true) | utility::options::OptionCollection | inline |
| operator()(IntegerOptionKey const &key, bool check_restricted_access=true) const | utility::options::OptionCollection | inline |
| operator()(IntegerOptionKey const &key, bool check_restricted_access=true) | utility::options::OptionCollection | inline |
| operator()(RealOptionKey const &key, bool check_restricted_access=true) const | utility::options::OptionCollection | inline |
| operator()(RealOptionKey const &key, bool check_restricted_access=true) | utility::options::OptionCollection | inline |
| operator()(StringOptionKey const &key, bool check_restricted_access=true) const | utility::options::OptionCollection | inline |
| operator()(StringOptionKey const &key, bool check_restricted_access=true) | utility::options::OptionCollection | inline |
| operator()(FileOptionKey const &key, bool check_restricted_access=true) const | utility::options::OptionCollection | inline |
| operator()(FileOptionKey const &key, bool check_restricted_access=true) | utility::options::OptionCollection | inline |
| operator()(PathOptionKey const &key, bool check_restricted_access=true) const | utility::options::OptionCollection | inline |
| operator()(PathOptionKey const &key, bool check_restricted_access=true) | utility::options::OptionCollection | inline |
| operator()(AnyOptionKey const &key, bool check_restricted_access=true) const | utility::options::OptionCollection | inline |
| operator()(AnyOptionKey const &key, bool check_restricted_access=true) | utility::options::OptionCollection | inline |
| operator()(AnyOptionKey const &key, bool check_restricted_access=true) const | utility::options::OptionCollection | inline |
| operator()(AnyOptionKey const &key, bool check_restricted_access=true) | utility::options::OptionCollection | inline |
| operator()(BooleanVectorOptionKey const &key, bool check_restricted_access=true) const | utility::options::OptionCollection | inline |
| operator()(BooleanVectorOptionKey const &key, bool check_restricted_access=true) | utility::options::OptionCollection | inline |
| operator()(IntegerVectorOptionKey const &key, bool check_restricted_access=true) const | utility::options::OptionCollection | inline |
| operator()(IntegerVectorOptionKey const &key, bool check_restricted_access=true) | utility::options::OptionCollection | inline |
| operator()(RealVectorOptionKey const &key, bool check_restricted_access=true) const | utility::options::OptionCollection | inline |
| operator()(RealVectorOptionKey const &key, bool check_restricted_access=true) | utility::options::OptionCollection | inline |
| operator()(ResidueChainVectorOptionKey const &key, bool check_restricted_access=true) const | utility::options::OptionCollection | inline |
| operator()(ResidueChainVectorOptionKey const &key, bool check_restricted_access=true) | utility::options::OptionCollection | inline |
| operator()(StringVectorOptionKey const &key, bool check_restricted_access=true) const | utility::options::OptionCollection | inline |
| operator()(StringVectorOptionKey const &key, bool check_restricted_access=true) | utility::options::OptionCollection | inline |
| operator()(FileVectorOptionKey const &key, bool check_restricted_access=true) const | utility::options::OptionCollection | inline |
| operator()(FileVectorOptionKey const &key, bool check_restricted_access=true) | utility::options::OptionCollection | inline |
| operator()(PathVectorOptionKey const &key, bool check_restricted_access=true) const | utility::options::OptionCollection | inline |
| operator()(PathVectorOptionKey const &key, bool check_restricted_access=true) | utility::options::OptionCollection | inline |
| operator()(AnyVectorOptionKey const &key, bool check_restricted_access=true) const | utility::options::OptionCollection | inline |
| operator()(AnyVectorOptionKey const &key, bool check_restricted_access=true) | utility::options::OptionCollection | inline |
| operator()(AnyVectorOptionKey const &key, bool check_restricted_access=true) const | utility::options::OptionCollection | inline |
| operator()(AnyVectorOptionKey const &key, bool check_restricted_access=true) | utility::options::OptionCollection | inline |
| operator()(OptionKey const &key, bool check_restricted_access=true) const | utility::options::OptionCollection | inline |
| operator()(OptionKey const &key, bool check_restricted_access=true) | utility::options::OptionCollection | inline |
| operator()(OptionKey const &key, bool check_restricted_access=true) const | utility::options::OptionCollection | inline |
| operator()(OptionKey const &key, bool check_restricted_access=true) | utility::options::OptionCollection | inline |
| operator<<(std::ostream &stream, OptionCollection const &options) | utility::options::OptionCollection | friend |
| operator=(OptionCollection const &src) | utility::options::OptionCollection | |
| utility::VirtualBase::operator=(VirtualBase const &)=default | utility::VirtualBase | |
| utility::VirtualBase::operator=(VirtualBase &&)=default | utility::VirtualBase | |
| operator[](BooleanOptionKey const &key) const | utility::options::OptionCollection | inline |
| operator[](BooleanOptionKey const &key) | utility::options::OptionCollection | inline |
| operator[](IntegerOptionKey const &key) const | utility::options::OptionCollection | inline |
| operator[](IntegerOptionKey const &key) | utility::options::OptionCollection | inline |
| operator[](RealOptionKey const &key) const | utility::options::OptionCollection | inline |
| operator[](RealOptionKey const &key) | utility::options::OptionCollection | inline |
| operator[](StringOptionKey const &key) const | utility::options::OptionCollection | inline |
| operator[](StringOptionKey const &key) | utility::options::OptionCollection | inline |
| operator[](FileOptionKey const &key) const | utility::options::OptionCollection | inline |
| operator[](FileOptionKey const &key) | utility::options::OptionCollection | inline |
| operator[](PathOptionKey const &key) const | utility::options::OptionCollection | inline |
| operator[](PathOptionKey const &key) | utility::options::OptionCollection | inline |
| operator[](AnyOptionKey const &key) const | utility::options::OptionCollection | inline |
| operator[](AnyOptionKey const &key) | utility::options::OptionCollection | inline |
| operator[](AnyOptionKey const &key) const | utility::options::OptionCollection | inline |
| operator[](AnyOptionKey const &key) | utility::options::OptionCollection | inline |
| operator[](BooleanVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| operator[](BooleanVectorOptionKey const &key) | utility::options::OptionCollection | inline |
| operator[](IntegerVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| operator[](IntegerVectorOptionKey const &key) | utility::options::OptionCollection | inline |
| operator[](RealVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| operator[](RealVectorOptionKey const &key) | utility::options::OptionCollection | inline |
| operator[](ResidueChainVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| operator[](ResidueChainVectorOptionKey const &key) | utility::options::OptionCollection | inline |
| operator[](StringVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| operator[](StringVectorOptionKey const &key) | utility::options::OptionCollection | inline |
| operator[](FileVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| operator[](FileVectorOptionKey const &key) | utility::options::OptionCollection | inline |
| operator[](PathVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| operator[](PathVectorOptionKey const &key) | utility::options::OptionCollection | inline |
| operator[](AnyVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| operator[](AnyVectorOptionKey const &key) | utility::options::OptionCollection | inline |
| operator[](AnyVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| operator[](AnyVectorOptionKey const &key) | utility::options::OptionCollection | inline |
| operator[](OptionKey const &key) const | utility::options::OptionCollection | inline |
| operator[](OptionKey const &key) | utility::options::OptionCollection | inline |
| operator[](OptionKey const &key) const | utility::options::OptionCollection | inline |
| operator[](OptionKey const &key) | utility::options::OptionCollection | inline |
| option(BooleanOptionKey const &key) const | utility::options::OptionCollection | inline |
| option(BooleanOptionKey const &key) | utility::options::OptionCollection | inline |
| option(IntegerOptionKey const &key) const | utility::options::OptionCollection | inline |
| option(IntegerOptionKey const &key) | utility::options::OptionCollection | inline |
| option(RealOptionKey const &key) const | utility::options::OptionCollection | inline |
| option(RealOptionKey const &key) | utility::options::OptionCollection | inline |
| option(StringOptionKey const &key) const | utility::options::OptionCollection | inline |
| option(StringOptionKey const &key) | utility::options::OptionCollection | inline |
| option(FileOptionKey const &key) const | utility::options::OptionCollection | inline |
| option(FileOptionKey const &key) | utility::options::OptionCollection | inline |
| option(PathOptionKey const &key) const | utility::options::OptionCollection | inline |
| option(PathOptionKey const &key) | utility::options::OptionCollection | inline |
| option(AnyOptionKey const &key) const | utility::options::OptionCollection | inline |
| option(AnyOptionKey const &key) | utility::options::OptionCollection | inline |
| option(AnyOptionKey const &key) const | utility::options::OptionCollection | inline |
| option(AnyOptionKey const &key) | utility::options::OptionCollection | inline |
| option(BooleanVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| option(BooleanVectorOptionKey const &key) | utility::options::OptionCollection | inline |
| option(IntegerVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| option(IntegerVectorOptionKey const &key) | utility::options::OptionCollection | inline |
| option(RealVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| option(RealVectorOptionKey const &key) | utility::options::OptionCollection | inline |
| option(StringVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| option(StringVectorOptionKey const &key) | utility::options::OptionCollection | inline |
| option(FileVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| option(FileVectorOptionKey const &key) | utility::options::OptionCollection | inline |
| option(PathVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| option(PathVectorOptionKey const &key) | utility::options::OptionCollection | inline |
| option(AnyVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| option(AnyVectorOptionKey const &key) | utility::options::OptionCollection | inline |
| option(AnyVectorOptionKey const &key) const | utility::options::OptionCollection | inline |
| option(AnyVectorOptionKey const &key) | utility::options::OptionCollection | inline |
| option(OptionKey const &key) const | utility::options::OptionCollection | inline |
| option(OptionKey const &key) | utility::options::OptionCollection | inline |
| option(OptionKey const &key) const | utility::options::OptionCollection | inline |
| option(OptionKey const &key) | utility::options::OptionCollection | inline |
| OptionCollection() | utility::options::OptionCollection | inline |
| OptionCollection(OptionCollection const &src) | utility::options::OptionCollection | |
| path_vectors_ | utility::options::OptionCollection | private |
| Paths typedef | utility::options::OptionCollection | private |
| paths_ | utility::options::OptionCollection | private |
| PathVectors typedef | utility::options::OptionCollection | private |
| prefix(std::string const &s, int const n=1) | utility::options::OptionCollection | static |
| real_vectors_ | utility::options::OptionCollection | private |
| Reals typedef | utility::options::OptionCollection | private |
| reals_ | utility::options::OptionCollection | private |
| RealVectors typedef | utility::options::OptionCollection | private |
| relevant_ | utility::options::OptionCollection | private |
| residue_chain_vectors_ | utility::options::OptionCollection | private |
| ResidueChainVectors typedef | utility::options::OptionCollection | private |
| set_option_value_cl(std::string const &key_id, ValueStrings &arg_strings) | utility::options::OptionCollection | private |
| set_option_value_file(std::string const &key_id, ValueStrings &val_strings) | utility::options::OptionCollection | private |
| set_show_accessed_options_flag(bool v) | utility::options::OptionCollection | inline |
| set_show_unused_options_flag(bool v) | utility::options::OptionCollection | inline |
| show_accessed_options(std::ostream &stream) const | utility::options::OptionCollection | |
| show_accessed_options_ | utility::options::OptionCollection | private |
| show_all(std::ostream &stream) const | utility::options::OptionCollection | |
| show_all_hier(std::ostream &stream) const | utility::options::OptionCollection | |
| show_help(std::ostream &stream) | utility::options::OptionCollection | |
| show_help_hier(std::ostream &stream) | utility::options::OptionCollection | |
| show_inaccessed_user_options(std::ostream &stream) const | utility::options::OptionCollection | |
| show_option_help(OptionKey const &, std::string &group, std::ostream &stream) | utility::options::OptionCollection | |
| show_option_help_hier(OptionKey const &, std::string &group, std::ostream &stream) | utility::options::OptionCollection | |
| show_table_text(std::ostream &stream) const | utility::options::OptionCollection | |
| show_table_Wiki(std::ostream &stream) const | utility::options::OptionCollection | |
| show_unused_options(std::ostream &stream) const | utility::options::OptionCollection | |
| show_unused_options_ | utility::options::OptionCollection | private |
| show_user(std::ostream &stream) const | utility::options::OptionCollection | |
| space_prefixed(std::string const &s, int const n=1) | utility::options::OptionCollection | inlinestatic |
| string_vectors_ | utility::options::OptionCollection | private |
| Strings typedef | utility::options::OptionCollection | private |
| strings_ | utility::options::OptionCollection | private |
| StringVectors typedef | utility::options::OptionCollection | private |
| suffix(std::string const &s, int const n=1) | utility::options::OptionCollection | static |
| tab_prefixed(std::string const &s, int const n=1) | utility::options::OptionCollection | inlinestatic |
| trim(std::string &s, int const n=1) | utility::options::OptionCollection | static |
| trimmed(std::string const &s, int const n=1) | utility::options::OptionCollection | static |
| ValueStrings typedef | utility::options::OptionCollection | private |
| VirtualBase()=default | utility::VirtualBase | |
| VirtualBase(VirtualBase const &)=default | utility::VirtualBase | |
| VirtualBase(VirtualBase &&)=default | utility::VirtualBase | |
| wrapped(std::string const &s, std::string::size_type indent=10, std::string::size_type width=80, std::string const &header_for_extra_lines="") | utility::options::OptionCollection | static |
| ~OptionCollection() override | utility::options::OptionCollection | |
| ~VirtualBase()=default | utility::VirtualBase | virtual |
