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Rosetta
3.7
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Namespaces | |
OptionKeys | |
Functions | |
OptionKey const & | key (std::string const &str) |
Get key for an option name. More... | |
bool | truefalseoption (std::string const &str) |
bool | truefalseoption (OptionKey const &key) |
double | realafteroption (std::string const &str) |
double | realafteroption (std::string const &str, double const opt_default) |
void | realafteroption (std::string const &str, double const opt_default, double &rnum) |
void | realafteroption (OptionKey const &key, double const opt_default, double &rnum) |
void | real2afteroption (std::string const &str, double const default1, double &rnum1, double const default2, double &rnum2) |
void | real2afteroption (OptionKey const &key, double const default1, double &rnum1, double const default2, double &rnum2) |
void | real3afteroption (std::string const &str, double const default1, double &rnum1, double const default2, double &rnum2, double const default3, double &rnum3) |
void | real3afteroption (OptionKey const &key, double const default1, double &rnum1, double const default2, double &rnum2, double const default3, double &rnum3) |
int | intafteroption (std::string const &str) |
int | intafteroption (std::string const &str, int const opt_default) |
void | intafteroption (std::string const &str, int const opt_default, int &inum) |
void | intafteroption (OptionKey const &key, int const opt_default, int &inum) |
void | optional_positive_intafteroption (std::string const &str, int const opt_default, int &inum) |
void | optional_positive_intafteroption (OptionKey const &key, int const opt_default, int &inum) |
void | int2afteroption (std::string const &str, int const opt_default, int &inum, int const opt_default2, int &inum2) |
void | int2afteroption (OptionKey const &key, int const opt_default, int &inum, int const opt_default2, int &inum2) |
std::string | stringafteroption (std::string const &str) |
std::string | stringafteroption (std::string const &str, std::string const &opt_default) |
void | stringafteroption (std::string const &str, std::string const &opt_default, std::string &cval) |
void | stringafteroption (OptionKey const &key, std::string const &opt_default, std::string &cval) |
void | stringafteroption (std::string const &str, char const opt_default, char &cval) |
void | stringafteroption (OptionKey const &key, char const opt_default, char &cval) |
static THREAD_LOCAL basic::Tracer | TR ("basic.options") |
int const | silent (0) |
Named verbosity levels. More... | |
int const | quiet (1) |
int const | standard (2) |
int const | inform (4) |
int const | chat (6) |
int const | yap (7) |
int const | gush (8) |
int const | verbose (9) |
OptionCollection & | initialize () |
Initialize the options. More... | |
OptionCollection & | process () |
Process the specified options. More... | |
template<typename T , typename K > | |
T | get_option (std::string const &id) |
template<typename T , typename K > | |
void | set_option (std::string const &id, T const &value) |
bool | get_boolean_option (std::string const &id) |
int | get_integer_option (std::string const &id) |
double | get_real_option (std::string const &id) |
std::string | get_string_option (std::string const &id) |
std::string | get_file_option (std::string const &id) |
void | set_boolean_option (std::string const &id, bool v) |
void | set_integer_option (std::string const &id, int v) |
void | set_real_option (std::string const &id, double v) |
void | set_string_option (std::string const &id, std::string const &v) |
void | set_file_option (std::string const &id, std::string const &v) |
utility::vector1< bool > | get_boolean_vector_option (std::string const &id) |
utility::vector1< int > | get_integer_vector_option (std::string const &id) |
utility::vector1< double > | get_real_vector_option (std::string const &id) |
utility::vector1< std::string > | get_string_vector_option (std::string const &id) |
utility::vector1< std::string > | get_file_vector_option (std::string const &id) |
void | set_boolean_vector_option (std::string const &id, utility::vector1< bool > const &v) |
void | set_integer_vector_option (std::string const &id, utility::vector1< int > const &v) |
void | set_real_vector_option (std::string const &id, utility::vector1< double > const &v) |
void | set_string_vector_option (std::string const &id, utility::vector1< std::string > const &v) |
void | set_file_vector_option (std::string const &id, utility::vector1< std::string > const &v) |
std::string | start_file () |
kind of like the old -s – just one file More... | |
utility::vector1< std::string > | start_files () |
void | add_anonymous_option (utility::options::OptionCollection &options, utility::options::OptionKey const &key) |
Add a base-class OptionKey to an OptionCollection by trying to perform a dynamic cast to each of the available option types until the correct derived class is found. More... | |
utility::options::OptionCollectionOP | read_subset_of_global_option_collection (utility::options::OptionKeyList const &opt_keys) |
Create an OptionCollection that knows about only the subset of option keys listed in the input OptionsKeys list. Load this new OptionCollection with the values and the defaults that are stored in the global option collection. More... | |
Variables | |
utility::options::OptionCollection | option |
OptionCollection global. More... | |
int const | silent |
Named verbosity levels. More... | |
int const | quiet |
int const | standard |
int const | inform |
int const | chat |
int const | yap |
int const | gush |
int const | verbose |
void basic::options::add_anonymous_option | ( | utility::options::OptionCollection & | options, |
utility::options::OptionKey const & | key | ||
) |
Add a base-class OptionKey to an OptionCollection by trying to perform a dynamic cast to each of the available option types until the correct derived class is found.
References utility::options::OptionCollection::add(), utility::keys::AutoKey< O, S, C >::id(), and options.
Referenced by read_subset_of_global_option_collection().
int const basic::options::chat | ( | 6 | ) |
bool basic::options::get_boolean_option | ( | std::string const & | id | ) |
utility::vector1< bool > basic::options::get_boolean_vector_option | ( | std::string const & | id | ) |
std::string basic::options::get_file_option | ( | std::string const & | id | ) |
utility::vector1< std::string > basic::options::get_file_vector_option | ( | std::string const & | id | ) |
int basic::options::get_integer_option | ( | std::string const & | id | ) |
utility::vector1< int > basic::options::get_integer_vector_option | ( | std::string const & | id | ) |
T basic::options::get_option | ( | std::string const & | id | ) |
References has, key, option, utility_exit_with_message, and value.
double basic::options::get_real_option | ( | std::string const & | id | ) |
utility::vector1< double > basic::options::get_real_vector_option | ( | std::string const & | id | ) |
std::string basic::options::get_string_option | ( | std::string const & | id | ) |
utility::vector1< std::string > basic::options::get_string_vector_option | ( | std::string const & | id | ) |
int const basic::options::gush | ( | 8 | ) |
int const basic::options::inform | ( | 4 | ) |
OptionCollection & basic::options::initialize | ( | ) |
Initialize the options.
References add_all_rosetta_options(), utility::options::OptionCollection::add_built_in_options(), utility::io::oc::cerr, utility::options::OptionCollection::check_specs(), utility::io::ocstream::flush(), option, and options.
void basic::options::int2afteroption | ( | std::string const & | str, |
int const | opt_default, | ||
int & | inum, | ||
int const | opt_default2, | ||
int & | inum2 | ||
) |
References key().
void basic::options::int2afteroption | ( | OptionKey const & | key, |
int const | opt_default, | ||
int & | inum, | ||
int const | opt_default2, | ||
int & | inum2 | ||
) |
References utility::io::oc::cerr, utility::io::oc::cout, BuildPackagedBindings::format, utility::keys::AutoKey< O, S, C >::id(), option, utility::options::OptionCollection::option(), utility::options::VectorOption_T_< K, T >::size(), ObjexxFCL::format::SS(), basic::options::OptionKeys::inout::dbms::user, and utility_exit.
int basic::options::intafteroption | ( | std::string const & | str | ) |
References utility::io::oc::cout, key(), truefalseoption(), and utility_exit.
Referenced by intafteroption().
References intafteroption(), and key().
References intafteroption(), and key().
OptionKey const& basic::options::key | ( | std::string const & | str | ) |
Get key for an option name.
References utility::options::OptionCollection::find_key_cl().
Referenced by int2afteroption(), intafteroption(), optional_positive_intafteroption(), real2afteroption(), real3afteroption(), realafteroption(), stringafteroption(), and truefalseoption().
void basic::options::optional_positive_intafteroption | ( | std::string const & | str, |
int const | opt_default, | ||
int & | inum | ||
) |
References key().
OptionCollection & basic::options::process | ( | ) |
Process the specified options.
References in::alternate_3_letter_codes(), utility::vectorL< SSize, T, A >::append(), database, basic::options::OptionKeys::in::path::fragments, carbohydrates::glycam_pdb_format(), in::include_sugars(), score::no_pro_close_ring_closure(), option, options, chemical::override_rsd_type_limit(), basic::options::OptionKeys::in::path::path, basic::options::OptionKeys::in::path::pdb, in::preserve_crystinfo(), basic::options::OptionKeys::AnchoredDesign::filters::score, symmetry::symmetry_definition(), TR(), and basic::options::OptionKeys::inout::dbms::user.
int const basic::options::quiet | ( | 1 | ) |
utility::options::OptionCollectionOP basic::options::read_subset_of_global_option_collection | ( | utility::options::OptionKeyList const & | opt_keys | ) |
Create an OptionCollection that knows about only the subset of option keys listed in the input OptionsKeys list. Load this new OptionCollection with the values and the defaults that are stored in the global option collection.
References add_anonymous_option(), debug_assert, utility::options::OptionCollection::has(), basic::options::OptionKeys::mp::mutate_relax::iter, option, options, and app.surface_docking.surface_docking::opts.
void basic::options::real2afteroption | ( | std::string const & | str, |
double const | default1, | ||
double & | rnum1, | ||
double const | default2, | ||
double & | rnum2 | ||
) |
References key().
void basic::options::real2afteroption | ( | OptionKey const & | key, |
double const | default1, | ||
double & | rnum1, | ||
double const | default2, | ||
double & | rnum2 | ||
) |
References utility::io::oc::cerr, utility::io::oc::cout, BuildPackagedBindings::format, utility::keys::AutoKey< O, S, C >::id(), option, utility::options::OptionCollection::option(), utility::options::VectorOption_T_< K, T >::size(), ObjexxFCL::format::SS(), basic::options::OptionKeys::inout::dbms::user, and utility_exit.
void basic::options::real3afteroption | ( | std::string const & | str, |
double const | default1, | ||
double & | rnum1, | ||
double const | default2, | ||
double & | rnum2, | ||
double const | default3, | ||
double & | rnum3 | ||
) |
References key().
void basic::options::real3afteroption | ( | OptionKey const & | key, |
double const | default1, | ||
double & | rnum1, | ||
double const | default2, | ||
double & | rnum2, | ||
double const | default3, | ||
double & | rnum3 | ||
) |
References utility::io::oc::cerr, utility::io::oc::cout, BuildPackagedBindings::format, utility::keys::AutoKey< O, S, C >::id(), option, utility::options::OptionCollection::option(), utility::options::VectorOption_T_< K, T >::size(), ObjexxFCL::format::SS(), basic::options::OptionKeys::inout::dbms::user, and utility_exit.
double basic::options::realafteroption | ( | std::string const & | str | ) |
References utility::io::oc::cerr, truefalseoption(), and utility_exit.
Referenced by realafteroption().
double basic::options::realafteroption | ( | std::string const & | str, |
double const | opt_default | ||
) |
References key(), realafteroption(), and value.
void basic::options::realafteroption | ( | std::string const & | str, |
double const | opt_default, | ||
double & | rnum | ||
) |
References key(), and realafteroption().
void basic::options::realafteroption | ( | OptionKey const & | key, |
double const | opt_default, | ||
double & | rnum | ||
) |
void basic::options::set_boolean_option | ( | std::string const & | id, |
bool | v | ||
) |
void basic::options::set_boolean_vector_option | ( | std::string const & | id, |
utility::vector1< bool > const & | v | ||
) |
References test.T850_SubClassing::v.
void basic::options::set_file_option | ( | std::string const & | id, |
std::string const & | v | ||
) |
References test.T850_SubClassing::v.
void basic::options::set_file_vector_option | ( | std::string const & | id, |
utility::vector1< std::string > const & | v | ||
) |
void basic::options::set_integer_option | ( | std::string const & | id, |
int | v | ||
) |
void basic::options::set_integer_vector_option | ( | std::string const & | id, |
utility::vector1< int > const & | v | ||
) |
References test.T850_SubClassing::v.
void basic::options::set_option | ( | std::string const & | id, |
T const & | value | ||
) |
References has, key, option, utility_exit_with_message, and value.
void basic::options::set_real_option | ( | std::string const & | id, |
double | v | ||
) |
References test.T850_SubClassing::v.
void basic::options::set_real_vector_option | ( | std::string const & | id, |
utility::vector1< double > const & | v | ||
) |
References test.T850_SubClassing::v.
void basic::options::set_string_option | ( | std::string const & | id, |
std::string const & | v | ||
) |
void basic::options::set_string_vector_option | ( | std::string const & | id, |
utility::vector1< std::string > const & | v | ||
) |
int const basic::options::silent | ( | 0 | ) |
Named verbosity levels.
int const basic::options::standard | ( | 2 | ) |
std::string basic::options::start_file | ( | ) |
kind of like the old -s – just one file
convenience functions
References runtime_assert, and start_files().
Referenced by densityTools(), main(), run_pep_prep(), and RunPepSpec().
utility::vector1< std::string > basic::options::start_files | ( | ) |
Retrieve all files specified using -l or -s NOTE:: will die if neither option is used!
References utility::io::izstream::close(), app.delta_score_per_mutation::data, basic::options::OptionKeys::in::file::file, utility::io::izstream::getline(), utility::io::izstream::good(), basic::options::OptionKeys::frags::j, basic::options::OptionKeys::in::file::l, basic::options::OptionKeys::in::file::list, name, option, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::in::file::screening_list, basic::T(), basic::options::OptionKeys::inout::dbms::user, utility_exit, and utility_exit_with_message.
Referenced by create_theozyme_pdb(), main(), match_main(), and start_file().
std::string basic::options::stringafteroption | ( | std::string const & | str | ) |
References utility::io::oc::cout, key(), truefalseoption(), and utility_exit.
Referenced by stringafteroption().
std::string basic::options::stringafteroption | ( | std::string const & | str, |
std::string const & | opt_default | ||
) |
References key(), and stringafteroption().
void basic::options::stringafteroption | ( | std::string const & | str, |
std::string const & | opt_default, | ||
std::string & | cval | ||
) |
References key(), and stringafteroption().
void basic::options::stringafteroption | ( | OptionKey const & | key, |
std::string const & | opt_default, | ||
std::string & | cval | ||
) |
void basic::options::stringafteroption | ( | std::string const & | str, |
char const | opt_default, | ||
char & | cval | ||
) |
References key(), and stringafteroption().
void basic::options::stringafteroption | ( | OptionKey const & | key, |
char const | opt_default, | ||
char & | cval | ||
) |
|
static |
Referenced by check_option_conflicts(), go_main(), load_loops_from_file(), main(), my_main(), process(), and validate_dunbrack_binaries().
bool basic::options::truefalseoption | ( | std::string const & | str | ) |
References key().
Referenced by intafteroption(), realafteroption(), and stringafteroption().
bool basic::options::truefalseoption | ( | OptionKey const & | key | ) |
int const basic::options::verbose | ( | 9 | ) |
int const basic::options::yap | ( | 7 | ) |
int const basic::options::chat |
int const basic::options::gush |
int const basic::options::inform |
OptionCollection basic::options::option |
OptionCollection global.
OptionCollection global
Referenced by apps::public1::scenarios::chemically_conjugated_docking::add_extra_bodies(), UBQ_GTPaseMover::analyze_and_filter(), UBQ_GTPase_disulfide_Mover::analyze_and_filter(), UBQ_E2Mover::analyze_and_filter(), AnchorFinderMover::AnchorFinderMover(), APDBCMover::APDBCMover(), IAMover::apply(), zinc1_homodimer_setup::apply(), AnchorFinderMover::apply(), zinc1_homodimer_design::apply(), ExposedStrandMover::apply(), APDBCMover::apply(), HDmakerMover::apply(), HDdesignMover::apply(), CaToAllAtom::apply(), supercharge::apply(), UBQ_GTPaseMover::apply(), UBQ_GTPase_disulfide_Mover::apply(), UBQ_E2Mover::apply(), IAMover::assign_IA_mover(), supercharge::AvNAPSA_values(), HDmakerMover::bb_score(), CaToAllAtom::CaToAllAtom(), check_option_conflicts(), check_required_options(), HDdesignMover::cloak_and_setup(), DockFragmentsMover::cluster_frags(), basic::ComparingTracer::ComparingTracer(), create_ensemble(), create_theozyme_pdb(), DockFragmentsMover::cut_from_map(), zinc2_homodimer_design::design_symmetric_homodimer_metal_interface(), supercharge::energy_comparison(), zinc2_homodimer_setup::filter_clashes(), zinc2_homodimer_setup::filter_metal_geom(), get_file_vector_option(), get_option(), get_option(), go_main(), graphics_main(), zinc2_homodimer_setup::gridsearch_symmetric_alignments(), UBQ_GTPase_disulfide_Mover::init_on_new_input(), UBQ_GTPaseMover::init_on_new_input(), UBQ_E2Mover::init_on_new_input(), initialize(), int2afteroption(), intafteroption(), load_loops_from_file(), main(), minimize_with_constraints(), my_main(), optimize_pose(), optional_positive_intafteroption(), output_general_base_pair_steps(), supercharge::prepack_input_structure(), process(), DockFragmentsMover::process_fragfile(), processRegions(), basic::prof_start_function_body(), basic::prof_stop_function_body(), APDBCMover::read_in_insert_loop_info(), read_native_sequence_for_entity_elements(), read_subset_of_global_option_collection(), real2afteroption(), real3afteroption(), realafteroption(), register_options(), rna_design_test(), rna_fullatom_minimize_test(), rna_score_test(), DockFragmentsMover::run(), ScoreFragmentSetMover::run(), SolutionRescoreMover::run(), run_mc(), set_option(), set_option(), supercharge::set_resfile_AvNAPSA(), supercharge::set_surface(), LigandDockBenchmark::setUp(), LigandDockScriptBenchmark::setUp(), setup_ca_constraints(), zinc1_homodimer_design::setup_metalsite_constraints(), zinc1_homodimer_design::setup_scorefunctions(), setup_segment_insert(), zinc2_homodimer_design::setup_taskfactory_scorefunction_movers(), start_files(), stringafteroption(), HDdesignMover::task_constraint_setup(), truefalseoption(), UBQ_E2Mover::UBQ_E2Mover(), validate_dunbrack_binaries(), and zinc2_homodimer_setup::zinc2_homodimer_setup().
int const basic::options::quiet |
int const basic::options::silent |
Named verbosity levels.
int const basic::options::standard |
int const basic::options::verbose |
int const basic::options::yap |