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basic::options Namespace Reference

Namespaces

 OptionKeys
 

Typedefs

typedef utility::options::OptionKey OptionKey
 
typedef
utility::options::BooleanOptionKey 
BooleanOptionKey
 
typedef
utility::options::IntegerOptionKey 
IntegerOptionKey
 
typedef
utility::options::RealOptionKey 
RealOptionKey
 
typedef
utility::options::StringOptionKey 
StringOptionKey
 
typedef
utility::options::FileOptionKey 
FileOptionKey
 
typedef
utility::options::PathOptionKey 
PathOptionKey
 
typedef
utility::options::BooleanVectorOptionKey 
BooleanVectorOptionKey
 
typedef
utility::options::IntegerVectorOptionKey 
IntegerVectorOptionKey
 
typedef
utility::options::RealVectorOptionKey 
RealVectorOptionKey
 
typedef
utility::options::ResidueChainVectorOptionKey 
ResidueChainVectorOptionKey
 
typedef
utility::options::StringVectorOptionKey 
StringVectorOptionKey
 
typedef
utility::options::FileVectorOptionKey 
FileVectorOptionKey
 
typedef
utility::options::PathVectorOptionKey 
PathVectorOptionKey
 
typedef
utility::options::OptionCollection 
OptionCollection
 
typedef utility::options::Option Option
 
typedef
utility::options::BooleanOption 
BooleanOption
 
typedef
utility::options::IntegerOption 
IntegerOption
 
typedef
utility::options::RealOption 
RealOption
 
typedef
utility::options::StringOption 
StringOption
 
typedef
utility::options::FileOption 
FileOption
 
typedef
utility::options::PathOption 
PathOption
 
typedef
utility::options::BooleanVectorOption 
BooleanVectorOption
 
typedef
utility::options::IntegerVectorOption 
IntegerVectorOption
 
typedef
utility::options::RealVectorOption 
RealVectorOption
 
typedef
utility::options::StringVectorOption 
StringVectorOption
 
typedef
utility::options::FileVectorOption 
FileVectorOption
 
typedef
utility::options::PathVectorOption 
PathVectorOption
 

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)
 
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)
 
OptionCollectioninitialize ()
 Initialize the options. More...
 
OptionCollectionpre_tracer_process ()
 Process the specified options - do this prior to. More...
 
OptionCollectionprocess ()
 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)
 
std::string get_path_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)
 
void set_path_option (std::string const &id, std::string const &v)
 
utility::vector1< boolget_boolean_vector_option (std::string const &id)
 
utility::vector1< intget_integer_vector_option (std::string const &id)
 
utility::vector1< doubleget_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)
 
utility::vector1< std::string > get_path_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)
 
void set_path_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...
 
std::string replace_option_namespace_colons_with_underscores (utility::options::OptionKey const &key)
 

Variables

static basic::Tracer TR ("basic.options")
 
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
 
static basic::Tracer TR ("basic.options.util")
 

Typedef Documentation

Function Documentation

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(), CREATE_EXCEPTION, utility::keys::AutoKey< O, S, C >::id(), and options.

Referenced by read_subset_of_global_option_collection().

int const basic::options::chat ( )
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)
template<typename T , typename K >
T basic::options::get_option ( std::string const &  id)
std::string basic::options::get_path_option ( std::string const &  id)
utility::vector1< std::string > basic::options::get_path_vector_option ( std::string const &  id)
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 ( )
int const basic::options::inform ( )
OptionCollection & basic::options::initialize ( )
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 
)
int basic::options::intafteroption ( std::string const &  str)
int basic::options::intafteroption ( std::string const &  str,
int const  opt_default 
)

References intafteroption(), and key().

void basic::options::intafteroption ( std::string const &  str,
int const  opt_default,
int inum 
)

References intafteroption(), and key().

void basic::options::intafteroption ( OptionKey const &  key,
int const  opt_default,
int inum 
)
OptionKey const& basic::options::key ( std::string const &  str)
void basic::options::optional_positive_intafteroption ( std::string const &  str,
int const  opt_default,
int inum 
)

References key().

void basic::options::optional_positive_intafteroption ( OptionKey const &  key,
int const  opt_default,
int inum 
)
OptionCollection & basic::options::pre_tracer_process ( )

Process the specified options - do this prior to.

Process complex option inter-dependencies, prior to Tracer initializations.

Note
Do more complex value setup and checks here than the option system provides.

References run::constant_seed(), testing::INTEGRATION_TEST(), out::mpi_tracer_to_file(), in::no_fconfig(), run::no_prof_info_in_silentout(), run::nodelay(), option, basic::options::OptionKeys::inout::dbms::user, and value.

OptionCollection & basic::options::process ( )
int const basic::options::quiet ( )
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(), option, and options.

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 
)
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 
)
double basic::options::realafteroption ( std::string const &  str)
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 
)
std::string basic::options::replace_option_namespace_colons_with_underscores ( utility::options::OptionKey const &  key)
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 
)
void basic::options::set_file_option ( std::string const &  id,
std::string const &  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 
)
template<typename T , typename K >
void basic::options::set_option ( std::string const &  id,
T const &  value 
)
void basic::options::set_path_option ( std::string const &  id,
std::string const &  v 
)
void basic::options::set_path_vector_option ( std::string const &  id,
utility::vector1< std::string > const &  v 
)
void basic::options::set_real_option ( std::string const &  id,
double  v 
)
void basic::options::set_real_vector_option ( std::string const &  id,
utility::vector1< double > const &  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 ( )

Named verbosity levels.

int const basic::options::standard ( )
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 ( )
std::string basic::options::stringafteroption ( std::string const &  str)
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 
)
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 ( )
int const basic::options::yap ( )

Variable Documentation

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_GTPase_disulfide_Mover::analyze_and_filter(), UBQ_E2Mover::analyze_and_filter(), AnchorFinderMover::AnchorFinderMover(), APDBCMover::APDBCMover(), IAMover::apply(), IdentifyCDRClusters::apply(), zinc1_homodimer_setup::apply(), MetalSiteFinderMover::apply(), AnchorFinderMover::apply(), zinc1_homodimer_design::apply(), ExposedStrandMover::apply(), APDBCMover::apply(), HDdesignMover::apply(), HDmakerMover::apply(), CaToAllAtom::apply(), supercharge::apply(), UBQ_GTPase_disulfide_Mover::apply(), UBQ_E2Mover::apply(), IAMover::assign_IA_mover(), supercharge::AvNAPSA_values(), BacksideHbondFinderMover::BacksideHbondFinderMover(), HDmakerMover::bb_score(), calculate_binding_energy(), CaToAllAtom::CaToAllAtom(), check_option_conflicts(), check_required_options(), HDdesignMover::cloak_and_setup(), DockFragmentsMover::cluster_frags(), basic::ComparingTracer::ComparingTracer(), RNA_DeNovoJobQueen::complete_larval_job_maturation(), convert(), correct_rama(), create_ensemble(), create_theozyme_pdb(), DockFragmentsMover::cut_from_map(), zinc2_homodimer_design::design_symmetric_homodimer_metal_interface(), do_color_by_score(), do_erraser2(), do_options_checks(), supercharge::energy_comparison(), basic::resource_manager::locator::FileSystemResourceLocator::FileSystemResourceLocator(), zinc2_homodimer_setup::filter_clashes(), zinc2_homodimer_setup::filter_metal_geom(), find_residues_around_mutation(), generate_dunbrack_binaries(), get_mutations_from_file(), get_option(), get_quota_per_silent(), get_unbound_protein_score(), go_main(), graphics_main(), zinc2_homodimer_setup::gridsearch_symmetric_alignments(), harvest_motifs(), harvest_motifs_one(), harvest_scores(), GlycanClashCheckMover::init(), MPDomainAssembly::init_from_cmd(), UBQ_GTPase_disulfide_Mover::init_on_new_input(), UBQ_E2Mover::init_on_new_input(), basic::random::init_random_number_generators(), initialize(), basic::resource_manager::ResourceManager::initialize_from_commandline(), MetalSiteFinderMover::initialize_from_options(), zinc_stats::ZincStatisticGenerator::initialize_from_options(), insert_stage_tag(), int2afteroption(), intafteroption(), key(), HBondReporter::load_job_data(), load_loops_from_file(), apps::pilot::frankdt::main(), main(), make_mutation_tag(), make_mutations(), merge_motifs(), minimize_with_constraints(), mutate_and_score_RNP(), my_main(), optimize_embedding(), optimize_pose(), optional_positive_intafteroption(), output_general_base_pair_steps(), output_results(), pre_tracer_process(), supercharge::prepack_input_structure(), print_motifs(), print_scores(), process(), DockFragmentsMover::process_fragfile(), processRegions(), basic::prof_start_function_body(), basic::prof_stop_function_body(), read_fasta(), APDBCMover::read_in_insert_loop_info(), read_membrane(), read_native_sequence_for_entity_elements(), read_silent_input_as_library(), read_subset_of_global_option_collection(), real2afteroption(), real3afteroption(), realafteroption(), register_options(), report_and_dump(), retag(), reverse_convert(), rna_denovo_legacy(), rna_design_test(), rna_fullatom_minimize_test(), rna_motif_test(), DockFragmentsMover::run(), ScoreFragmentSetMover::run(), SolutionRescoreMover::run(), run_mc(), set_option(), supercharge::set_resfile_AvNAPSA(), supercharge::set_surface(), LigandDockBenchmark::setUp(), InteractionGraphPerformanceBenchmark::setUp(), LigandDockScriptBenchmark::setUp(), setup_ca_constraints(), zinc1_homodimer_design::setup_metalsite_constraints(), setup_score_function(), zinc1_homodimer_design::setup_scorefunctions(), setup_segment_insert(), zinc2_homodimer_design::setup_taskfactory_scorefunction_movers(), simple_minimization(), skipping_relax(), start_files(), stringafteroption(), HDdesignMover::task_constraint_setup(), truefalseoption(), UBQ_E2Mover::UBQ_E2Mover(), unbound_protein_minimization(), 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
basic::Tracer basic::options::TR("basic.options.util")
static
basic::Tracer basic::options::TR("basic.options")
static
int const basic::options::verbose
int const basic::options::yap