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)
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 ()

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

Typedef Documentation

typedef utility::options::BooleanOption basic::options::BooleanOption

typedef utility::options::BooleanOptionKey basic::options::BooleanOptionKey

typedef utility::options::BooleanVectorOption basic::options::BooleanVectorOption

typedef utility::options::BooleanVectorOptionKey basic::options::BooleanVectorOptionKey

typedef utility::options::FileOption basic::options::FileOption

typedef utility::options::FileOptionKey basic::options::FileOptionKey

typedef utility::options::FileVectorOption basic::options::FileVectorOption

typedef utility::options::FileVectorOptionKey basic::options::FileVectorOptionKey

typedef utility::options::IntegerOption basic::options::IntegerOption

typedef utility::options::IntegerOptionKey basic::options::IntegerOptionKey

typedef utility::options::IntegerVectorOption basic::options::IntegerVectorOption

typedef utility::options::IntegerVectorOptionKey basic::options::IntegerVectorOptionKey

typedef utility::options::Option basic::options::Option

typedef utility::options::OptionCollection basic::options::OptionCollection

typedef utility::options::OptionKey basic::options::OptionKey

typedef utility::options::PathOption basic::options::PathOption

typedef utility::options::PathOptionKey basic::options::PathOptionKey

typedef utility::options::PathVectorOption basic::options::PathVectorOption

typedef utility::options::PathVectorOptionKey basic::options::PathVectorOptionKey

typedef utility::options::RealOption basic::options::RealOption

typedef utility::options::RealOptionKey basic::options::RealOptionKey

typedef utility::options::RealVectorOption basic::options::RealVectorOption

typedef utility::options::RealVectorOptionKey basic::options::RealVectorOptionKey

typedef utility::options::ResidueChainVectorOptionKey basic::options::ResidueChainVectorOptionKey

typedef utility::options::StringOption basic::options::StringOption

typedef utility::options::StringOptionKey basic::options::StringOptionKey

typedef utility::options::StringVectorOption basic::options::StringVectorOption

typedef utility::options::StringVectorOptionKey basic::options::StringVectorOptionKey

Function Documentation

int const basic::options::chat

(

6

)

bool basic::options::get_boolean_option

(

std::string const &

id

)

Referenced by app.pyrosetta_toolkit.window_modules.clean_pdb.FixPDBWindow.FixPDBWindow::load_cleaned_pdb().

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

)

Referenced by app.pyrosetta_toolkit.modules.protocols.AnalysisProtocols.AnalysisProtocols::analyze_vip().

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

)

References has, key, option, utility_exit_with_message, and value.

double basic::options::get_real_option

(

std::string const &

id

)

Referenced by app.pyrosetta_toolkit.modules.protocols.MinimizationProtocols.MinimizationProtocols::minimize().

utility::vector1< double > basic::options::get_real_vector_option

(

std::string const &

id

)

std::string basic::options::get_string_option

(

std::string const &

id

)

Referenced by app.pyrosetta_toolkit.modules.protocols.DesignProtocols.DesignWrapper::apply(), and app.pyrosetta_toolkit.modules.protocols.MinimizationProtocols.MinimizationProtocols::minimize().

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, 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().

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
	)

References utility::io::oc::cout, utility::keys::AutoKey< O, S, C >::id(), key(), option, utility::options::OptionCollection::option(), ObjexxFCL::format::SS(), and basic::options::OptionKeys::inout::dbms::user.

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().

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

References utility::io::oc::cout, utility::keys::AutoKey< O, S, C >::id(), option, utility::options::OptionCollection::option(), utility::options::VectorOption_T_< K, T >::size(), ObjexxFCL::format::SS(), and basic::options::OptionKeys::inout::dbms::user.

OptionCollection & basic::options::process

(

)

Process the specified options.

Note

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

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, basic::options::OptionKeys::AnchoredDesign::filters::score, and TR().

int const basic::options::quiet

(

1

)

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, 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, 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
	)

References utility::io::oc::cout, utility::keys::AutoKey< O, S, C >::id(), key(), option, utility::options::OptionCollection::option(), ObjexxFCL::format::SS(), and basic::options::OptionKeys::inout::dbms::user.

void basic::options::set_boolean_option	(	std::string const &	id,
		bool	v
	)

References test.T850_SubClassing::v.

Referenced by app.pyrosetta_toolkit.modules.protocols.FloppyTailProtocol.FloppyTailProtocol::setup_mover_and_run().

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
	)

References test.T850_SubClassing::v.

Referenced by app.pyrosetta_toolkit.modules.protocols.FloppyTailProtocol.FloppyTailProtocol::setup_mover_and_run().

void basic::options::set_integer_option	(	std::string const &	id,
		int	v
	)

References test.T850_SubClassing::v.

Referenced by app.pyrosetta_toolkit.modules.protocols.FloppyTailProtocol.FloppyTailProtocol::setup_mover_and_run().

void basic::options::set_integer_vector_option	(	std::string const &	id,
		utility::vector1< int > const &	v
	)

References test.T850_SubClassing::v.

template<typename T , typename K >

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
	)

References test.T850_SubClassing::v.

Referenced by app.pyrosetta_toolkit.modules.protocols.FloppyTailProtocol.FloppyTailProtocol::setup_mover_and_run().

void basic::options::set_string_vector_option	(	std::string const &	id,
		utility::vector1< std::string > const &	v
	)

References test.T850_SubClassing::v.

Referenced by app.pyrosetta_toolkit.modules.protocols.FloppyTailProtocol.FloppyTailProtocol::setup_mover_and_run().

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
	)

References utility::io::oc::cout, utility::keys::AutoKey< O, S, C >::id(), key(), option, utility::options::OptionCollection::option(), and basic::options::OptionKeys::inout::dbms::user.

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
	)

References utility::io::oc::cout, utility::keys::AutoKey< O, S, C >::id(), option, utility::options::OptionCollection::option(), and basic::options::OptionKeys::inout::dbms::user.

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

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

)

References utility::io::oc::cout, utility::keys::AutoKey< O, S, C >::id(), option, and basic::options::OptionKeys::inout::dbms::user.

int const basic::options::verbose

(

9

)

int const basic::options::yap

(

7

)

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_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_filename(), 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(), real2afteroption(), real3afteroption(), realafteroption(), register_options(), rna_design_test(), rna_fullatom_minimize_test(), rna_score_test(), DockFragmentsMover::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