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

Definition at line 42 of file option.hh.

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

Definition at line 103 of file OptionKeys.hh.

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

Definition at line 48 of file option.hh.

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

Definition at line 109 of file OptionKeys.hh.

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

Definition at line 46 of file option.hh.

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

Definition at line 107 of file OptionKeys.hh.

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

Definition at line 52 of file option.hh.

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

Definition at line 114 of file OptionKeys.hh.

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

Definition at line 43 of file option.hh.

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

Definition at line 104 of file OptionKeys.hh.

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

Definition at line 49 of file option.hh.

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

Definition at line 110 of file OptionKeys.hh.

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

Definition at line 41 of file option.hh.

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

Definition at line 40 of file option.hh.

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

Definition at line 35 of file after_opts.hh.

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

Definition at line 47 of file option.hh.

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

Definition at line 108 of file OptionKeys.hh.

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

Definition at line 53 of file option.hh.

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

Definition at line 115 of file OptionKeys.hh.

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

Definition at line 44 of file option.hh.

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

Definition at line 105 of file OptionKeys.hh.

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

Definition at line 50 of file option.hh.

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

Definition at line 111 of file OptionKeys.hh.

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

Definition at line 112 of file OptionKeys.hh.

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

Definition at line 45 of file option.hh.

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

Definition at line 106 of file OptionKeys.hh.

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

Definition at line 51 of file option.hh.

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

Definition at line 113 of file OptionKeys.hh.

Function Documentation

int const basic::options::chat ( 6 )

bool basic::options::get_boolean_option ( std::string const & id )

Definition at line 60 of file PyRosettaFunctions.cc.

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 )

Definition at line 73 of file PyRosettaFunctions.cc.

std::string basic::options::get_file_option ( std::string const & id )

Definition at line 64 of file PyRosettaFunctions.cc.

utility::vector1< std::string > basic::options::get_file_vector_option ( std::string const & id )

Definition at line 77 of file PyRosettaFunctions.cc.

int basic::options::get_integer_option ( std::string const & id )

Definition at line 61 of file PyRosettaFunctions.cc.

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

utility::vector1< int > basic::options::get_integer_vector_option ( std::string const & id )

Definition at line 74 of file PyRosettaFunctions.cc.

template<typename T , typename K >

T basic::options::get_option ( std::string const & id )

Definition at line 44 of file PyRosettaFunctions.cc.

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

double basic::options::get_real_option ( std::string const & id )

Definition at line 62 of file PyRosettaFunctions.cc.

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

utility::vector1< double > basic::options::get_real_vector_option ( std::string const & id )

Definition at line 75 of file PyRosettaFunctions.cc.

std::string basic::options::get_string_option ( std::string const & id )

Definition at line 63 of file PyRosettaFunctions.cc.

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 )

Definition at line 76 of file PyRosettaFunctions.cc.

int const basic::options::gush ( 8 )

int const basic::options::inform ( 4 )

OptionCollection & basic::options::initialize ( )

Initialize the options.

Definition at line 61 of file option.cc.

References 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
	)

Definition at line 302 of file after_opts.cc.

References key().

void basic::options::int2afteroption	(	OptionKey const &	key,
		int const	opt_default,
		int &	inum,
		int const	opt_default2,
		int &	inum2
	)

Definition at line 315 of file after_opts.cc.

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(), utility::options::OptionKeys::options::user, and utility_exit.

int basic::options::intafteroption ( std::string const & str )

Definition at line 211 of file after_opts.cc.

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
	)

Definition at line 226 of file after_opts.cc.

References intafteroption(), and key().

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

Definition at line 238 of file after_opts.cc.

References intafteroption(), and key().

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

Definition at line 249 of file after_opts.cc.

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

OptionKey const& basic::options::key ( std::string const & str )

Get key for an option name.

Definition at line 42 of file after_opts.cc.

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
	)

Definition at line 267 of file after_opts.cc.

References key().

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

Definition at line 278 of file after_opts.cc.

References 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(), and utility::options::OptionKeys::options::user.

OptionCollection & basic::options::process ( )

Process the specified options.

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

Definition at line 94 of file option.cc.

References utility::vectorL< SSize, T, A >::append(), database, option, options, app.surface_docking.surface_docking::path, contacts::pdb, test.G100_Functions_Input::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
	)

Definition at line 125 of file after_opts.cc.

References key().

void basic::options::real2afteroption	(	OptionKey const &	key,
		double const	default1,
		double &	rnum1,
		double const	default2,
		double &	rnum2
	)

Definition at line 138 of file after_opts.cc.

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(), utility::options::OptionKeys::options::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
	)

Definition at line 165 of file after_opts.cc.

References key().

void basic::options::real3afteroption	(	OptionKey const &	key,
		double const	default1,
		double &	rnum1,
		double const	default2,
		double &	rnum2,
		double const	default3,
		double &	rnum3
	)

Definition at line 180 of file after_opts.cc.

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(), utility::options::OptionKeys::options::user, and utility_exit.

double basic::options::realafteroption ( std::string const & str )

Definition at line 69 of file after_opts.cc.

References utility::io::oc::cerr, truefalseoption(), and utility_exit.

Referenced by realafteroption().

double basic::options::realafteroption	(	std::string const &	str,
		double const	opt_default
	)

Definition at line 84 of file after_opts.cc.

References key(), realafteroption(), and value.

void basic::options::realafteroption	(	std::string const &	str,
		double const	opt_default,
		double &	rnum
	)

Definition at line 96 of file after_opts.cc.

References key(), and realafteroption().

void basic::options::realafteroption	(	OptionKey const &	key,
		double const	opt_default,
		double &	rnum
	)

Definition at line 107 of file after_opts.cc.

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

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

Definition at line 66 of file PyRosettaFunctions.cc.

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
	)

Definition at line 80 of file PyRosettaFunctions.cc.

References test.T850_SubClassing::v.

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

Definition at line 70 of file PyRosettaFunctions.cc.

References test.T850_SubClassing::v.

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

Definition at line 84 of file PyRosettaFunctions.cc.

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
	)

Definition at line 67 of file PyRosettaFunctions.cc.

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
	)

Definition at line 81 of file PyRosettaFunctions.cc.

References test.T850_SubClassing::v.

template<typename T , typename K >

void basic::options::set_option	(	std::string const &	id,
		T const &	value
	)

Definition at line 52 of file PyRosettaFunctions.cc.

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

void basic::options::set_real_option	(	std::string const &	id,
		double	v
	)

Definition at line 68 of file PyRosettaFunctions.cc.

References test.T850_SubClassing::v.

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

Definition at line 82 of file PyRosettaFunctions.cc.

References test.T850_SubClassing::v.

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

Definition at line 69 of file PyRosettaFunctions.cc.

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
	)

Definition at line 83 of file PyRosettaFunctions.cc.

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

Definition at line 41 of file util.cc.

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!

Definition at line 53 of file util.cc.

References utility::io::izstream::close(), app.delta_score_per_mutation::data, utility::io::izstream::getline(), utility::io::izstream::good(), name, option, app.pyrosetta_toolkit.modules.SQLPDB::s, basic::T(), utility::options::OptionKeys::options::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 )

Definition at line 344 of file after_opts.cc.

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
	)

Definition at line 359 of file after_opts.cc.

References key(), and stringafteroption().

void basic::options::stringafteroption	(	std::string const &	str,
		std::string const &	opt_default,
		std::string &	cval
	)

Definition at line 371 of file after_opts.cc.

References key(), and stringafteroption().

void basic::options::stringafteroption	(	OptionKey const &	key,
		std::string const &	opt_default,
		std::string &	cval
	)

Definition at line 382 of file after_opts.cc.

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

void basic::options::stringafteroption	(	std::string const &	str,
		char const	opt_default,
		char &	cval
	)

Definition at line 399 of file after_opts.cc.

References key(), and stringafteroption().

void basic::options::stringafteroption	(	OptionKey const &	key,
		char const	opt_default,
		char &	cval
	)

Definition at line 410 of file after_opts.cc.

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

Definition at line 49 of file after_opts.cc.

References key().

Referenced by intafteroption(), realafteroption(), and stringafteroption().

bool basic::options::truefalseoption ( OptionKey const & key )

Definition at line 56 of file after_opts.cc.

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

Definition at line 45 of file option.cc.

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(), 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.

Referenced by align_pdbs(), calc_rms_test(), calculate_pairwise_RMSD(), cluster_outfile_test(), cluster_test(), extract_pdbs_test(), fill_optional_options(), filter_combine_long_loop(), main(), mg_modeler_test(), minimize_with_constraints(), mutate_residues_wrapper(), nucleobase_probe_score_test(), pdb_to_silent_file(), post_rebuild_bulge_assembly(), read_structures(), rebuild_test(), register_options(), rna_build_helix_test(), rna_fullatom_minimize_test(), rna_sample_virtual_sugar(), rna_score_test(), DockFragmentsMover::run(), ScoreFragmentSetMover::run(), FragmentAssemblyMover::run(), ConsensusFragmentMover::run(), SolutionRescoreMover::run(), run_mc(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), stepwise_monte_carlo(), swa_rna_cluster(), swa_rna_sample(), and write_base_pair_step_to_silent_struct().

int const basic::options::standard

int const basic::options::verbose

Referenced by densityTools(), main(), and FragmentAssemblyMover::score().

int const basic::options::yap

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