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)
OptionCollection &	initialize ()
	Initialize the options. More...
OptionCollection &	pre_tracer_process ()
	Process the specified options - do this prior to. 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)
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< 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)
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

BooleanOption

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

BooleanOptionKey

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

BooleanVectorOption

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

BooleanVectorOptionKey

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

FileOption

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

FileOptionKey

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

FileVectorOption

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

FileVectorOptionKey

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

IntegerOption

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

IntegerOptionKey

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

IntegerVectorOption

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

IntegerVectorOptionKey

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

Option

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

OptionCollection

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

OptionKey

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

PathOption

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

PathOptionKey

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

PathVectorOption

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

PathVectorOptionKey

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

RealOption

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

RealOptionKey

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

RealVectorOption

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

RealVectorOptionKey

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

ResidueChainVectorOptionKey

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

StringOption

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

StringOptionKey

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

StringVectorOption

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

StringVectorOptionKey

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

Function Documentation

add_anonymous_option()

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

Referenced by read_subset_of_global_option_collection().

chat()

int const basic::options::chat

(

6

)

get_boolean_option()

bool basic::options::get_boolean_option

(

std::string const &

id

)

get_boolean_vector_option()

utility::vector1< bool > basic::options::get_boolean_vector_option

(

std::string const &

id

)

get_file_option()

std::string basic::options::get_file_option

(

std::string const &

id

)

get_file_vector_option()

utility::vector1< std::string > basic::options::get_file_vector_option

(

std::string const &

id

)

get_integer_option()

int basic::options::get_integer_option

(

std::string const &

id

)

get_integer_vector_option()

utility::vector1< int > basic::options::get_integer_vector_option

(

std::string const &

id

)

get_option()

template<typename T , typename K >

T basic::options::get_option

(

std::string const &

id

)

References has, PREcst::K, subloop_histogram::key, option, utility_exit_with_message, and value.

get_path_option()

std::string basic::options::get_path_option

(

std::string const &

id

)

get_path_vector_option()

utility::vector1< std::string > basic::options::get_path_vector_option

(

std::string const &

id

)

get_real_option()

double basic::options::get_real_option

(

std::string const &

id

)

get_real_vector_option()

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

(

std::string const &

id

)

get_string_option()

std::string basic::options::get_string_option

(

std::string const &

id

)

get_string_vector_option()

utility::vector1< std::string > basic::options::get_string_vector_option

(

std::string const &

id

)

gush()

int const basic::options::gush

(

8

)

inform()

int const basic::options::inform

(

4

)

initialize()

OptionCollection & basic::options::initialize

(

)

Initialize the options.

References utility::options::OptionCollection::add_built_in_options(), utility::options::OptionCollection::check_specs(), and option.

Referenced by PoseWrap::align_orig_pose(), CountContact::apply(), CountContact::CountContact(), dump_clash_pdb(), find_dna_rotamers(), setup_atom_number(), PoseWrap::switch_to_cen(), and PoseWrap::switch_to_fa().

int2afteroption() [1/2]

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(), key(), option, utility::options::OptionCollection::option(), utility::options::VectorOption_T_< K, T >::size(), SS, basic::options::OptionKeys::inout::dbms::user, and utility_exit.

int2afteroption() [2/2]

void basic::options::int2afteroption	(	std::string const &	str,
		int const	opt_default,
		int &	inum,
		int const	opt_default2,
		int &	inum2
	)

References key(), and str().

intafteroption() [1/4]

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(), SS, and basic::options::OptionKeys::inout::dbms::user.

intafteroption() [2/4]

int basic::options::intafteroption

(

std::string const &

str

)

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

Referenced by intafteroption().

intafteroption() [3/4]

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

References intafteroption(), key(), and str().

intafteroption() [4/4]

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

References intafteroption(), key(), and str().

key()

OptionKey const& basic::options::key

(

std::string const &

str

)

Get key for an option name.

References utility::options::OptionCollection::find_key_cl(), option, and str().

Referenced by add_anonymous_option(), harvest_scores(), int2afteroption(), intafteroption(), main(), optional_positive_intafteroption(), real2afteroption(), real3afteroption(), realafteroption(), replace_option_namespace_colons_with_underscores(), sicdock_thread_num(), stringafteroption(), and truefalseoption().

optional_positive_intafteroption() [1/2]

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(), key(), option, utility::options::OptionCollection::option(), utility::options::VectorOption_T_< K, T >::size(), SS, and basic::options::OptionKeys::inout::dbms::user.

optional_positive_intafteroption() [2/2]

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

References key(), and str().

pre_tracer_process()

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.

process()

OptionCollection & basic::options::process

(

)

Process the specified options.

Process complex option inter-dependencies (after tracer system is initialized)

Note

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

References in::alternate_3_letter_codes(), utility::vectorL< L, T, A >::append(), kic_runner::database, basic::Tracer::flush(), basic::options::OptionKeys::in::path::fragments, carbohydrates::glycam_pdb_format(), option, closure_error::path, kic_runner::pdb, in::preserve_crystinfo(), create_a3b_hbs::score, symmetry::symmetry_definition(), TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by ui::task::open_file_viewer().

quiet()

int const basic::options::quiet

(

1

)

read_subset_of_global_option_collection()

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(), and option.

real2afteroption() [1/2]

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(), key(), option, utility::options::OptionCollection::option(), utility::options::VectorOption_T_< K, T >::size(), SS, basic::options::OptionKeys::inout::dbms::user, and utility_exit.

real2afteroption() [2/2]

void basic::options::real2afteroption	(	std::string const &	str,
		double const	default1,
		double &	rnum1,
		double const	default2,
		double &	rnum2
	)

References key(), and str().

real3afteroption() [1/2]

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(), key(), option, utility::options::OptionCollection::option(), utility::options::VectorOption_T_< K, T >::size(), SS, basic::options::OptionKeys::inout::dbms::user, and utility_exit.

real3afteroption() [2/2]

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(), and str().

realafteroption() [1/4]

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(), SS, and basic::options::OptionKeys::inout::dbms::user.

realafteroption() [2/4]

double basic::options::realafteroption

(

std::string const &

str

)

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

Referenced by realafteroption().

realafteroption() [3/4]

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

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

realafteroption() [4/4]

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

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

replace_option_namespace_colons_with_underscores()

std::string basic::options::replace_option_namespace_colons_with_underscores

(

utility::options::OptionKey const &

key

)

References utility::keys::AutoKey< O, S, C >::identifier(), and key().

set_boolean_option()

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

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

set_boolean_vector_option()

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

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

set_file_option()

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

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

set_file_vector_option()

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

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

set_integer_option()

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

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

set_integer_vector_option()

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

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

set_option()

template<typename T , typename K >

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

References has, PREcst::K, subloop_histogram::key, option, utility_exit_with_message, and value.

set_path_option()

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

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

set_path_vector_option()

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

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

set_real_option()

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

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

set_real_vector_option()

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

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

set_string_option()

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

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

set_string_vector_option()

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

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

silent()

int const basic::options::silent

(

0

)

Named verbosity levels.

standard()

int const basic::options::standard

(

2

)

start_file()

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 analyze_interface_test(), bk_test(), bzip_test(), capri_t033_loop_test(), capri_t033_trim_dock_test(), compare_dna_energies(), compare_energies(), densityTools(), design_test(), dna_deriv_test_old(), dna_dr_loop_test(), dump_dna_kinemage(), endo_test(), get_native_pdb_names(), lk_ball_wtd_deriv_test(), loop_modeling_test(), loop_rebuilding_test(), luxr_setup(), luxr_test(), main(), my_main(), not1_loop_test(), not1_test(), proclose_test(), read_write(), rebuild_test(), relax_test(), RotamerAnalysis(), run_pep_prep(), RunPepSpec(), simple_loop_modeling_test(), simple_opte_test(), small_min_test(), start_file_test(), SymmAbRelaxTest(), SymmDataTest(), SymmSilentFileTest(), test_gb(), water_test(), water_test_fixed_O(), and zf_relax_test().

start_files()

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(), data, basic::Tracer::Fatal, evaluate_beta_mutants::file, utility::io::izstream::getline(), utility::io::izstream::good(), create_a3b_hbs::i, create_a3b_hbs::j, basic::options::OptionKeys::in::file::l, basic::options::OptionKeys::in::file::list, run_backbone::names, option, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::in::file::screening_list, TR, basic::options::OptionKeys::inout::dbms::user, utility_exit, and utility_exit_with_message.

Referenced by atom_vdw_test(), bk_test2(), capri_t033_centroid_trim_dock_test(), centroid_rescore_test(), create_theozyme_pdb(), cst_relax_test(), design_test(), dna_chain_check(), dna_design_test(), dna_geometry(), dna_io_test(), dna_motif_matcher(), dna_nbr_radii_test(), dna_specificity_test(), dna_stats(), find_dna_rotamers(), hbond_stats(), interface_repack_test(), intra_dna_stats(), kono_sarai_stats(), kono_sarai_zscore(), ligrot_test(), main(), match_main(), motif_dna_packer_design(), motif_scan(), phosphate_stats(), process_file_list(), rescore_test(), simple_opte_test(), ss_test(), start_file(), start_file_test(), tf_specificity_test(), trim_dock_rebuild_relax_test(), trim_dock_rebuild_relax_test_rhiju(), and zf_test().

stringafteroption() [1/6]

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(), key(), option, utility::options::OptionCollection::option(), and basic::options::OptionKeys::inout::dbms::user.

stringafteroption() [2/6]

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.

stringafteroption() [3/6]

std::string basic::options::stringafteroption

(

std::string const &

str

)

References utility::io::oc::cout, key(), str(), truefalseoption(), and utility_exit.

Referenced by stringafteroption().

stringafteroption() [4/6]

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

References key(), str(), and stringafteroption().

stringafteroption() [5/6]

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

References key(), str(), and stringafteroption().

stringafteroption() [6/6]

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

References key(), str(), and stringafteroption().

truefalseoption() [1/2]

bool basic::options::truefalseoption

(

OptionKey const &

key

)

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

truefalseoption() [2/2]

bool basic::options::truefalseoption

(

std::string const &

str

)

References key(), and str().

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

verbose()

int const basic::options::verbose

(

9

)

yap()

int const basic::options::yap

(

7

)

Variable Documentation

chat

int const basic::options::chat

extern

gush

int const basic::options::gush

extern

inform

int const basic::options::inform

extern

option

OptionCollection basic::options::option

OptionCollection global.

OptionCollection global

Referenced by TCDock::__dock_base__(), BuriedUnsatPolarsFinder::acc_geom_check(), PoseWrap::add_apcs_local(), apps::public1::scenarios::chemically_conjugated_docking::add_extra_bodies(), PoseWrap::add_floating_sc_csts(), add_my_options(), add_user_constraints(), addcc(), align_helix(), Tet4HMatchAligner::align_info(), UBQ_E2Mover::analyze_and_filter(), UBQ_GTPase_disulfide_Mover::analyze_and_filter(), AnchorFinderMover::AnchorFinderMover(), APDBCMover::APDBCMover(), zinc1_homodimer_setup::apply(), xtal_water_bunsat::apply(), ZincMinimize::apply(), HemeReplace::apply(), InverseRotlibDumpMover::apply(), FloppyTailMover::apply(), HECTMover::apply(), UBQ_E2Mover::apply(), IAMover::apply(), HolesTrainingDataMover::apply(), ChallengeMover::apply(), PBPotentialMover::apply(), Packing_energies::apply(), SSM_energies::apply(), MinTestMover::apply(), HotspotPlacementMover::apply(), MinPackMinMover::apply(), RosettaHolesMover::apply(), IdentifyCDRClusters::apply(), APDBCMover::apply(), AnchorFinderMover::apply(), ExposedStrandMover::apply(), HDdesignMover::apply(), HDmakerMover::apply(), CaToAllAtom::apply(), UBQ_GTPase_disulfide_Mover::apply(), MetalSiteFinderMover::apply(), ZincSiteEvaluator::apply(), HBondReporter::apply(), MyProtocol::apply(), zinc1_homodimer_design::apply(), BuriedUnsatPolarsFinder::apply(), generate_hbond_geometry::apply(), compute_Irmsd::apply(), run_score_patchdock_hotspot::apply(), run_score_hotspot::apply(), apply_linked_constraints(), IAMover::assign_IA_mover(), BacksideHbondFinderMover::BacksideHbondFinderMover(), HDmakerMover::bb_score(), BBG_Cyclic_Mover::BBG_Cyclic_Mover(), calc_B_values(), calc_ddg(), calc_sequence_score(), CalcIrms::CalcIrms(), CalcsTestMover::CalcsTestMover(), calculate_binding_energy(), calculate_distances(), CaToAllAtom::CaToAllAtom(), cen_fold(), protocols::abinitio::JumpSpecificAbrelax::check_filters(), check_inputs_for_errors(), check_option_conflicts(), check_required(), check_required_options(), check_structures(), checkresiduecount(), CL::CL(), ClashCheck::ClashCheck(), HDdesignMover::cloak_and_setup(), DockFragmentsMover::cluster_frags(), cluster_silent(), collect_residue_types(), collect_stats(), combine_refinement(), combine_search(), basic::ComparingTracer::ComparingTracer(), compute_bb_motif_score(), compute_chem_shift_RMSD(), ComputeSAXSSpectrum::ComputeSAXSSpectrum(), ConstraintConfig::ConstraintConfig(), containment_and_clash_checks(), convert(), correct_rama(), count_contacts(), create_ensemble(), create_MPpose(), create_theozyme_pdb(), MatchSet::cross(), MatchSet::cross_homodimer(), cs_rosetta_rna_pdb(), DockFragmentsMover::cut_from_map(), cxdock_design(), define_variables(), design(), design_cluster(), design_hits(), zinc2_homodimer_design::design_symmetric_homodimer_metal_interface(), design_target(), determine_allowed_dofs(), determine_output_name(), distribute_jobs(), dna_motif_matcher(), do_color_by_score(), do_erraser2(), do_event_prediction(), do_options_checks(), do_refinement(), do_search(), dock(), doit(), BuriedUnsatPolarsFinder::don_geom_check(), dostuff(), dump_efactor_pdb(), TCDock::dump_onecomp(), TCDock::dump_pdb(), PoseWrap::dump_pdb(), TCDock::dump_top_hits(), ZincSiteEvaluator::evaluate_ligand_sasa(), evaluate_score(), ZincSiteEvaluator::evaluate_zinc_neighbors(), fa_refine_and_design(), basic::resource_manager::locator::FileSystemResourceLocator::FileSystemResourceLocator(), InterfaceDDGBindJobInputter::fill_jobs(), fillPoseAndDataList(), zinc2_homodimer_setup::filter_clashes(), zinc2_homodimer_setup::filter_metal_geom(), find_clusters(), find_residues_around_mutation(), ZincSiteEvaluator::find_zinc_site(), fit_helix_in_map(), BBG_Cyclic_Mover::fix_disulf(), FloppyTailMover::FloppyTailMover(), flxbb_nobu(), TCDock::gather_hits(), SetupHotspotMover::generate_csts(), generate_disulfide_conformations(), generate_dunbrack_binaries(), get_aln(), get_ang_samp(), get_area(), get_atom_vdw(), TCDock::get_best_sub1_contact_delta_rotations(), TCDock::get_contacts_by_component(), get_deriv(), get_distance_around_rna_base(), get_distances_around_rna_backbone(), get_filename(), get_fragment_sets(), get_interface_type(), get_mutations_from_file(), get_num_nbrs(), get_option(), get_options(), get_pts(), get_quota_per_silent(), get_radius(), get_rmsd(), get_rsrpl(), get_scanres(), get_symm_residue_name(), get_tasks_from_command_line(), get_unbound_protein_score(), get_vallfrags(), protocols::jd2::RECONMPIJobDistributor::go(), go_main(), gpu_refold_test(), gpu_score_test(), HbondZinc::graft_match(), HbondZincBackbone::graft_match(), graphics_main(), zinc2_homodimer_setup::gridsearch_symmetric_alignments(), harvest_motifs(), harvest_motifs_one(), harvest_scores(), HECTMover::HECTMover(), HemeReplace::HemeReplace(), HubDenovo::HubDenovo(), IAMover::IAMover(), GlycanClashCheckMover::init(), TCDock::init(), MatchSet::init(), MPDomainAssembly::init_from_cmd(), UBQ_E2Mover::init_on_new_input(), UBQ_GTPase_disulfide_Mover::init_on_new_input(), AbInitio_MPI::init_on_new_input(), FloppyTailMover::init_on_new_input(), basic::random::init_random_number_generators(), initialize(), basic::resource_manager::ResourceManager::initialize_from_commandline(), HemeBindingMover::initialize_from_options(), MetalSiteFinderMover::initialize_from_options(), zinc_stats::ZincStatisticGenerator::initialize_from_options(), initialize_initalizeZNcst(), initialize_pose(), insert_stage_tag(), int2afteroption(), intafteroption(), JDtestmover::JDtestmover(), TCDock::justone(), key(), largest_cluster(), ligand_dock_main_jd1(), load_as_fullatom(), load_coordinates_from_database(), HBondReporter::load_job_data(), load_loops_from_file(), LoopBuild_main(), ClosabilityScore::loophash_query(), main(), make_active_site_grid(), HECTMover::make_frags(), make_mutation_tag(), make_mutations(), make_pose(), HubDenovo::make_start_pose(), makesplitwork(), makesplitwork_3bpy(), manual_refine(), measure_sequence_recovery(), merge_motifs(), BuriedUnsatPolarsFinder::metal_check(), TCDock::min_termini_dis(), TCDock::min_termini_proj(), minimize_with_constraints(), molten_get_vallfrags(), motif_dna_packer_design(), mutate_and_score_RNP(), mutate_to_sequence(), my_main(), optimize_embedding(), optimize_pose(), optional_positive_intafteroption(), output_general_base_pair_steps(), output_residue_types(), output_results(), output_single_motif(), Packing_energies::Packing_energies(), ConstraintConfig::parse_config_file(), parse_extra_atom_list(), parse_nonstandard_angles(), parse_nonstandard_bondlengths(), passes_quality_check(), perturb_bb_and_relax(), UniformPerturber::perturb_chain(), PerturbStruct::PerturbStruct(), ConstraintConfig::pick_sequence(), place_waters_and_minimize(), plot_scoreterm(), PoseWrap::PoseWrap(), pre_tracer_process(), TCDock::precompute_intra(), predict_AE(), print_hbonds_test(), print_motifs(), print_scores(), process(), process_file_list(), process_for_motifs(), DockFragmentsMover::process_fragfile(), processChild(), processChildren(), processChildrenIntensification(), processRegions(), basic::prof_start_function_body(), basic::prof_stop_function_body(), RBSegmentRelax_test(), read_B_vals(), protocols::antibody::design::AntibodyDesignMoverGenerator::read_command_line_options(), read_complex_type(), read_covalent_connections_file(), read_ERMS(), read_fasta(), read_FileVector(), read_in_extension(), APDBCMover::read_in_insert_loop_info(), read_membrane(), read_native_sequence_for_entity_elements(), read_PCAfile(), read_silent_input_as_library(), read_sphere(), read_subset_of_global_option_collection(), read_template_structures(), read_tensor_test(), real2afteroption(), real3afteroption(), realafteroption(), rebuild_test(), CalcsTestMover::register_calculators(), register_metrics(), register_options(), apps::pilot::momeara::HBondConformation::relax_pose_around_hbond(), HbondZinc::repack(), HbondZincBackbone::repack(), repack_cluster(), report(), report_and_dump(), rescore(), RescoreSAXS::RescoreSAXS(), HubDenovo::reset_hub(), results_to_pdb(), retag(), reverse_convert(), rna_denovo_legacy(), rna_design_test(), rna_motif_test(), RosettaHolesMover::RosettaHolesMover(), protocols::abinitio::JumpSpecificAbrelax::run(), run(), TCDock::run(), DockFragmentsMover::run(), ScoreFragmentSetMover::run(), SolutionRescoreMover::run(), core::pack::annealer::FixbbSimAnnealer::run(), HubDenovo::run(), run_3bpy(), run_aio(), run_diiron_glu(), apps::pilot::momeara::HBondConformation::run_example_hbond_sweep(), run_hd(), run_hh(), run_m8(), run_mc(), run_parallel_docking(), run_sf4h(), run_trace(), run_tyr_his(), run_zn2his(), sasa_bunsats(), scheme_score(), score_rnp(), scoreall(), sequence_tolerance_mf_main(), set_basic_dock_options(), set_file_output(), set_option(), ZincMinimize::set_scorefunction(), set_to_state(), InteractionGraphPerformanceBenchmark::setUp(), LigandDockBenchmark::setUp(), setup_ca_constraints(), setup_coord_csts(), setup_favor_native(), InteractionGraphPerformanceBenchmark::setup_for_denseig(), InteractionGraphPerformanceBenchmark::setup_for_linmemig(), InteractionGraphPerformanceBenchmark::setup_for_pdig(), setup_fragment_mover(), zinc1_homodimer_design::setup_metalsite_constraints(), setup_score_function(), zinc1_homodimer_design::setup_scorefunctions(), setup_segment_insert(), setup_start_coords(), HemeReplace::setup_task_factory(), zinc2_homodimer_design::setup_taskfactory_scorefunction_movers(), sicdock_thread_num(), simple_minimization(), skipping_relax(), SSM_energies::SSM_energies(), start_files(), store_backbone(), stringafteroption(), BuriedUnsatPolarsFinder::sulphur_bond_check(), sweep_params_from_match_constraint_file(), PoseWrap::switch_to_cen(), PoseWrap::switch_to_fa(), HDdesignMover::task_constraint_setup(), TCDock::TCDock(), TCDock::termini_score(), test(), test_kc(), test_kc2(), test_protein_rna(), myspace::test_relax(), test_replicate_xform(), InterfaceFeaturesTests::test_reporter(), thread_fxn(), traceCAs(), truefalseoption(), UBQ_E2Mover::UBQ_E2Mover(), unbound_protein_minimization(), PoseWrap::update_designable_packable(), use_in_rmsd(), validate_dunbrack_binaries(), MatchSet::write_to_file(), zinc2_homodimer_setup::zinc2_homodimer_setup(), and ZincMinimize::zn_min_pack().

quiet

int const basic::options::quiet

extern

Referenced by main(), OutputManager::OutputManager(), and OutputManager::write_progress().

silent

int const basic::options::silent

extern

Named verbosity levels.

standard

int const basic::options::standard

extern

Referenced by FixbbJobQueen::complete_larval_job_maturation(), RelaxJobQueen::complete_larval_job_maturation(), detail::chrono_formatter< FormatContext, OutputIt, Rep, Period >::on_12_hour(), detail::chrono_formatter< FormatContext, OutputIt, Rep, Period >::on_24_hour(), detail::chrono_formatter< FormatContext, OutputIt, Rep, Period >::on_minute(), detail::chrono_formatter< FormatContext, OutputIt, Rep, Period >::on_second(), and detail::parse_chrono_format().

TR [1/2]

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

static

Referenced by JDtestmover::apply(), HotspotPlacementMover::apply(), GlycanClashCheckMover::apply(), DetectSymmetry::apply(), SwapElementsMover1::apply(), SwapElementsMover2::apply(), BBG_Cyclic_Mover::apply(), MyProtocol::apply(), BuriedUnsatPolarsFinder::apply(), ConstraintConfig::apply_dcsts(), ConstraintConfig::apply_fa_csts(), apply_linked_constraints(), build_polymer(), calc_B_values(), calc_RMSE(), GlycanClashCheckMover::calculate_atom_clashes(), calculate_average_residue_scores(), calculate_binding_energy(), calculate_disorder(), calculate_percent_disorder(), HubDenovo::cen_fold(), check_6D_potential(), check_interface_symmetry(), check_multilinear_interpolation(), check_number_of_poses(), check_option_conflicts(), check_spline(), check_structures(), check_tensor(), Tet4HMatchAligner::checkalign(), cluster_silent(), collect_residue_types(), compute_num_bins(), ConstraintConfig::ConstraintConfig(), count_analytically(), count_analytically_cyclic(), count_analytically_improper_rotational(), count_numerically(), count_semi_analytically_improper_rotational(), MatchSet::cross(), MatchSet::cross_homodimer(), define_variables(), HubDenovo::design(), design_hits(), dnabase_test(), do_options_checks(), dock(), doit(), energy_cluster(), facts_test(), find_residues_around_mutation(), fit_helix_in_map(), genborn_test(), generate_dunbrack_binaries(), get_ang_samp(), get_backbone_segment(), get_mutations_from_file(), get_options_from_options_collection(), get_pose_chains(), get_pose_resnum(), get_quota_per_silent(), get_resmap(), get_simple_RNA_protein_fold_tree(), get_unbound_protein_score(), go_main(), gpu_refold_test(), gpu_score_test(), harvest_motifs(), harvest_scores(), helix_from_sequence(), HubDenovo::HubDenovo(), hxl_test(), ik_his_clamp(), MatchSet::init(), load_loops_from_file(), load_set(), main(), make_motif_task(), make_mutations(), HubDenovo::make_start_pose(), makesplitwork(), makesplitwork_3bpy(), merge_motifs(), mutate_and_score_RNP(), my_main(), optimize_embedding(), output_residue_types(), pairE_test(), ConstraintConfig::parse_config_file(), SwapElementsMover1::pick_fragments(), SwapElementsMover2::pick_fragments(), ConstraintConfig::pick_sequence(), plot_scoreterm(), predict_disorder(), print_atom_info(), print_hb_counts(), print_scores(), print_tree(), process(), rama2b_test(), rama_prepro_test(), rama_test(), RBSegmentRelax_test(), read_complex_type(), read_ERMS(), read_fasta(), read_in_pdbs(), read_membrane(), read_silent_input_as_library(), read_sphere(), read_tensor_test(), rebuild_test(), report_and_dump(), GlycanClashCheckMover::report_data(), reroot_restype(), rna_motif_test(), run(), HubDenovo::run(), run_3bpy(), run_aio(), run_diiron_glu(), run_m8(), run_sf4h(), run_tyr_his(), run_zn2his(), score_rnp(), set_basic_dock_options(), set_file_output(), setup_favor_native(), BBG_Cyclic_Mover::setup_locker(), sicdock_thread_num(), simple_minimization(), simple_packing(), simulate_ERMS(), skipping_relax(), start_files(), RerootRestypeVisitor::start_vertex(), HubDenovo::stupid_ddg(), target_constraints(), TCDock::TCDock(), test_refold(), testone(), thread_fxn(), unbound_protein_minimization(), validate_dunbrack_binaries(), visualize(), and MatchSet::write_to_file().

TR [2/2]

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

static

verbose

int const basic::options::verbose

extern

yap

int const basic::options::yap

extern