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Typedefs
typedef OptionKey	KeyType
	Lookup functors. More...

Variables
basic::options::BooleanOptionKey const	minimize_sidechains ("minimize_sidechains")

basic::options::BooleanOptionKey const	min_pack ("min_pack")

basic::options::BooleanOptionKey const	off_rotamer_pack ("off_rotamer_pack")

basic::options::FileOptionKey const	stublist_filename ("stublist")

basic::options::StringOptionKey const	lsmdef ("lsmdef")

basic::options::RealOptionKey const	angle_sampling ("angle_sampling")

basic::options::RealOptionKey const	translocation_sampling ("translocation_sampling")

basic::options::RealOptionKey const	max_radius ("max_radius")

basic::options::RealOptionKey const	distance_sampling ("distance_sampling")

basic::options::RealOptionKey const	max_distance ("max_distance")

basic::options::BooleanOptionKey const	constrain_grid ("constrain_grid")

utility::options::FileOptionKey const	extension ("extension")

basic::options::IntegerOptionKey const	flexible_start_resnum ("flexible_start_resnum")

basic::options::IntegerOptionKey const	flexible_stop_resnum ("flexible_stop_resnum")

basic::options::StringOptionKey const	flexible_chain ("flexible_chain")

basic::options::RealOptionKey const	shear_on ("shear_on")

basic::options::RealOptionKey const	short_tail_fraction ("short_tail_fraction")

basic::options::RealOptionKey const	short_tail_off ("short_tail_off")

basic::options::BooleanOptionKey const	pair_off ("pair_off")

basic::options::BooleanOptionKey const	publication ("publication")

basic::options::BooleanOptionKey const	C_root ("C_root")

basic::options::IntegerOptionKey const	e3_hinge_start_resnum ("e3_hinge_start_resnum")

basic::options::IntegerOptionKey const	e3_hinge_stop_resnum ("e3_hinge_stop_resnum")

basic::options::StringOptionKey const	e3_hinge_chain ("e3_hinge_chain")

basic::options::IntegerOptionKey const	e3_catalytic_resnum ("e3_catalytic_resnum")

basic::options::IntegerOptionKey const	UBQ_tail_start_resnum ("UBQ_tail_start_resnum")

basic::options::StringOptionKey const	UBQ_tail_chain ("UBQ_tail_chain")

basic::options::StringOptionKey const	e2_chain ("e2_chain")

basic::options::IntegerOptionKey const	e2_catalytic_resnum ("e2_catalytic_resnum")

basic::options::BooleanOptionKey const	debug_skip_fragment_generation ("debug_skip_fragment_generation")

basic::options::BooleanOptionKey const	debug ("debug")

basic::options::IntegerOptionKey const	cycles ("cycles")

basic::options::IntegerOptionKey const	repack_cycles ("cycles")

basic::options::RealOptionKey const	catalytic_cst_sd ("catalytic_cst_sd")

basic::options::RealOptionKey const	ubq_cst_sd ("ubq_cst_sd")

Typedef Documentation

◆ KeyType

typedef OptionKey basic::options::OptionKeys::KeyType

Lookup functors.

Variable Documentation

◆ angle_sampling

basic::options::RealOptionKey const basic::options::OptionKeys::angle_sampling("angle_sampling") ( "angle_sampling" )

Referenced by main().

◆ C_root

basic::options::BooleanOptionKey const basic::options::OptionKeys::C_root("C_root") ( "C_root" )

Referenced by FloppyTailMover::init_on_new_input(), and main().

◆ catalytic_cst_sd

basic::options::RealOptionKey const basic::options::OptionKeys::catalytic_cst_sd("catalytic_cst_sd") ( "catalytic_cst_sd" )

Referenced by HECTAllMover::init_on_new_input(), and register_options().

◆ constrain_grid

basic::options::BooleanOptionKey const basic::options::OptionKeys::constrain_grid("constrain_grid") ( "constrain_grid" )

Referenced by main().

◆ cycles

basic::options::IntegerOptionKey const basic::options::OptionKeys::cycles("cycles") ( "cycles" )

Referenced by HECTMover::apply(), APDBCMover::apply(), coarse_rb_test(), coarse_rna_denovo_test(), erraser_monte_carlo(), main(), rb_entropy_test(), register_options(), SamplingManager::setup(), and setup_transform_mover().

◆ debug

basic::options::BooleanOptionKey const basic::options::OptionKeys::debug("debug") ( "debug" )

Referenced by HECTAllMover::init_on_new_input(), HECTUBQMover::init_on_new_input(), main(), and register_options().

◆ debug_skip_fragment_generation

basic::options::BooleanOptionKey const basic::options::OptionKeys::debug_skip_fragment_generation("debug_skip_fragment_generation") ( "debug_skip_fragment_generation" )

Referenced by HECTMover::make_frags(), and register_options().

◆ distance_sampling

basic::options::RealOptionKey const basic::options::OptionKeys::distance_sampling("distance_sampling") ( "distance_sampling" )

Referenced by main().

◆ e2_catalytic_resnum

basic::options::IntegerOptionKey const basic::options::OptionKeys::e2_catalytic_resnum("e2_catalytic_resnum") ( "e2_catalytic_resnum" )

Referenced by HECTMover::parse_options(), and register_options().

◆ e2_chain

basic::options::StringOptionKey const basic::options::OptionKeys::e2_chain("e2_chain") ( "e2_chain" )

Referenced by HECTMover::parse_options(), and register_options().

◆ e3_catalytic_resnum

basic::options::IntegerOptionKey const basic::options::OptionKeys::e3_catalytic_resnum("e3_catalytic_resnum") ( "e3_catalytic_resnum" )

Referenced by HECTMover::parse_options(), and register_options().

◆ e3_hinge_chain

basic::options::StringOptionKey const basic::options::OptionKeys::e3_hinge_chain("e3_hinge_chain") ( "e3_hinge_chain" )

Referenced by HECTMover::parse_options(), and register_options().

◆ e3_hinge_start_resnum

basic::options::IntegerOptionKey const basic::options::OptionKeys::e3_hinge_start_resnum("e3_hinge_start_resnum") ( "e3_hinge_start_resnum" )

Referenced by HECTMover::parse_options(), and register_options().

◆ e3_hinge_stop_resnum

basic::options::IntegerOptionKey const basic::options::OptionKeys::e3_hinge_stop_resnum("e3_hinge_stop_resnum") ( "e3_hinge_stop_resnum" )

Referenced by HECTMover::parse_options(), and register_options().

◆ extension

utility::options::FileOptionKey const basic::options::OptionKeys::extension("extension") ( "extension" )

Referenced by determine_output_name(), main(), output_single_motif(), and read_in_extension().

◆ flexible_chain

basic::options::StringOptionKey const basic::options::OptionKeys::flexible_chain("flexible_chain") ( "flexible_chain" )

Referenced by FloppyTailMover::init_on_new_input(), and main().

◆ flexible_start_resnum

basic::options::IntegerOptionKey const basic::options::OptionKeys::flexible_start_resnum("flexible_start_resnum") ( "flexible_start_resnum" )

Referenced by FloppyTailMover::init_on_new_input(), and main().

◆ flexible_stop_resnum

basic::options::IntegerOptionKey const basic::options::OptionKeys::flexible_stop_resnum("flexible_stop_resnum") ( "flexible_stop_resnum" )

Referenced by FloppyTailMover::init_on_new_input(), and main().

◆ lsmdef

basic::options::StringOptionKey const basic::options::OptionKeys::lsmdef("lsmdef") ( "lsmdef" )

Referenced by main().

◆ max_distance

basic::options::RealOptionKey const basic::options::OptionKeys::max_distance("max_distance") ( "max_distance" )

Referenced by numeric::find_nearest_value(), and main().

◆ max_radius

basic::options::RealOptionKey const basic::options::OptionKeys::max_radius("max_radius") ( "max_radius" )

Referenced by numeric::geometry::hashing::SixDOffsetTree::init(), main(), and numeric::geometry::hashing::SixDCoordinateBinner::tree_init().

◆ min_pack

basic::options::BooleanOptionKey const basic::options::OptionKeys::min_pack ( "min_pack" )

Referenced by FixbbJobQueen::FixbbJobQueen(), lk_ball_wtd_deriv_test(), main(), repack_cluster(), and repack_step().

◆ minimize_sidechains

basic::options::BooleanOptionKey const basic::options::OptionKeys::minimize_sidechains ( "minimize_sidechains" )

Referenced by SymFixbbMover::apply(), FixbbJobQueen::complete_larval_job_maturation(), FixbbJobQueen::FixbbJobQueen(), and main().

◆ off_rotamer_pack

basic::options::BooleanOptionKey const basic::options::OptionKeys::off_rotamer_pack ( "off_rotamer_pack" )

Referenced by FixbbJobQueen::FixbbJobQueen(), and main().

◆ pair_off

basic::options::BooleanOptionKey const basic::options::OptionKeys::pair_off("pair_off") ( "pair_off" )

Referenced by FloppyTailMover::FloppyTailMover(), and main().

◆ publication

basic::options::BooleanOptionKey const basic::options::OptionKeys::publication("publication") ( "publication" )

Referenced by FloppyTailMover::apply(), and main().

◆ repack_cycles

basic::options::IntegerOptionKey const basic::options::OptionKeys::repack_cycles("cycles") ( "cycles" )

Referenced by FloppyTailMover::apply(), HECTMover::apply(), UBQ_E2Mover::apply(), UBQ_GTPase_disulfide_Mover::apply(), and register_options().

◆ shear_on

basic::options::RealOptionKey const basic::options::OptionKeys::shear_on("shear_on") ( "shear_on" )

Referenced by FloppyTailMover::apply(), and main().

◆ short_tail_fraction

basic::options::RealOptionKey const basic::options::OptionKeys::short_tail_fraction("short_tail_fraction") ( "short_tail_fraction" )

Referenced by FloppyTailMover::init_on_new_input(), and main().

◆ short_tail_off

basic::options::RealOptionKey const basic::options::OptionKeys::short_tail_off("short_tail_off") ( "short_tail_off" )

Referenced by FloppyTailMover::apply(), FloppyTailMover::init_on_new_input(), and main().

◆ stublist_filename

basic::options::FileOptionKey const basic::options::OptionKeys::stublist_filename("stublist") ( "stublist" )

Referenced by main().

◆ translocation_sampling

basic::options::RealOptionKey const basic::options::OptionKeys::translocation_sampling("translocation_sampling") ( "translocation_sampling" )

Referenced by main().

◆ ubq_cst_sd

basic::options::RealOptionKey const basic::options::OptionKeys::ubq_cst_sd("ubq_cst_sd") ( "ubq_cst_sd" )

Referenced by register_options(), and HECTMover::ubq_constraints().

◆ UBQ_tail_chain

basic::options::StringOptionKey const basic::options::OptionKeys::UBQ_tail_chain("UBQ_tail_chain") ( "UBQ_tail_chain" )

Referenced by HECTMover::parse_options(), and register_options().

◆ UBQ_tail_start_resnum

basic::options::IntegerOptionKey const basic::options::OptionKeys::UBQ_tail_start_resnum("UBQ_tail_start_resnum") ( "UBQ_tail_start_resnum" )

Referenced by HECTMover::parse_options(), and register_options().

Namespaces

Typedefs

Variables

Typedef Documentation

◆ KeyType

Variable Documentation

◆ angle_sampling

◆ C_root

◆ catalytic_cst_sd

◆ constrain_grid

◆ cycles

◆ debug

◆ debug_skip_fragment_generation

◆ distance_sampling

◆ e2_catalytic_resnum

◆ e2_chain

◆ e3_catalytic_resnum

◆ e3_hinge_chain

◆ e3_hinge_start_resnum

◆ e3_hinge_stop_resnum

◆ extension

◆ flexible_chain

◆ flexible_start_resnum

◆ flexible_stop_resnum

◆ lsmdef

◆ max_distance

◆ max_radius

◆ min_pack

◆ minimize_sidechains

◆ off_rotamer_pack

◆ pair_off

◆ publication

◆ repack_cycles

◆ shear_on

◆ short_tail_fraction

◆ short_tail_off

◆ stublist_filename

◆ translocation_sampling

◆ ubq_cst_sd

◆ UBQ_tail_chain

◆ UBQ_tail_start_resnum