local Namespace Reference

Classes
struct	HbondInfo

Variables
basic::options::BooleanOptionKey const	AvNAPSA_positive ("AvNAPSA_positive")
basic::options::BooleanOptionKey const	AvNAPSA_negative ("AvNAPSA_negative")
basic::options::BooleanOptionKey const	target_net_charge_active ("target_net_charge_active")
basic::options::IntegerOptionKey const	target_net_charge ("target_net_charge")
basic::options::IntegerOptionKey const	surface_atom_cutoff ("surface_atom_cutoff")
basic::options::IntegerOptionKey const	surface_residue_cutoff ("surface_residue_cutoff")
basic::options::BooleanOptionKey const	include_arg ("include_arg")
basic::options::BooleanOptionKey const	include_lys ("include_lys")
basic::options::BooleanOptionKey const	include_asp ("include_asp")
basic::options::BooleanOptionKey const	include_glu ("include_glu")
basic::options::RealOptionKey const	refweight_arg ("refweight_arg")
basic::options::RealOptionKey const	refweight_lys ("refweight_lys")
basic::options::RealOptionKey const	refweight_asp ("refweight_asp")
basic::options::RealOptionKey const	refweight_glu ("refweight_glu")
basic::options::BooleanOptionKey const	dont_mutate_glyprocys ("dont_mutate_glyprocys")
basic::options::BooleanOptionKey const	dont_mutate_correct_charge ("dont_mutate_correct_charge")
basic::options::BooleanOptionKey const	dont_mutate_hbonded_sidechains ("dont_mutate_hbonded_sidechains")
basic::options::BooleanOptionKey const	pre_packminpack ("pre_packminpack")
basic::options::IntegerOptionKey const	nstruct ("nstruct")
basic::options::BooleanOptionKey const	compare_residue_energies_all ("compare_residue_energies_all")
basic::options::BooleanOptionKey const	compare_residue_energies_mut ("compare_residue_energies_mut")
basic::options::FileOptionKey const	partner1 ("partner1")
basic::options::FileOptionKey const	partner2 ("partner2")
basic::options::FileOptionKey const	match_pdb ("match_pdb")
basic::options::IntegerOptionKey const	partner2_residue ("partner2_residue")
basic::options::BooleanOptionKey const	skip_sitegraft_repack ("skip_sitegraft_repack")
basic::options::RealOptionKey const	atom_sasa_cutoff ("atom_sasa_cutoff")
basic::options::RealOptionKey const	neighbor_distance_cutoff ("neighbor_distance_cutoff")
basic::options::IntegerOptionKey const	window_width ("window_width")
basic::options::IntegerOptionKey const	helix_length ("helix_length")
basic::options::StringOptionKey const	reference_zinc_site ("reference_zinc_site")
basic::options::IntegerOptionKey const	first_ref_his ("first_ref_his")
basic::options::IntegerOptionKey const	ref_zinc ("ref_zinc")
basic::options::RealOptionKey const	temperature ("temperature")
basic::options::IntegerOptionKey const	n_moves ("n_moves")
basic::options::RealOptionKey const	constraint_weight ("constraint_weight")
basic::options::RealOptionKey const	max_angle ("max_angle")
basic::options::IntegerOptionKey const	small_moves ("small_moves")
basic::options::IntegerOptionKey const	shear_moves ("shear_moves")
basic::options::StringOptionKey const	metal_type ("metal_type")
basic::options::RealOptionKey const	metal_ligand_distance_cutoff ("metal_ligand_distance_cutoff")
basic::options::IntegerOptionKey const	min_total_coord_atoms ("min_total_coord_atoms")
basic::options::IntegerOptionKey const	min_local_coord_atoms ("min_local_coord_atoms")
basic::options::IntegerOptionKey const	min_coord_res ("min_coord_res")
basic::options::IntegerOptionKey const	max_res_span ("max_res_span")
basic::options::BooleanOptionKey const	require_bordering_ss ("require_bordering_ss")
basic::options::IntegerOptionKey const	max_loop_size ("max_loop_size")
basic::options::BooleanOptionKey const	helices_only ("helices_only")
basic::options::BooleanOptionKey const	strict_ss_changes ("strict_ss_changes")
basic::options::BooleanOptionKey const	append_nonlocal_residues ("append_nonlocal_residues")
basic::options::StringOptionKey const	allowed_elements ("allowed_elements")
basic::options::BooleanOptionKey const	allow_his ("allow_his")
basic::options::BooleanOptionKey const	allow_de ("allow_de")
basic::options::StringOptionKey const	secstruct ("secstruct")
basic::options::RealOptionKey const	sampling_range ("sampling_range")
basic::options::RealOptionKey const	sampling_increment ("sampling_increment")
basic::options::StringOptionKey const	output_name ("output_name")

Variable Documentation

basic::options::BooleanOptionKey const local::allow_de("allow_de")

Referenced by zinc_stats::ZincStatisticGenerator::initialize_from_options(), and main().

basic::options::BooleanOptionKey const local::allow_his("allow_his")

Referenced by zinc_stats::ZincStatisticGenerator::initialize_from_options(), and main().

basic::options::StringOptionKey const local::allowed_elements("allowed_elements")

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

basic::options::BooleanOptionKey const local::append_nonlocal_residues("append_nonlocal_residues")

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

basic::options::RealOptionKey const local::atom_sasa_cutoff("atom_sasa_cutoff")

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

basic::options::BooleanOptionKey const local::AvNAPSA_negative("AvNAPSA_negative")

Referenced by supercharge::apply(), supercharge::AvNAPSA_values(), main(), and supercharge::set_resfile_AvNAPSA().

basic::options::BooleanOptionKey const local::AvNAPSA_positive("AvNAPSA_positive")

Referenced by supercharge::apply(), supercharge::AvNAPSA_values(), supercharge::design_supercharge_AvNAPSA(), main(), and supercharge::set_resfile_AvNAPSA().

basic::options::BooleanOptionKey const local::compare_residue_energies_all("compare_residue_energies_all")

Referenced by supercharge::apply(), supercharge::energy_comparison(), and main().

basic::options::BooleanOptionKey const local::compare_residue_energies_mut("compare_residue_energies_mut")

Referenced by supercharge::apply(), supercharge::energy_comparison(), and main().

basic::options::RealOptionKey const local::constraint_weight("constraint_weight")

Referenced by add_rosetta_options_7(), main(), and setup_ca_constraints().

basic::options::BooleanOptionKey const local::dont_mutate_correct_charge("dont_mutate_correct_charge")

Referenced by main(), and supercharge::set_resfile().

basic::options::BooleanOptionKey const local::dont_mutate_glyprocys("dont_mutate_glyprocys")

Referenced by main(), and supercharge::set_resfile().

basic::options::BooleanOptionKey const local::dont_mutate_hbonded_sidechains("dont_mutate_hbonded_sidechains")

Referenced by main(), and supercharge::set_resfile().

basic::options::IntegerOptionKey const local::first_ref_his("first_ref_his")

Referenced by main().

basic::options::BooleanOptionKey const local::helices_only("helices_only")

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

basic::options::IntegerOptionKey const local::helix_length("helix_length")

Referenced by main().

basic::options::BooleanOptionKey const local::include_arg("include_arg")

Referenced by supercharge::apply(), supercharge::design_supercharge(), main(), and supercharge::set_resfile().

basic::options::BooleanOptionKey const local::include_asp("include_asp")

Referenced by supercharge::apply(), supercharge::design_supercharge(), main(), and supercharge::set_resfile().

basic::options::BooleanOptionKey const local::include_glu("include_glu")

Referenced by supercharge::apply(), supercharge::design_supercharge(), main(), and supercharge::set_resfile().

basic::options::BooleanOptionKey const local::include_lys("include_lys")

Referenced by supercharge::apply(), supercharge::design_supercharge(), main(), and supercharge::set_resfile().

basic::options::FileOptionKey const local::match_pdb("match_pdb")

Referenced by main().

basic::options::RealOptionKey const local::max_angle("max_angle")

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

basic::options::IntegerOptionKey const local::max_loop_size("max_loop_size")

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

basic::options::IntegerOptionKey const local::max_res_span("max_res_span")

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

basic::options::RealOptionKey const local::metal_ligand_distance_cutoff("metal_ligand_distance_cutoff")

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

basic::options::StringOptionKey const local::metal_type("metal_type")

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

basic::options::IntegerOptionKey const local::min_coord_res("min_coord_res")

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

basic::options::IntegerOptionKey const local::min_local_coord_atoms("min_local_coord_atoms")

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

basic::options::IntegerOptionKey const local::min_total_coord_atoms("min_total_coord_atoms")

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

basic::options::IntegerOptionKey const local::n_moves("n_moves")

Referenced by main().

basic::options::RealOptionKey const local::neighbor_distance_cutoff("neighbor_distance_cutoff")

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

basic::options::IntegerOptionKey const local::nstruct("nstruct")

Referenced by add_rosetta_options_0(), supercharge::design_supercharge(), erraser2_test(), fill_required_options(), insert_stage_tag(), main(), report_and_dump(), rna_build_helix_test(), rna_design_test(), FragmentAssemblyMover::run(), and StepWiseJobQueen::StepWiseJobQueen().

basic::options::StringOptionKey const local::output_name("output_name")

Referenced by MetalSiteFinderMover::apply(), zinc_stats::ZincStatisticGenerator::initialize_from_options(), main(), and zinc1_homodimer_design::setup_output_tag().

basic::options::FileOptionKey const local::partner1("partner1")

Referenced by main().

basic::options::FileOptionKey const local::partner2("partner2")

Referenced by main().

basic::options::IntegerOptionKey const local::partner2_residue("partner2_residue")

Referenced by main().

basic::options::BooleanOptionKey const local::pre_packminpack("pre_packminpack")

Referenced by main(), and supercharge::prepack_input_structure().

basic::options::IntegerOptionKey const local::ref_zinc("ref_zinc")

Referenced by main().

basic::options::StringOptionKey const local::reference_zinc_site("reference_zinc_site")

Referenced by main().

basic::options::RealOptionKey const local::refweight_arg("refweight_arg")

Referenced by main(), and supercharge::set_reference_energies().

basic::options::RealOptionKey const local::refweight_asp("refweight_asp")

Referenced by main(), and supercharge::set_reference_energies().

basic::options::RealOptionKey const local::refweight_glu("refweight_glu")

Referenced by main(), and supercharge::set_reference_energies().

basic::options::RealOptionKey const local::refweight_lys("refweight_lys")

Referenced by main(), and supercharge::set_reference_energies().

basic::options::BooleanOptionKey const local::require_bordering_ss("require_bordering_ss")

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

basic::options::RealOptionKey const local::sampling_increment("sampling_increment")

Referenced by zinc_stats::ZincStatisticGenerator::initialize_from_options(), and main().

basic::options::RealOptionKey const local::sampling_range("sampling_range")

Referenced by zinc_stats::ZincStatisticGenerator::initialize_from_options(), and main().

basic::options::StringOptionKey const local::secstruct("secstruct")

Referenced by add_rosetta_options_13(), add_rosetta_options_4(), MetalSiteFinderMover::apply(), MPDomainAssembly::apply(), zinc_stats::ZincStatisticGenerator::initialize_from_options(), zinc_stats::ZincStatisticGenerator::iterate_over_residues(), main(), rebuild_test(), rna_fullatom_minimize_test(), and spanfile_from_pdb().

basic::options::IntegerOptionKey const local::shear_moves("shear_moves")

Referenced by add_rosetta_options_7(), and main().

basic::options::BooleanOptionKey const local::skip_sitegraft_repack("skip_sitegraft_repack")

Referenced by main().

basic::options::IntegerOptionKey const local::small_moves("small_moves")

Referenced by add_rosetta_options_12(), and main().

basic::options::BooleanOptionKey const local::strict_ss_changes("strict_ss_changes")

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

basic::options::IntegerOptionKey const local::surface_atom_cutoff("surface_atom_cutoff")

Referenced by main(), supercharge::set_resfile_AvNAPSA(), and supercharge::set_surface().

basic::options::IntegerOptionKey const local::surface_residue_cutoff("surface_residue_cutoff")

Referenced by main(), and supercharge::set_surface().

basic::options::IntegerOptionKey const local::target_net_charge("target_net_charge")

Referenced by supercharge::apply(), supercharge::design_supercharge(), main(), and supercharge::set_resfile_AvNAPSA().

basic::options::BooleanOptionKey const local::target_net_charge_active("target_net_charge_active")

Referenced by supercharge::apply(), supercharge::design_supercharge(), main(), and supercharge::set_resfile_AvNAPSA().

basic::options::RealOptionKey const local::temperature("temperature")

Referenced by add_rosetta_options_10(), add_rosetta_options_13(), add_rosetta_options_14(), add_rosetta_options_15(), add_rosetta_options_4(), add_rosetta_options_7(), create_ensemble(), and main().

basic::options::IntegerOptionKey const local::window_width("window_width")

Referenced by main().