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Namespaces | Variables
basic::options::OptionKeys::in Namespace Reference

Namespaces

 dbms
 
 file
 
 path
 
 rdf
 

Variables

BooleanOptionKey const in
 
FileVectorOptionKey const fconfig
 
BooleanOptionKey const no_fconfig
 
BooleanOptionKey const skip_classic_cart_setup
 
BooleanOptionKey const skip_new_cart_setup
 
StringOptionKey const Ntermini
 
StringOptionKey const Ctermini
 
BooleanOptionKey const use_truncated_termini
 
BooleanOptionKey const ignore_unrecognized_res
 
BooleanOptionKey const ignore_waters
 
StringOptionKey const water_type_if_unspecified
 
BooleanOptionKey const guarantee_no_DNA
 
BooleanOptionKey const add_orbitals
 
BooleanOptionKey const show_all_fixes
 
BooleanOptionKey const include_sugars
 
BooleanOptionKey const include_lipids
 
BooleanOptionKey const include_surfaces
 
BooleanOptionKey const read_only_ATOM_entries
 
BooleanOptionKey const auto_detect_glycan_connections
 
RealOptionKey const max_bond_length
 
RealOptionKey const min_bond_length
 
RealOptionKey const glycan_virtual_offset
 
BooleanOptionKey const membrane
 
RealOptionKey const tuning_param
 
BooleanOptionKey const remember_unrecognized_res
 
BooleanOptionKey const remember_unrecognized_water
 
BooleanOptionKey const preserve_crystinfo
 
BooleanOptionKey const fast_restyping
 
BooleanOptionKey const detect_oops
 
BooleanOptionKey const obey_ssbond
 
BooleanOptionKey const detect_disulf
 
RealOptionKey const detect_disulf_tolerance
 
BooleanOptionKey const constraints_from_link_records
 
BooleanOptionKey const auto_setup_metals
 
BooleanOptionKey const prevent_auto_setup_metal_bb_variants
 
RealOptionKey const metals_detection_LJ_multiplier
 
RealOptionKey const metals_distance_constraint_multiplier
 
RealOptionKey const metals_angle_constraint_multiplier
 
StringVectorOptionKey const name3_property_codes
 
StringVectorOptionKey const alternate_3_letter_codes
 
BooleanOptionKey const maintain_links
 
FileOptionKey const fix_disulf
 
BooleanOptionKey const missing_density_to_jump
 
IntegerVectorOptionKey const target_residues
 
IntegerVectorOptionKey const replonly_residues
 
BooleanOptionKey const replonly_loops
 
BooleanOptionKey const use_database
 
StringVectorOptionKey const select_structures_from_database
 

Variable Documentation

◆ add_orbitals

BooleanOptionKey const basic::options::OptionKeys::in::add_orbitals
extern

Referenced by add_rosetta_options_0().

◆ alternate_3_letter_codes

StringVectorOptionKey const basic::options::OptionKeys::in::alternate_3_letter_codes
extern

Referenced by add_rosetta_options_0().

◆ auto_detect_glycan_connections

BooleanOptionKey const basic::options::OptionKeys::in::auto_detect_glycan_connections
extern

Referenced by add_rosetta_options_0().

◆ auto_setup_metals

BooleanOptionKey const basic::options::OptionKeys::in::auto_setup_metals
extern

Referenced by add_rosetta_options_0().

◆ constraints_from_link_records

BooleanOptionKey const basic::options::OptionKeys::in::constraints_from_link_records
extern

Referenced by add_rosetta_options_0(), and main().

◆ Ctermini

StringOptionKey const basic::options::OptionKeys::in::Ctermini
extern

Referenced by add_rosetta_options_0().

◆ detect_disulf

BooleanOptionKey const basic::options::OptionKeys::in::detect_disulf
extern

Referenced by add_rosetta_options_0().

◆ detect_disulf_tolerance

RealOptionKey const basic::options::OptionKeys::in::detect_disulf_tolerance
extern

Referenced by add_rosetta_options_0().

◆ detect_oops

BooleanOptionKey const basic::options::OptionKeys::in::detect_oops
extern

Referenced by add_rosetta_options_0().

◆ fast_restyping

BooleanOptionKey const basic::options::OptionKeys::in::fast_restyping
extern

Referenced by add_rosetta_options_0().

◆ fconfig

FileVectorOptionKey const basic::options::OptionKeys::in::fconfig
extern

Referenced by add_rosetta_options_0().

◆ fix_disulf

FileOptionKey const basic::options::OptionKeys::in::fix_disulf
extern

Referenced by add_rosetta_options_0(), BBG_Cyclic_Mover::fix_disulf(), and BBG_Cyclic_Mover::setup_locker().

◆ glycan_virtual_offset

RealOptionKey const basic::options::OptionKeys::in::glycan_virtual_offset
extern

Referenced by add_rosetta_options_0().

◆ guarantee_no_DNA

BooleanOptionKey const basic::options::OptionKeys::in::guarantee_no_DNA
extern

Referenced by add_rosetta_options_0().

◆ ignore_unrecognized_res

BooleanOptionKey const basic::options::OptionKeys::in::ignore_unrecognized_res
extern

Referenced by add_rosetta_options_0(), and main().

◆ ignore_waters

BooleanOptionKey const basic::options::OptionKeys::in::ignore_waters
extern

Referenced by add_rosetta_options_0(), and main().

◆ in

BooleanOptionKey const basic::options::OptionKeys::in::in
extern

Referenced by add_rosetta_options_0(), CrystCluster::apply(), basic::ComparingTracer::ComparingTracer(), compute_intrinsic_deviation(), correct_dunbrack(), correct_rama(), utility::tag::Tag::create(), design(), design_homodimer(), basic::random::determine_random_number_seed(), dock(), utility::file::file_size(), get_aln(), get_frags_map(), get_out_number(), utility::file::gzip(), load_loops_from_file(), main(), make_frag_set_9mers(), my_main(), ui::task::ProjectView::on_action_open_project_triggered(), utility::io::izstream::open(), utility::io::ozstream::open(), utility::io::izstream::open_ifstream(), operator>>(), ui::task::operator>>(), output_packstat(), output_packstat_pdb(), ConstraintConfig::parse_config_file(), parsefilelist(), posewrap_from_command_line(), read_covalent_connections_file(), DisulfEposDatabase::read_data_file(), read_ddg_file(), read_equivalent_position_file(), read_frags(), read_input_weights(), read_jumpcut_file(), numeric::read_probabilities_or_die(), read_res_list(), SphereSample::read_sphere_data(), numeric::read_tensor_from_file(), readFile(), recover_clustered_frags(), register_options(), run(), FragmentAssemblyMover::run(), run_3bpy(), SphereSample::sanity_check(), Solver_NU::select_working_set(), setup_activity_table(), basic::resource_manager::locator::FileSystemResourceLocator::show(), test(), NodeTest::test_node_serialization(), NodeTest::test_project_serialization(), NodeTest::test_task_serialization(), test_vs_dots(), utility::file::trytry_ifstream_open(), utility::file::trytry_ofstream_open(), and write_cluster_frags().

◆ include_lipids

BooleanOptionKey const basic::options::OptionKeys::in::include_lipids
extern

Referenced by add_rosetta_options_0().

◆ include_sugars

BooleanOptionKey const basic::options::OptionKeys::in::include_sugars
extern

Referenced by add_rosetta_options_0().

◆ include_surfaces

BooleanOptionKey const basic::options::OptionKeys::in::include_surfaces
extern

Referenced by add_rosetta_options_0().

◆ maintain_links

BooleanOptionKey const basic::options::OptionKeys::in::maintain_links
extern

Referenced by add_rosetta_options_0().

◆ max_bond_length

RealOptionKey const basic::options::OptionKeys::in::max_bond_length
extern

Referenced by add_rosetta_options_0().

◆ membrane

BooleanOptionKey const basic::options::OptionKeys::in::membrane
extern

Referenced by add_rosetta_options_0(), create_MPpose(), and main().

◆ metals_angle_constraint_multiplier

RealOptionKey const basic::options::OptionKeys::in::metals_angle_constraint_multiplier
extern

Referenced by add_rosetta_options_0().

◆ metals_detection_LJ_multiplier

RealOptionKey const basic::options::OptionKeys::in::metals_detection_LJ_multiplier
extern

Referenced by add_rosetta_options_0().

◆ metals_distance_constraint_multiplier

RealOptionKey const basic::options::OptionKeys::in::metals_distance_constraint_multiplier
extern

Referenced by add_rosetta_options_0().

◆ min_bond_length

RealOptionKey const basic::options::OptionKeys::in::min_bond_length
extern

Referenced by add_rosetta_options_0().

◆ missing_density_to_jump

BooleanOptionKey const basic::options::OptionKeys::in::missing_density_to_jump
extern

Referenced by add_rosetta_options_0(), and main().

◆ name3_property_codes

StringVectorOptionKey const basic::options::OptionKeys::in::name3_property_codes
extern

Referenced by add_rosetta_options_0().

◆ no_fconfig

BooleanOptionKey const basic::options::OptionKeys::in::no_fconfig
extern

Referenced by add_rosetta_options_0().

◆ Ntermini

StringOptionKey const basic::options::OptionKeys::in::Ntermini
extern

Referenced by add_rosetta_options_0().

◆ obey_ssbond

BooleanOptionKey const basic::options::OptionKeys::in::obey_ssbond
extern

Referenced by add_rosetta_options_0().

◆ preserve_crystinfo

BooleanOptionKey const basic::options::OptionKeys::in::preserve_crystinfo
extern

Referenced by add_rosetta_options_0(), and my_main().

◆ prevent_auto_setup_metal_bb_variants

BooleanOptionKey const basic::options::OptionKeys::in::prevent_auto_setup_metal_bb_variants
extern

Referenced by add_rosetta_options_0().

◆ read_only_ATOM_entries

BooleanOptionKey const basic::options::OptionKeys::in::read_only_ATOM_entries
extern

Referenced by add_rosetta_options_0().

◆ remember_unrecognized_res

BooleanOptionKey const basic::options::OptionKeys::in::remember_unrecognized_res
extern

Referenced by add_rosetta_options_0().

◆ remember_unrecognized_water

BooleanOptionKey const basic::options::OptionKeys::in::remember_unrecognized_water
extern

Referenced by add_rosetta_options_0().

◆ replonly_loops

BooleanOptionKey const basic::options::OptionKeys::in::replonly_loops
extern

Referenced by add_rosetta_options_0().

◆ replonly_residues

IntegerVectorOptionKey const basic::options::OptionKeys::in::replonly_residues
extern

Referenced by add_rosetta_options_0().

◆ select_structures_from_database

StringVectorOptionKey const basic::options::OptionKeys::in::select_structures_from_database
extern

Referenced by add_rosetta_options_0(), and main().

◆ show_all_fixes

BooleanOptionKey const basic::options::OptionKeys::in::show_all_fixes
extern

Referenced by add_rosetta_options_0().

◆ skip_classic_cart_setup

BooleanOptionKey const basic::options::OptionKeys::in::skip_classic_cart_setup
extern

Referenced by add_rosetta_options_0().

◆ skip_new_cart_setup

BooleanOptionKey const basic::options::OptionKeys::in::skip_new_cart_setup
extern

Referenced by add_rosetta_options_0().

◆ target_residues

IntegerVectorOptionKey const basic::options::OptionKeys::in::target_residues
extern

Referenced by add_rosetta_options_0(), Bola::Bola(), design_target(), main(), and register_options().

◆ tuning_param

RealOptionKey const basic::options::OptionKeys::in::tuning_param
extern

Referenced by add_rosetta_options_0(), and main().

◆ use_database

BooleanOptionKey const basic::options::OptionKeys::in::use_database
extern

Referenced by add_rosetta_options_0(), and main().

◆ use_truncated_termini

BooleanOptionKey const basic::options::OptionKeys::in::use_truncated_termini
extern

Referenced by add_rosetta_options_0().

◆ water_type_if_unspecified

StringOptionKey const basic::options::OptionKeys::in::water_type_if_unspecified
extern

Referenced by add_rosetta_options_0().

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