Rosetta
Variables
basic::options::OptionKeys::out::file Namespace Reference

Variables

BooleanOptionKey const file
 
StringOptionKey const o
 
FileOptionKey const design_contrast
 
StringOptionKey const residue_type_set
 
BooleanOptionKey const srlz
 
StringOptionKey const atom_tree_diff
 
IntegerOptionKey const atom_tree_diff_bb
 
IntegerOptionKey const atom_tree_diff_sc
 
IntegerOptionKey const atom_tree_diff_bl
 
StringOptionKey const alignment
 
StringOptionKey const score_only
 
StringOptionKey const scorefile
 
StringOptionKey const scorefile_format
 
StringOptionKey const silent
 
StringOptionKey const silent_struct_type
 
BooleanOptionKey const silent_print_all_score_headers
 
BooleanOptionKey const raw
 
BooleanOptionKey const weight_silent_scores
 
BooleanOptionKey const silent_preserve_H
 
BooleanOptionKey const fullatom
 
BooleanOptionKey const suppress_zero_occ_pdb_output
 
BooleanOptionKey const output_ligands_as_separate_chains
 
BooleanOptionKey const output_virtual
 
BooleanOptionKey const output_virtual_zero_occ
 
BooleanOptionKey const no_chainend_ter
 
BooleanOptionKey const no_output_cen
 
BooleanOptionKey const output_orbitals
 
BooleanOptionKey const renumber_pdb
 
BooleanOptionKey const pdb_parents
 
BooleanOptionKey const per_chain_renumbering
 
BooleanOptionKey const output_secondary_structure
 
BooleanOptionKey const do_not_autoassign_SS
 
BooleanOptionKey const output_torsions
 
BooleanOptionKey const use_occurrence_data
 
BooleanOptionKey const pdb_comments
 
BooleanOptionKey const force_nonideal_structure
 
StringOptionKey const set_pdb_author
 
BooleanOptionKey const write_pdb_title_section_records
 
BooleanOptionKey const write_pdb_link_records
 
BooleanOptionKey const use_pdb_format_HETNAM_records
 
BooleanOptionKey const write_pdb_parametric_info
 
BooleanOptionKey const write_glycan_pdb_codes
 
BooleanOptionKey const write_seqres_records
 
BooleanOptionKey const output_pose_energies_table
 
BooleanOptionKey const output_pose_cache_data
 
BooleanOptionKey const output_pose_fold_tree
 
BooleanOptionKey const output_only_asymmetric_unit
 
BooleanOptionKey const cif_extra_data_separate_file
 
BooleanOptionKey const dont_rewrite_dunbrack_database
 
StringOptionKey const frag_prefix
 
BooleanOptionKey const no_extra_sdf_data
 
BooleanOptionKey const no_scores_in_pdb
 

Variable Documentation

◆ alignment

StringOptionKey const basic::options::OptionKeys::out::file::alignment
extern

Referenced by add_rosetta_options_0().

◆ atom_tree_diff

StringOptionKey const basic::options::OptionKeys::out::file::atom_tree_diff
extern

Referenced by add_rosetta_options_0(), and main().

◆ atom_tree_diff_bb

IntegerOptionKey const basic::options::OptionKeys::out::file::atom_tree_diff_bb
extern

Referenced by add_rosetta_options_0().

◆ atom_tree_diff_bl

IntegerOptionKey const basic::options::OptionKeys::out::file::atom_tree_diff_bl
extern

Referenced by add_rosetta_options_0().

◆ atom_tree_diff_sc

IntegerOptionKey const basic::options::OptionKeys::out::file::atom_tree_diff_sc
extern

Referenced by add_rosetta_options_0().

◆ cif_extra_data_separate_file

BooleanOptionKey const basic::options::OptionKeys::out::file::cif_extra_data_separate_file
extern

Referenced by add_rosetta_options_0().

◆ design_contrast

FileOptionKey const basic::options::OptionKeys::out::file::design_contrast
extern

Referenced by add_rosetta_options_0().

◆ do_not_autoassign_SS

BooleanOptionKey const basic::options::OptionKeys::out::file::do_not_autoassign_SS
extern

Referenced by add_rosetta_options_0().

◆ dont_rewrite_dunbrack_database

BooleanOptionKey const basic::options::OptionKeys::out::file::dont_rewrite_dunbrack_database
extern

Referenced by add_rosetta_options_0().

◆ file

BooleanOptionKey const basic::options::OptionKeys::out::file::file
extern

Referenced by add_rosetta_options_0().

◆ force_nonideal_structure

BooleanOptionKey const basic::options::OptionKeys::out::file::force_nonideal_structure
extern

Referenced by add_rosetta_options_0().

◆ frag_prefix

StringOptionKey const basic::options::OptionKeys::out::file::frag_prefix
extern

Referenced by add_rosetta_options_0(), and main().

◆ fullatom

BooleanOptionKey const basic::options::OptionKeys::out::file::fullatom
extern

Referenced by add_rosetta_options_0().

◆ no_chainend_ter

BooleanOptionKey const basic::options::OptionKeys::out::file::no_chainend_ter
extern

Referenced by add_rosetta_options_0().

◆ no_extra_sdf_data

BooleanOptionKey const basic::options::OptionKeys::out::file::no_extra_sdf_data
extern

Referenced by add_rosetta_options_0().

◆ no_output_cen

BooleanOptionKey const basic::options::OptionKeys::out::file::no_output_cen
extern

Referenced by add_rosetta_options_0().

◆ no_scores_in_pdb

BooleanOptionKey const basic::options::OptionKeys::out::file::no_scores_in_pdb
extern

Referenced by add_rosetta_options_0().

◆ o

StringOptionKey const basic::options::OptionKeys::out::file::o
extern

Referenced by ObjexxFCL::internal::ObserverMediator::acyclic(), add_rosetta_options_0(), align_carboxyl_diiron(), align_carboxyl_diiron_OLD(), RosettaHolesMover::apply(), numeric::xyzTransform< T >::approx_lever_distance(), ui::network::as_hexadecimal(), bind_std_forward_list(), bind_std_functional_hash(), bind_std_stl_deque(), bind_std_stl_function(), bind_std_stl_list(), bind_std_stl_multiset(), bind_std_stl_vector(), bind_std_stl_vector_1(), bind_std_unordered_map(), bind_std_unordered_set(), bind_T05_default(), bind_T07_class(), bind_T07_class_match_args(), bind_T10_inheritance(), bind_T10_virtual_inheritance(), bind_T12_insertion_operator(), bind_T12_insertion_operator_1(), bind_T12_insertion_operator_2(), bind_T12_insertion_operator_3(), bind_T12_insertion_operator_4(), bind_T15_copy(), bind_T31_include_for_class_incl_a_include(), bind_T80_custom_trampoline(), PyCallBack_Mammal_1_t::Breathe(), PyCallBack_Dog_1_t::Breathe(), Link::clashes(), utility::py::COP_to_Python_converter< T >::convert(), ui::network::create_argument(), MatchSet::cross(), MatchSet::cross_homodimer(), cxdock_design(), design_hits(), design_test(), MyRT::distance_squared(), do_event_prediction(), dock(), doit(), PoseWrap::dump_pdb(), dump_points_pdb(), dump_points_pdb_contacts(), PyCallBack_Animal_1_t::Eat(), PyCallBack_Mammal_1_t::Eat(), PyCallBack_Dog_1_t::Eat(), HBondedPairIterator::equal(), basic::Emitter::escape_string(), PyCallBack_A2::f(), PyCallBack_A3::f(), PyCallBack_Base::f_v(), PyCallBack_Derived::f_v(), PyCallBack_Delete::f_v(), PyCallBack_Base::f_v_2(), PyCallBack_Derived::f_v_2(), PyCallBack_Delete::f_v_2(), PyCallBack_X::f_v_2(), fill_optional_options(), PyCallBack_Base::foo(), PyCallBack_n1_A::foo(), PyCallBack_n1_n2_A::foo(), PyCallBack_Base::foo_int(), PyCallBack_Base::foo_protected(), PyCallBack_Derived::foo_protected(), PyCallBack_Delete::foo_protected(), PyCallBack_X::foo_protected(), PyCallBack_Base::foo_sring(), PyCallBack_Base::foo_sring_r(), PyCallBack_Base::foo_void(), PyCallBack_Base::foo_void_pure(), generate_disulfide_conformations(), ui::task::Updater::get(), get_hbond_rotation_samples(), harvest_motifs(), harvest_motifs_one(), intersecting_bpy_axes(), intersecting_disulfide_axes(), PyCallBack_Animal_1_t::isDog(), PyCallBack_Mammal_1_t::isDog(), PyCallBack_Dog_1_t::isDog(), TCDock::justone(), main(), utility::options::OptionCollection::merged(), utility::Enumerate1::operator!=(), numeric::random::WeightedReservoirItem< T >::operator<(), operator<<(), PyCallBack_A4::operator=(), utility::Enumerate1::operator==(), numeric::VoxelArray< _Float, _Value >::operator==(), output_results(), RBSegmentRelax_test(), register_options(), report(), rescore(), ThisApplication::run(), run(), core::pack::annealer::FixbbSimAnnealer::run(), HubDenovo::run(), run_diiron_glu(), run_parallel_docking(), protocols::abinitio::JumpSpecificAbrelax::setup_jumps(), sicdock_thread_num(), small_min_test(), ui::task::TaskSyncer_TaskStrategy::subscribe(), and ui::task::Task::task_data().

◆ output_ligands_as_separate_chains

BooleanOptionKey const basic::options::OptionKeys::out::file::output_ligands_as_separate_chains
extern

Referenced by add_rosetta_options_0().

◆ output_only_asymmetric_unit

BooleanOptionKey const basic::options::OptionKeys::out::file::output_only_asymmetric_unit
extern

Referenced by add_rosetta_options_0().

◆ output_orbitals

BooleanOptionKey const basic::options::OptionKeys::out::file::output_orbitals
extern

Referenced by add_rosetta_options_0().

◆ output_pose_cache_data

BooleanOptionKey const basic::options::OptionKeys::out::file::output_pose_cache_data
extern

Referenced by add_rosetta_options_0().

◆ output_pose_energies_table

BooleanOptionKey const basic::options::OptionKeys::out::file::output_pose_energies_table
extern

Referenced by add_rosetta_options_0().

◆ output_pose_fold_tree

BooleanOptionKey const basic::options::OptionKeys::out::file::output_pose_fold_tree
extern

Referenced by add_rosetta_options_0().

◆ output_secondary_structure

BooleanOptionKey const basic::options::OptionKeys::out::file::output_secondary_structure
extern

Referenced by add_rosetta_options_0().

◆ output_torsions

BooleanOptionKey const basic::options::OptionKeys::out::file::output_torsions
extern

Referenced by add_rosetta_options_0().

◆ output_virtual

BooleanOptionKey const basic::options::OptionKeys::out::file::output_virtual
extern

Referenced by add_rosetta_options_0(), dump_efactor_pdb(), report(), and MatchSet::write_to_file().

◆ output_virtual_zero_occ

BooleanOptionKey const basic::options::OptionKeys::out::file::output_virtual_zero_occ
extern

Referenced by add_rosetta_options_0().

◆ pdb_comments

BooleanOptionKey const basic::options::OptionKeys::out::file::pdb_comments
extern

Referenced by add_rosetta_options_0().

◆ pdb_parents

BooleanOptionKey const basic::options::OptionKeys::out::file::pdb_parents
extern

Referenced by add_rosetta_options_0().

◆ per_chain_renumbering

BooleanOptionKey const basic::options::OptionKeys::out::file::per_chain_renumbering
extern

Referenced by add_rosetta_options_0().

◆ raw

BooleanOptionKey const basic::options::OptionKeys::out::file::raw
extern

Referenced by add_rosetta_options_0(), and basic::Tracer::set_ios_hook().

◆ renumber_pdb

BooleanOptionKey const basic::options::OptionKeys::out::file::renumber_pdb
extern

Referenced by add_rosetta_options_0(), and main().

◆ residue_type_set

StringOptionKey const basic::options::OptionKeys::out::file::residue_type_set
extern

Referenced by add_rosetta_options_0(), and main().

◆ score_only

StringOptionKey const basic::options::OptionKeys::out::file::score_only
extern

Referenced by add_rosetta_options_0(), and main().

◆ scorefile

StringOptionKey const basic::options::OptionKeys::out::file::scorefile
extern

Referenced by add_rosetta_options_0(), and main().

◆ scorefile_format

StringOptionKey const basic::options::OptionKeys::out::file::scorefile_format
extern

Referenced by add_rosetta_options_0().

◆ set_pdb_author

StringOptionKey const basic::options::OptionKeys::out::file::set_pdb_author
extern

Referenced by add_rosetta_options_0().

◆ silent

StringOptionKey const basic::options::OptionKeys::out::file::silent
extern

Referenced by add_rosetta_options_0(), check_structures(), MatchSet::cross(), MatchSet::cross_homodimer(), cxdock_design(), dock(), fill_optional_options(), protocols::abinitio::JumpSpecificAbrelax::fold(), main(), report_and_dump(), rescore(), run(), HubDenovo::run(), run_aio(), set_basic_dock_options(), set_file_output(), and StepWiseJobQueen::StepWiseJobQueen().

◆ silent_preserve_H

BooleanOptionKey const basic::options::OptionKeys::out::file::silent_preserve_H
extern

Referenced by add_rosetta_options_0().

◆ silent_print_all_score_headers

BooleanOptionKey const basic::options::OptionKeys::out::file::silent_print_all_score_headers
extern

Referenced by add_rosetta_options_0(), and main().

◆ silent_struct_type

StringOptionKey const basic::options::OptionKeys::out::file::silent_struct_type
extern

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

◆ srlz

BooleanOptionKey const basic::options::OptionKeys::out::file::srlz
extern

Referenced by add_rosetta_options_0().

◆ suppress_zero_occ_pdb_output

BooleanOptionKey const basic::options::OptionKeys::out::file::suppress_zero_occ_pdb_output
extern

Referenced by add_rosetta_options_0().

◆ use_occurrence_data

BooleanOptionKey const basic::options::OptionKeys::out::file::use_occurrence_data
extern

Referenced by add_rosetta_options_0().

◆ use_pdb_format_HETNAM_records

BooleanOptionKey const basic::options::OptionKeys::out::file::use_pdb_format_HETNAM_records
extern

Referenced by add_rosetta_options_0().

◆ weight_silent_scores

BooleanOptionKey const basic::options::OptionKeys::out::file::weight_silent_scores
extern

Referenced by add_rosetta_options_0().

◆ write_glycan_pdb_codes

BooleanOptionKey const basic::options::OptionKeys::out::file::write_glycan_pdb_codes
extern

Referenced by add_rosetta_options_0().

◆ write_pdb_link_records

BooleanOptionKey const basic::options::OptionKeys::out::file::write_pdb_link_records
extern

Referenced by add_rosetta_options_0(), and main().

◆ write_pdb_parametric_info

BooleanOptionKey const basic::options::OptionKeys::out::file::write_pdb_parametric_info
extern

Referenced by add_rosetta_options_0().

◆ write_pdb_title_section_records

BooleanOptionKey const basic::options::OptionKeys::out::file::write_pdb_title_section_records
extern

Referenced by add_rosetta_options_0().

◆ write_seqres_records

BooleanOptionKey const basic::options::OptionKeys::out::file::write_seqres_records
extern

Referenced by add_rosetta_options_0().

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