basic::options::OptionKeys::in::file Namespace Reference

Variables
BooleanOptionKey const	file
FileVectorOptionKey const	s
FileVectorOptionKey const	t
FileVectorOptionKey const	l
FileOptionKey const	job_definition_file
FileVectorOptionKey const	list
BooleanOptionKey const	srlz
BooleanOptionKey const	srlz_override
FileVectorOptionKey const	screening_list
FileOptionKey const	screening_job_file
BooleanOptionKey const	shuffle_screening_jobs
FileOptionKey const	native
FileOptionKey const	torsion_bin_probs
FileOptionKey const	PCS_frag_cst
FileOptionKey const	talos_phi_psi
FileOptionKey const	talos_cs
FileOptionKey const	ambig_talos_cs_A
FileOptionKey const	ambig_talos_cs_B
IntegerVectorOptionKey const	native_exclude_res
BooleanOptionKey const	no_detect_pseudobonds
StringVectorOptionKey const	tags
StringVectorOptionKey const	user_tags
FileOptionKey const	tagfile
FileVectorOptionKey const	frag_files
StringVectorOptionKey const	remap_pdb_atom_names_for
FileVectorOptionKey const	extra_res
FileVectorOptionKey const	extra_res_fa
BooleanOptionKey const	override_database_params
FileVectorOptionKey const	extra_res_mol
FileVectorOptionKey const	extra_res_mmCIF
BooleanOptionKey const	load_PDB_components
StringOptionKey const	PDB_components_directory
StringVectorOptionKey const	PDB_components_overrides
BooleanOptionKey const	check_all_PDB_components
StringOptionKey const	extra_res_database
StringOptionKey const	extra_res_pq_schema
StringOptionKey const	extra_res_database_mode
FileOptionKey const	extra_res_database_resname_list
FileVectorOptionKey const	extra_res_cen
PathVectorOptionKey const	extra_res_path
PathVectorOptionKey const	extra_rot_lib_path
PathVectorOptionKey const	override_rot_lib_path
PathVectorOptionKey const	extra_res_batch_path
FileVectorOptionKey const	extra_patch_fa
FileVectorOptionKey const	extra_patch_cen
StringOptionKey const	frag3
StringOptionKey const	frag9
StringOptionKey const	fragA
StringOptionKey const	fragB
StringOptionKey const	surface_vectors
StringOptionKey const	xyz
BooleanOptionKey const	keep_input_scores
BooleanOptionKey const	lazy_silent
FileVectorOptionKey const	silent
BooleanOptionKey const	force_silent_bitflip_on_read
FileVectorOptionKey const	atom_tree_diff
StringOptionKey const	zip
FileVectorOptionKey const	boinc_wu_zip
BooleanOptionKey const	fullatom
BooleanOptionKey const	centroid_input
BooleanOptionKey const	centroid
BooleanOptionKey const	assign_gasteiger_atom_types
StringOptionKey const	treat_residues_in_these_chains_as_separate_chemical_entities
StringOptionKey const	residue_type_set
FileOptionKey const	pca
RealOptionKey const	silent_energy_cut
FileVectorOptionKey const	silent_list
BooleanOptionKey const	silent_renumber
StringOptionKey const	silent_struct_type
BooleanOptionKey const	silent_read_through_errors
StringOptionKey const	silent_score_prefix
IntegerOptionKey const	silent_select_random
IntegerOptionKey const	silent_select_range_start
IntegerOptionKey const	silent_select_range_mul
IntegerOptionKey const	silent_select_range_len
BooleanOptionKey const	skip_failed_simulations
StringVectorOptionKey const	silent_scores_wanted
FileVectorOptionKey const	fasta
FileVectorOptionKey const	pssm
StringVectorOptionKey const	seq
FileOptionKey const	checkpoint
FileOptionKey const	binary_chk
FileVectorOptionKey const	alignment
FileVectorOptionKey const	alignment2
FileOptionKey const	rama2b_map
FileOptionKey const	psipred_ss2
FileOptionKey const	dssp
BooleanOptionKey const	fail_on_bad_hbond
FileOptionKey const	movemap
BooleanOptionKey const	repair_sidechains
BooleanOptionKey const	no_binary_dunlib
IntegerOptionKey const	extended_pose
FileVectorOptionKey const	template_pdb
FileOptionKey const	template_silent
FileVectorOptionKey const	rdc
FileVectorOptionKey const	csa
FileVectorOptionKey const	dc
FileVectorOptionKey const	burial
FileOptionKey const	hrf_ms_labeling
FileVectorOptionKey const	vall
BooleanOptionKey const	rescore
StringOptionKey const	spanfile
StringOptionKey const	lipofile
StringOptionKey const	HDX
RealOptionKey const	d2h_sa_reweight
FileOptionKey const	sucker_params
FileOptionKey const	fold_tree
BooleanOptionKey const	obey_ENDMDL
BooleanOptionKey const	new_chain_order
FileOptionKey const	ddg_predictions_file
ResidueChainVectorOptionKey const	input_res
IntegerVectorOptionKey const	minimize_res
StringOptionKey const	md_schfile
FileOptionKey const	native_contacts

Variable Documentation

alignment

FileVectorOptionKey const basic::options::OptionKeys::in::file::alignment

extern

Referenced by add_rosetta_options_0(), FastThreadingMover::apply(), check_required(), and main().

alignment2

FileVectorOptionKey const basic::options::OptionKeys::in::file::alignment2

extern

Referenced by add_rosetta_options_0().

ambig_talos_cs_A

FileOptionKey const basic::options::OptionKeys::in::file::ambig_talos_cs_A

extern

Referenced by add_rosetta_options_0().

ambig_talos_cs_B

FileOptionKey const basic::options::OptionKeys::in::file::ambig_talos_cs_B

extern

Referenced by add_rosetta_options_0().

assign_gasteiger_atom_types

BooleanOptionKey const basic::options::OptionKeys::in::file::assign_gasteiger_atom_types

extern

Referenced by add_rosetta_options_0(), and main().

atom_tree_diff

FileVectorOptionKey const basic::options::OptionKeys::in::file::atom_tree_diff

extern

Referenced by add_rosetta_options_0(), and main().

binary_chk

FileOptionKey const basic::options::OptionKeys::in::file::binary_chk

extern

Referenced by add_rosetta_options_0().

boinc_wu_zip

FileVectorOptionKey const basic::options::OptionKeys::in::file::boinc_wu_zip

extern

Referenced by add_rosetta_options_0(), and main().

burial

FileVectorOptionKey const basic::options::OptionKeys::in::file::burial

extern

Referenced by add_rosetta_options_0(), calc_burial(), calculate_burial(), and main().

centroid

BooleanOptionKey const basic::options::OptionKeys::in::file::centroid

extern

Referenced by add_rosetta_options_0(), aro_pack_output(), get_base_coordinate_system(), get_base_pair_coordinate_system(), get_centroid(), get_phosphate_stub(), get_repl_xyz(), get_ring_centroids_and_stubs(), main(), mg_pdbstats_from_pose(), my_main(), polar_pdbstats_from_pose(), rebuild_test(), register_options(), reorient_to_base_pair_coordinate_system(), rotate_into_nucleobase_frame(), save_torsion_M_v(), setup_symmetric_dimer(), test_actcoord(), and numeric::geometry::vector_normal_to_ring_plane_of_best_fit().

centroid_input

BooleanOptionKey const basic::options::OptionKeys::in::file::centroid_input

extern

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

check_all_PDB_components

BooleanOptionKey const basic::options::OptionKeys::in::file::check_all_PDB_components

extern

Referenced by add_rosetta_options_0().

checkpoint

FileOptionKey const basic::options::OptionKeys::in::file::checkpoint

extern

Referenced by add_rosetta_options_0().

csa

FileVectorOptionKey const basic::options::OptionKeys::in::file::csa

extern

Referenced by add_rosetta_options_0().

d2h_sa_reweight

RealOptionKey const basic::options::OptionKeys::in::file::d2h_sa_reweight

extern

Referenced by add_rosetta_options_0().

dc

FileVectorOptionKey const basic::options::OptionKeys::in::file::dc

extern

Referenced by add_rosetta_options_0().

ddg_predictions_file

FileOptionKey const basic::options::OptionKeys::in::file::ddg_predictions_file

extern

Referenced by add_rosetta_options_0().

dssp

FileOptionKey const basic::options::OptionKeys::in::file::dssp

extern

Referenced by add_rosetta_options_0(), CountContact::apply(), zinc_helix_cap::apply(), PairDistance::apply(), PickBAB::apply(), Sasa::apply(), FoldTreeOutputter::apply(), HelicalPdbGeneratorMover::apply(), InterfaceStrandFinderMover::apply(), RDF_Mover::apply(), SSM_energies::apply(), Foldptn::apply(), AnchorFinderMover::apply(), ExposedStrandMover::apply(), RescoreCenrot::apply(), HBondReporter::apply(), CrystFFTDock::apply(), HDdesignMover::calc_bb_E(), calc_rama_scores(), compute_motif_score(), dock(), get_avail_don_acc(), get_centered_pose(), harvest_motifs(), harvest_motifs_one(), CenRotRBRelaxMover::init(), CenRotDockingMover::init(), ligand_test(), LoopBuild_main(), main(), make_fragments(), PoseWrap::PoseWrap(), rescore_pose(), run(), setup_secstruct_dssp(), sicdock_thread_num(), strip_termini(), and vlb_test().

extended_pose

IntegerOptionKey const basic::options::OptionKeys::in::file::extended_pose

extern

Referenced by add_rosetta_options_0(), protocols::abinitio::Application::copy_native_structure(), protocols::abinitio::JumpSpecificAbrelax::copy_native_structure(), protocols::abinitio::JumpSpecificAbrelax::copy_structure(), figure_out_icoord_test(), protocols::abinitio::JumpSpecificAbrelax::generate_extended_pose(), generate_extended_pose(), protocols::abinitio::ApplicationContext::generateExtendedPose(), main(), replace_torsion_angles(), set_ideal_geometry(), protocols::abinitio::JumpSpecificAbrelax::setup_fold(), protocols::abinitio::JumpSpecificAbrelax::setup_jumps(), sugar_geometry_RNA_test(), and SymmAbRelaxTest().

extra_patch_cen

FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_patch_cen

extern

Referenced by add_rosetta_options_0().

extra_patch_fa

FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_patch_fa

extern

Referenced by add_rosetta_options_0().

extra_res

FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res

extern

Referenced by add_rosetta_options_0().

extra_res_batch_path

PathVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_batch_path

extern

Referenced by add_rosetta_options_0().

extra_res_cen

FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_cen

extern

Referenced by add_rosetta_options_0(), collect_residue_types(), and register_options().

extra_res_database

StringOptionKey const basic::options::OptionKeys::in::file::extra_res_database

extern

Referenced by add_rosetta_options_0(), and main().

extra_res_database_mode

StringOptionKey const basic::options::OptionKeys::in::file::extra_res_database_mode

extern

Referenced by add_rosetta_options_0().

extra_res_database_resname_list

FileOptionKey const basic::options::OptionKeys::in::file::extra_res_database_resname_list

extern

Referenced by add_rosetta_options_0().

extra_res_fa

FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_fa

extern

Referenced by add_rosetta_options_0(), collect_residue_types(), main(), and register_options().

extra_res_mmCIF

FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_mmCIF

extern

Referenced by add_rosetta_options_0(), load_as_fullatom(), and register_options().

extra_res_mol

FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_mol

extern

Referenced by add_rosetta_options_0(), load_as_fullatom(), and register_options().

extra_res_path

PathVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_path

extern

Referenced by add_rosetta_options_0().

extra_res_pq_schema

StringOptionKey const basic::options::OptionKeys::in::file::extra_res_pq_schema

extern

Referenced by add_rosetta_options_0().

extra_rot_lib_path

PathVectorOptionKey const basic::options::OptionKeys::in::file::extra_rot_lib_path

extern

Referenced by add_rosetta_options_0().

fail_on_bad_hbond

BooleanOptionKey const basic::options::OptionKeys::in::file::fail_on_bad_hbond

extern

Referenced by add_rosetta_options_0().

fasta

FileVectorOptionKey const basic::options::OptionKeys::in::file::fasta

extern

Referenced by add_rosetta_options_0(), MPFoldingMover::apply(), check_required(), get_options_from_options_collection(), MPDomainAssembly::init_from_cmd(), AbInitio_MPI::init_on_new_input(), main(), predict_ss(), read_fasta(), register_options(), MPDomainAssembly::register_options(), rna_denovo(), rna_fullatom_minimize_test(), and run().

file

BooleanOptionKey const basic::options::OptionKeys::in::file::file

extern

Referenced by add_rosetta_options_0().

fold_tree

FileOptionKey const basic::options::OptionKeys::in::file::fold_tree

extern

Referenced by add_rosetta_options_0(), cluster_rotamers(), hermann_phase_two_minimize(), main(), apps::pilot::frankdt::main(), minimize_pdb(), native_frag_CA_RMSD(), protocols::abinitio::Application::register_options(), protocols::abinitio::Application::run(), and DockFragmentsMover::run().

force_silent_bitflip_on_read

BooleanOptionKey const basic::options::OptionKeys::in::file::force_silent_bitflip_on_read

extern

Referenced by add_rosetta_options_0().

frag3

StringOptionKey const basic::options::OptionKeys::in::file::frag3

extern

Referenced by add_rosetta_options_0(), check_required(), FloppyTailMover::FloppyTailMover(), MPDomainAssembly::init_from_cmd(), AbInitio_MPI::init_on_new_input(), main(), and MPDomainAssembly::register_options().

frag9

StringOptionKey const basic::options::OptionKeys::in::file::frag9

extern

Referenced by add_rosetta_options_0(), check_required(), MPDomainAssembly::init_from_cmd(), AbInitio_MPI::init_on_new_input(), main(), and MPDomainAssembly::register_options().

frag_files

FileVectorOptionKey const basic::options::OptionKeys::in::file::frag_files

extern

Referenced by add_rosetta_options_0().

fragA

StringOptionKey const basic::options::OptionKeys::in::file::fragA

extern

Referenced by add_rosetta_options_0().

fragB

StringOptionKey const basic::options::OptionKeys::in::file::fragB

extern

Referenced by add_rosetta_options_0().

fullatom

BooleanOptionKey const basic::options::OptionKeys::in::file::fullatom

extern

Referenced by PoseWrap::add_apcs_local(), add_rosetta_options_0(), add_virtual_res(), CartRefineWrapperMover::apply(), protocols::abinitio::JumpSpecificAbrelax::generate_scorefxn(), get_disulfides_from_aln(), load_as_fullatom(), LoopBuild_main(), and main().

HDX

StringOptionKey const basic::options::OptionKeys::in::file::HDX

extern

Referenced by add_rosetta_options_0(), and main().

hrf_ms_labeling

FileOptionKey const basic::options::OptionKeys::in::file::hrf_ms_labeling

extern

Referenced by add_rosetta_options_0().

input_res

ResidueChainVectorOptionKey const basic::options::OptionKeys::in::file::input_res

extern

Referenced by add_rosetta_options_0(), coarse_rna_denovo_test(), copy_DOFS_local(), general_initialize(), get_input_res(), main(), and swa_rna_sample().

job_definition_file

FileOptionKey const basic::options::OptionKeys::in::file::job_definition_file

extern

Referenced by add_rosetta_options_0(), convert(), and reverse_convert().

keep_input_scores

BooleanOptionKey const basic::options::OptionKeys::in::file::keep_input_scores

extern

Referenced by add_rosetta_options_0(), and main().

l

FileVectorOptionKey const basic::options::OptionKeys::in::file::l

extern

Referenced by add_rosetta_options_0(), main(), read_FileVector(), register_options(), run(), scheme_score(), and basic::options::start_files().

lazy_silent

BooleanOptionKey const basic::options::OptionKeys::in::file::lazy_silent

extern

Referenced by add_rosetta_options_0().

lipofile

StringOptionKey const basic::options::OptionKeys::in::file::lipofile

extern

Referenced by add_rosetta_options_0().

list

FileVectorOptionKey const basic::options::OptionKeys::in::file::list

extern

Referenced by pyrosetta.bindings.pose.PoseResidueLabelAccessor::__str__(), pyrosetta.distributed.docs.MoverDocs::_component_names(), pyrosetta.distributed.docs.FilterDocs::_component_names(), pyrosetta.distributed.cluster.io.IO::_filter_scores_dict(), pyrosetta.distributed.cluster.io.IO::_get_output_dir(), pyrosetta.distributed.cluster.converters::_parse_protocols(), pyrosetta.distributed.viewer.modules::_pose_to_residue_chain_tuples(), pyrosetta.distributed.cluster.io.IO::_process_kwargs(), pyrosetta.bindings.pose.PoseResidueLabelAccessor::_repr_pretty_(), pyrosetta.distributed.cluster.base.TaskBase::_setup_protocols_protocol_seed(), add_rosetta_options_0(), pyrosetta.bindings.pose.PoseScoreAccessor::all(), pyrosetta.bindings.homogeneous_transform::as_array(), pyrosetta.bindings.rt::as_array(), bind_std_forward_list(), bind_std_functional_hash(), bind_std_stl_list(), bind_std_stl_multiset(), bind_std_stl_vector_1(), bind_std_unordered_map(), bind_T42_stl_names(), bind_T42_stl_names_map(), bind_T42_stl_names_multi(), bind_T42_stl_names_multimap(), bind_T42_stl_names_set(), bind_T43_stl_pybind11_include_stl(), bind_T60_pybind11(), utility::graph::ArrayPool< T >::clear(), pyrosetta.distributed.cluster.logging_handlers.MsgpackHmacSocketHandler::clear_masked_keys(), cluster_rigid_body_settings_test(), ui::task::create_viewer_for_file(), pyrosetta.toolbox.atom_pair_energy::dump_atom_pair_energy_table(), pyrosetta.toolbox.atom_pair_energy::dump_residue_pair_energies(), pyrosetta.bindings.pose.PoseScoreAccessor::extra(), mutant_modeler::figure_out_WT_seq(), fillPoseAndDataList(), erraser_util::find_error_res(), mutant_modeler::find_pairs(), setup_for_complex_scoring_general::find_pairs(), DRRAFTER::find_pairs(), DRRAFTER_util::find_pairs(), build::generate_bindings(), build::generate_rosetta_external_cmake_files(), update_ui_project::generate_rosetta_external_project_files(), mutant_modeler.MutantModeler::get_med_res_command_lines(), pyrosetta.bindings.residue_selectors::get_residues(), has_element(), inlist(), join(), pyrosetta.io.silent_file_map.SilentFilePoseAccessor::keys(), pyrosetta.io.silent_file_map.SilentFileEnergyAccessor::keys(), pyrosetta.protocols.structure_search.alignment::length_grouped_broadcast_metric(), pyrosetta.protocols.structure_search.alignment::length_grouped_pairwise_metric(), PyMOL-Rosetta-relay-client.PR_UDPServer::listen(), PyMOL-RosettaServer.PR_UDPServer::listen(), pyrosetta.network.rosetta_udp_to_tcp_bridge.PR_UDPServer::listen(), pyrosetta.PyMOLRosettaServer.PR_UDPServer::listen(), setup_for_complex_scoring_general::main(), main(), make_1mer_frags(), make_bindings_via_cmake::make_all_includes(), make_frags(), HECTMover::make_frags(), utility::graph::ArrayPool< T >::mine(), pyrosetta.mpi::MPIJobDistributor(), MSA_design_main(), pyrosetta.tests.distributed.cluster.test_smoke.GeneratorTest::my_pyrosetta_protocol_2(), pyrosetta.toolbox.py_jobdistributor::output_scorefile(), pyrosetta.protocols.structure_search.StructureSearchManager::pair_query(), DRRAFTER_util::parse_tag(), util::parse_tag(), erraser_util::pdb2rosetta(), pyrosetta.toolbox.extract_coords_pose::pose_coords_as_cols(), pyrosetta.toolbox.extract_coords_pose::pose_coords_as_rows(), pyrosetta.io::pose_from_pdbstring(), processChildren(), processChildrenIntensification(), read_FileVector(), pyrosetta.bindings.energies::residue_pair_energies_array(), run(), pyrosetta.distributed.cluster.logging_handlers.MsgpackHmacSocketHandler::sanitize_record_args(), demo.D090_Ala_scan::scanning(), drrafter_rna::setup_next_round(), pyrosetta.protocols.structure_search.StructureSearchManager::single_query(), basic::citation_manager::CitationManager::split_citations(), basic::options::start_files(), pyrosetta.io.silent_file_map.SilentFileMap::tags(), pyrosetta.tests.distributed.test_concurrency.TestConcurrentScripts::test_concurrent_multi_task(), pyrosetta.tests.distributed.test_concurrency.TestConcurrentScripts::test_concurrent_on_task(), pyrosetta.tests.distributed.cluster.test_smoke.GeneratorTest::test_generate_builtin_clients(), pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor::test_labels(), pyrosetta.tests.bindings.core.test_pose.TestPoseIO::test_multimodel_pdb_io(), pyrosetta.tests.bindings.core.test_pose.TestPoseCacheAccessor::test_pose_cache(), pyrosetta.tests.bindings.core.test_pose.TestPoseIO::test_pose_io(), pyrosetta.tests.distributed.test_smoke.SmokeTestDistributed::test_poses_from_sequences_io(), pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent::test_poses_to_silent(), pyrosetta.tests.distributed.cluster.test_reproducibility.TestReproducibilityMulti::test_reproducibility_from_reproduce(), pyrosetta.tests.distributed.cluster.test_reproducibility.TestReproducibilityMulti::test_reproducibility_packer_nstruct_multi(), pyrosetta.tests.distributed.cluster.test_reproducibility.TestReproducibilityMulti::test_reproducibility_packer_nstruct_multi_decoy_ids(), pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor::test_residues(), pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor::test_score_serialization(), pyrosetta.tests.distributed.cluster.test_smoke.SmokeTestMulti::test_smoke_multi(), pyrosetta.utility.array::to_structured_array(), and basic::citation_manager::CitationManager::write_all_citations_and_unpublished_author_info_from_list_to_stream().

load_PDB_components

BooleanOptionKey const basic::options::OptionKeys::in::file::load_PDB_components

extern

Referenced by add_rosetta_options_0().

md_schfile

StringOptionKey const basic::options::OptionKeys::in::file::md_schfile

extern

Referenced by add_rosetta_options_0().

minimize_res

IntegerVectorOptionKey const basic::options::OptionKeys::in::file::minimize_res

extern

Referenced by add_rosetta_options_0(), get_fixed_res(), hermann_phase_two_minimize(), main(), and minimize_pdb().

movemap

FileOptionKey const basic::options::OptionKeys::in::file::movemap

extern

Referenced by add_rosetta_options_0(), MinToolMover::apply(), RDCToolMover::apply(), TestMMOP::apply(), PhDocking::apply(), PepMinMover::apply(), MikeLinkerMover::apply(), FindOptimalHydrophobicThk::apply(), LigandRepackMinimizeProtocol::apply(), MinPackMinMover::apply(), SwapElementsMover1::apply(), SwapElementsMover2::apply(), MembraneMinMover::apply(), MembraneRelaxMover::apply(), MembraneSampleMover::apply(), CrystRelax::apply(), Minimize::apply(), aramid_main(), MinPackMin::backbone_minimization(), bk_test(), ccd_loop_close(), HubDenovo::cen_fold(), protocols::abinitio::JumpSpecificAbrelax::close_loops(), FixbbJobQueen::complete_larval_job_maturation(), compute_folding_energies(), copying_side_chains(), copying_side_chains_swap_loop(), define_movemap_extending_chain(), derive_MoveMap_from_cluster_lst(), design(), design_pose_motifs_only(), do_centroid_stuff(), do_sc_min(), do_sc_relax(), dock(), extending_chain(), HubDenovo::HubDenovo(), AbInitio_MPI::init_on_new_input(), protocols::abinitio::JumpSpecificAbrelax::insert_template_frags(), linmin(), loop_closure_test(), main(), make_float_sc_min_mover(), make_move_map(), HubDenovo::min_as_poly_ala(), minimize(), MoveThenFixHMin::MoveThenFixHMin(), my_main(), MainWindow::on_button_run_minimizer_clicked(), print_movemap(), rebuild_test(), refine(), apps::pilot::momeara::HBondConformation::relax_pose_around_hbond(), repack_all(), repackmin(), MinPackMin::rigid_body_minimization(), run(), myspace::Scheduler::run_md(), run_test(), ZincMinimize::set_min_mover(), protocols::abinitio::JumpSpecificAbrelax::setup_fold(), setup_for_folding(), abbinding::setup_RepulsiveRampMover(), sidechain_fastrelax(), SmoothFragRepackMover::SmoothFragRepackMover(), T400_Refinement(), test(), myspace::GraftTester::test_rb_min_graft(), and TestQuickRelaxMover::TestQuickRelaxMover().

native

FileOptionKey const basic::options::OptionKeys::in::file::native

extern

Referenced by add_rosetta_options_0(), LoopHash_Analyze::apply(), compute_Irmsd::apply(), CaToAllAtom::CaToAllAtom(), check_inputs_for_errors(), RelaxJobQueen::complete_larval_job_maturation(), DeleteSegments::DeleteSegments(), Foldptn::Foldptn(), HECTMover::HECTMover(), HemeReplace::HemeReplace(), LoopBuild_main(), main(), MyScoreMover::MyScoreMover(), register_options(), RosettaHolesMover::RosettaHolesMover(), run(), and run_parallel_docking().

native_contacts

FileOptionKey const basic::options::OptionKeys::in::file::native_contacts

extern

Referenced by add_rosetta_options_0().

native_exclude_res

IntegerVectorOptionKey const basic::options::OptionKeys::in::file::native_exclude_res

extern

Referenced by add_rosetta_options_0().

new_chain_order

BooleanOptionKey const basic::options::OptionKeys::in::file::new_chain_order

extern

Referenced by add_rosetta_options_0().

no_binary_dunlib

BooleanOptionKey const basic::options::OptionKeys::in::file::no_binary_dunlib

extern

Referenced by add_rosetta_options_0(), and validate_dunbrack_binaries().

no_detect_pseudobonds

BooleanOptionKey const basic::options::OptionKeys::in::file::no_detect_pseudobonds

extern

Referenced by add_rosetta_options_0().

obey_ENDMDL

BooleanOptionKey const basic::options::OptionKeys::in::file::obey_ENDMDL

extern

Referenced by add_rosetta_options_0().

override_database_params

BooleanOptionKey const basic::options::OptionKeys::in::file::override_database_params

extern

Referenced by add_rosetta_options_0().

override_rot_lib_path

PathVectorOptionKey const basic::options::OptionKeys::in::file::override_rot_lib_path

extern

Referenced by add_rosetta_options_0().

pca

FileOptionKey const basic::options::OptionKeys::in::file::pca

extern

Referenced by add_rosetta_options_0(), protocols::abinitio::JumpSpecificAbrelax::register_options(), and protocols::abinitio::JumpSpecificAbrelax::setup().

PCS_frag_cst

FileOptionKey const basic::options::OptionKeys::in::file::PCS_frag_cst

extern

Referenced by add_rosetta_options_0().

PDB_components_directory

StringOptionKey const basic::options::OptionKeys::in::file::PDB_components_directory

extern

Referenced by add_rosetta_options_0().

PDB_components_overrides

StringVectorOptionKey const basic::options::OptionKeys::in::file::PDB_components_overrides

extern

Referenced by add_rosetta_options_0().

psipred_ss2

FileOptionKey const basic::options::OptionKeys::in::file::psipred_ss2

extern

Referenced by add_rosetta_options_0(), apps::pilot::CustomStarTreeMover::apply(), ChallengeMover::initialize_pose(), main(), set_secstruct_from_psipred_ss2(), apps::pilot::SampleSecondaryStructureAlignmentMover::setup_startree(), SymmAbRelaxTest(), and SymmSilentFileTest().

pssm

FileVectorOptionKey const basic::options::OptionKeys::in::file::pssm

extern

Referenced by add_rosetta_options_0(), and MSA_design().

rama2b_map

FileOptionKey const basic::options::OptionKeys::in::file::rama2b_map

extern

Referenced by add_rosetta_options_0().

rdc

FileVectorOptionKey const basic::options::OptionKeys::in::file::rdc

extern

Referenced by add_rosetta_options_0(), and register_options().

remap_pdb_atom_names_for

StringVectorOptionKey const basic::options::OptionKeys::in::file::remap_pdb_atom_names_for

extern

Referenced by add_rosetta_options_0().

repair_sidechains

BooleanOptionKey const basic::options::OptionKeys::in::file::repair_sidechains

extern

Referenced by add_rosetta_options_0().

rescore

BooleanOptionKey const basic::options::OptionKeys::in::file::rescore

extern

Referenced by add_rosetta_options_0().

residue_type_set

StringOptionKey const basic::options::OptionKeys::in::file::residue_type_set

extern

Referenced by add_rosetta_options_0(), add_symm_sf4(), add_symm_zns(), add_vrts(), addcyclicconstraints(), align_sf4(), align_zns(), mtransferase::apply(), HotspotPlacementMover::apply(), PeptoidDesignMover::apply(), hbs_creator::apply(), atom_types_test(), HECTMover::build_AtomID_vec(), apps::pilot::momeara::HBondConformation::build_residue(), build_toy_pose(), cendnapose_from_file(), cenpose_from_file(), check_centroid(), check_fullatom(), ChiMover::ChiMover(), myspace::collect_silent(), MPDomainAssembly::create_residue_from_olc(), MPDomainAssembly::create_residue_from_resn(), create_theozyme_pdb(), dna_test(), protocols::abinitio::JumpSpecificAbrelax::do_rerun(), apps::pilot::momeara::HBondConformation::example_OH_pose(), protocols::abinitio::JumpSpecificAbrelax::generate_extended_pose(), protocols::abinitio::ApplicationContext::generateExtendedPose(), get_pose_by_id(), get_radius_in_frag_set(), get_residue(), get_vanilla_dna_residue(), get_vanilla_protein_residue(), graphics_main(), HubDenovo::HubDenovo(), UBQ_E2Mover::init_on_new_input(), UBQ_GTPase_disulfide_Mover::init_on_new_input(), AbInitio_MPI::init_on_new_input(), HECTAllMover::init_on_new_input(), HECTUBQMover::init_on_new_input(), lariat_modeling(), load_loops_from_file(), main(), apps::pilot::momeara::HBondConformation::make_conformation(), make_helix(), make_pose(), make_sequence_change(), match_main(), mg_modeler_test(), mg_pdbstats_test(), mutate_to_ala(), my_main(), native_frag_CA_RMSD(), output_pdb(), output_single_motif(), pdb_scoring(), place_water_acceptor(), place_water_donor(), pose_from_scratch(), myspace::pose_from_scratch(), print_all_torsions_test(), process_for_motifs(), rb_test(), register_options(), rna_denovo(), run(), DockFragmentsMover::run(), apps::pilot::momeara::HBondConformation::run_example_hbond_sweep(), set_fullatom_flag_test(), simple_centroid_test(), simple_frag_test(), ss_test(), sweep_params_from_match_constraint_file(), SymmAbRelaxTest(), test(), and HECTMover::ubq_constraints().

s

FileVectorOptionKey const basic::options::OptionKeys::in::file::s

extern

Referenced by add_rosetta_options_0(), calc_B_values(), calculate_distances(), check_inputs_for_errors(), check_structures(), combine_search(), create_theozyme_pdb(), do_refinement(), do_search(), fill_optional_options(), get_filename(), get_pts(), get_tasks_from_command_line(), gpu_refold_test(), gpu_score_test(), graphics_main(), main(), makesplitwork(), makesplitwork_3bpy(), manual_refine(), OPT_1GRP_KEY(), register_options(), results_to_pdb(), rna_motif_test(), run(), run_3bpy(), run_aio(), run_diiron_glu(), run_m8(), run_parallel_docking(), run_sf4h(), run_tyr_his(), run_zn2his(), scheme_score(), score_rnp(), set_basic_dock_options(), LigandDockBenchmark::setUp(), setup_coord_csts(), sicdock_thread_num(), basic::options::start_files(), test_protein_rna(), test_replicate_xform(), and thread_fxn().

screening_job_file

FileOptionKey const basic::options::OptionKeys::in::file::screening_job_file

extern

Referenced by add_rosetta_options_0().

screening_list

FileVectorOptionKey const basic::options::OptionKeys::in::file::screening_list

extern

Referenced by add_rosetta_options_0(), and basic::options::start_files().

seq

StringVectorOptionKey const basic::options::OptionKeys::in::file::seq

extern

Referenced by add_rosetta_options_0(), and main().

shuffle_screening_jobs

BooleanOptionKey const basic::options::OptionKeys::in::file::shuffle_screening_jobs

extern

Referenced by add_rosetta_options_0().

silent

FileVectorOptionKey const basic::options::OptionKeys::in::file::silent

extern

Referenced by add_rosetta_options_0(), align_pdbs(), align_pdbs_function(), analyze_base_pair_test(), AssignClusterToolMover::apply(), LoopHashRelax_Sampler::apply(), RNA_ScoreMover::apply(), apply_filter_base_stack_direction(), assign_rigid_body_settings_to_clusters_test(), base_doublet_rmsd_test(), base_pair_to_base_pair_test(), benzene_pair_score_test(), build_next_nucleotide_test(), calc_rms_test(), calc_rmsd_test(), calculate_distances(), calculate_pairwise_RMSD(), calculate_theoretical_RNA_length(), calculate_theoretical_RNA_length_with_bond_angle_dependence(), check_structures(), cluster_outfile_test_OLD(), cluster_rigid_body_settings_test(), cluster_rotamers(), cluster_silent(), cluster_silent_file_data(), coarse_frag_test(), coarse_rb_test(), combine_refinement(), connectivity_test(), convert_silent_file_to_pose_data_list(), convert_to_coarse_test(), convert_to_native_test(), count_contacts(), cst_relax_test(), define_states_test(), delta_chi_correction_test(), dinucleotide_test(), dist_matrix_test(), protocols::abinitio::JumpSpecificAbrelax::do_distributed_rerun(), protocols::abinitio::JumpSpecificAbrelax::do_rerun(), do_the_match(), each_aa_test(), entropy_calculate_test(), env_sugar_test(), erraser_monte_carlo(), basic::execute(), expand_chi_for_silent_structs(), extract_pdbs_test(), extract_replica(), fill_optional_options(), finely_sample_base_pair_test(), frag_extract_test(), general_initialize(), get_contacts(), get_pose_energy_breakdown(), get_rmsd(), get_RNA_binding_residues(), grid_matcher(), hermann_phase_two(), hermann_phase_two_minimize(), initialize_rigid_body_sampler(), journal_club_syn_chi(), loop_closure_test(), main(), minimize_poses(), minimizer_test(), mismatch_test(), modeler_closure_test(), modeler_map_test(), mutate_residues_wrapper(), my_main(), myspace::Scheduler::NM_linesearch(), nucleobase_probe_score_test(), output_centroid_silent_struct(), output_to_silent(), parse_pathway_test(), pdb_little_motif_test(), pdb_to_silent_file(), pdb_to_silent_file_simple(), peptide_plane_test(), peptide_plane_test_OLD(), ThisApplication::pick_frags(), post_rebuild_bulge_assembly(), print_hbonds_test(), protein_helix_test(), read_rigid_body_settings(), rebuild_centroid_test(), rebuild_test(), register_options(), repack_test(), reverse_doublet_test(), rna_assemble_all_combinations_test(), rna_assemble_test(), rna_build_helix_test(), rna_build_helix_test_OLD(), rna_build_helix_test_precompute(), rna_denovo(), rna_fullatom_minimize_silent_test(), rna_fullatom_multiscore_test(), rna_fullatom_score_test(), rna_lores_score_silent_test(), rna_motif_test(), rna_o2prime_test(), rotamerize_rna_test(), run(), sample_rama_test(), sample_state_to_state(), sample_trp_test(), sample_trp_tyr_test(), sasa_test(), score12_plot_test(), score_and_minimize(), score_rnp(), search_translations(), setup_dinucleotide_pose(), setup_double_helix_pose(), setup_one_chain_pose(), setup_pose(), setup_two_base_pair_pose(), setup_two_base_pair_pose_with_chainbreak(), sidechain_sample(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), split_silent_file_data(), stepwise_template_test(), sugar_frag_RNA_test(), sugar_geometry_RNA_test(), swa_rna_sample(), tar_motif_test(), test_function(), thermal_sampler(), two_base_pairs_test(), write_base_pair_step_to_silent_struct(), write_for_resnum(), and write_output_files().

silent_energy_cut

RealOptionKey const basic::options::OptionKeys::in::file::silent_energy_cut

extern

Referenced by add_rosetta_options_0(), doit(), and report().

silent_list

FileVectorOptionKey const basic::options::OptionKeys::in::file::silent_list

extern

Referenced by add_rosetta_options_0().

silent_read_through_errors

BooleanOptionKey const basic::options::OptionKeys::in::file::silent_read_through_errors

extern

Referenced by add_rosetta_options_0(), and main().

silent_renumber

BooleanOptionKey const basic::options::OptionKeys::in::file::silent_renumber

extern

Referenced by add_rosetta_options_0(), and main().

silent_score_prefix

StringOptionKey const basic::options::OptionKeys::in::file::silent_score_prefix

extern

Referenced by add_rosetta_options_0().

silent_scores_wanted

StringVectorOptionKey const basic::options::OptionKeys::in::file::silent_scores_wanted

extern

Referenced by add_rosetta_options_0().

silent_select_random

IntegerOptionKey const basic::options::OptionKeys::in::file::silent_select_random

extern

Referenced by add_rosetta_options_0().

silent_select_range_len

IntegerOptionKey const basic::options::OptionKeys::in::file::silent_select_range_len

extern

Referenced by add_rosetta_options_0().

silent_select_range_mul

IntegerOptionKey const basic::options::OptionKeys::in::file::silent_select_range_mul

extern

Referenced by add_rosetta_options_0().

silent_select_range_start

IntegerOptionKey const basic::options::OptionKeys::in::file::silent_select_range_start

extern

Referenced by add_rosetta_options_0().

silent_struct_type

StringOptionKey const basic::options::OptionKeys::in::file::silent_struct_type

extern

Referenced by add_rosetta_options_0(), and main().

skip_failed_simulations

BooleanOptionKey const basic::options::OptionKeys::in::file::skip_failed_simulations

extern

Referenced by add_rosetta_options_0().

spanfile

StringOptionKey const basic::options::OptionKeys::in::file::spanfile

extern

Referenced by add_rosetta_options_0(), main(), spanfile_for_each_chain(), and spanfile_from_pdb().

srlz

BooleanOptionKey const basic::options::OptionKeys::in::file::srlz

extern

Referenced by add_rosetta_options_0().

srlz_override

BooleanOptionKey const basic::options::OptionKeys::in::file::srlz_override

extern

Referenced by add_rosetta_options_0().

sucker_params

FileOptionKey const basic::options::OptionKeys::in::file::sucker_params

extern

Referenced by add_rosetta_options_0().

surface_vectors

StringOptionKey const basic::options::OptionKeys::in::file::surface_vectors

extern

Referenced by add_rosetta_options_0().

t

FileVectorOptionKey const basic::options::OptionKeys::in::file::t

extern

Referenced by add_rosetta_options_0().

tagfile

FileOptionKey const basic::options::OptionKeys::in::file::tagfile

extern

Referenced by add_rosetta_options_0().

tags

StringVectorOptionKey const basic::options::OptionKeys::in::file::tags

extern

Referenced by add_rosetta_options_0(), calculate_distances(), check_structures(), main(), and rna_motif_test().

talos_cs

FileOptionKey const basic::options::OptionKeys::in::file::talos_cs

extern

Referenced by add_rosetta_options_0().

talos_phi_psi

FileOptionKey const basic::options::OptionKeys::in::file::talos_phi_psi

extern

Referenced by add_rosetta_options_0().

template_pdb

FileVectorOptionKey const basic::options::OptionKeys::in::file::template_pdb

extern

Referenced by add_rosetta_options_0(), check_required(), main(), and my_main().

template_silent

FileOptionKey const basic::options::OptionKeys::in::file::template_silent

extern

Referenced by add_rosetta_options_0(), and main().

torsion_bin_probs

FileOptionKey const basic::options::OptionKeys::in::file::torsion_bin_probs

extern

Referenced by add_rosetta_options_0().

treat_residues_in_these_chains_as_separate_chemical_entities

StringOptionKey const basic::options::OptionKeys::in::file::treat_residues_in_these_chains_as_separate_chemical_entities

extern

Referenced by add_rosetta_options_0().

user_tags

StringVectorOptionKey const basic::options::OptionKeys::in::file::user_tags

extern

Referenced by add_rosetta_options_0(), and main().

vall

FileVectorOptionKey const basic::options::OptionKeys::in::file::vall

extern

Referenced by add_rosetta_options_0(), fill_optional_options(), get_fragment_sets(), main(), RunPepSpec(), setup_fragment_mover(), setup_loops_fragment_libraries_with_ss(), simple_frag_test(), and simple_loop_modeling_test().

xyz

StringOptionKey const basic::options::OptionKeys::in::file::xyz

extern

Referenced by add_rosetta_options_0(), CrystFFTDock::apply(), pyrosetta.distributed.viewer.modules.setHydrogenBonds::apply(), pyrosetta.distributed.viewer.modules.setHydrogens::apply(), array2vecs(), atom_line(), InterfaceStrandFinderMover::bb_score(), ExposedStrandMover::bb_score(), HDmakerMover::bb_score(), Bola::Bola(), best_beta_backbones::bump_check(), demo.D090_Ala_scan::calc_binding_energy(), check_silent_error(), ClashCheck::clash_check(), ClashCheck::clash_check_trimer(), numeric::comma_seperated_string_to_xyz(), CollectCoordinates::copy_coordinates(), MainWindow::create_pose(), cyclic_perm(), design(), devel_main(), dock(), find_closest_atom(), lactamize::find_lactams(), for(), MPInterfaceStatistics::get_inout_orientation(), get_sphere_xyz(), demo.D060_Folding::guess_disulfides(), numeric::geometry::hashing::MinimalClashHash::init(), local_rms(), main(), apps::pilot::frankdt::main(), measure_sequence_recovery(), MainWindow::paintGL(), ui::ui_core::pose_draw::SimplePoseDrawOpenGLWidget::paintGL(), pose2bin(), process_the_pose(), randvec(), relax_with_restraints_on_constres(), pyrosetta.toolbox.mutants::restrict_non_nbrs_from_repacking(), pyrosetta.tests.distributed.test_smoke.SmokeTestDistributed::roundtrip(), run(), SphereGrinder(), numeric::spherical_to_xyz(), pyrosetta.tests.bindings.core.test_pose.TestPoseIO::test_cif_io(), pyrosetta.tests.bindings.core.test_pose.TestPoseIO::test_file_io(), pyrosetta.tests.bindings.core.test_pose.TestPoseIO::test_mmtf_io(), pyrosetta.tests.bindings.core.test_pose.TestPoseIO::test_multimodel_pdb_io(), pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor::test_score_serialization(), pyrosetta.tests.distributed.cluster.test_smoke.SmokeTestMulti::test_smoke_multi(), water_test_fixed_O(), and numeric::xyz_to_spherical().

zip

StringOptionKey const basic::options::OptionKeys::in::file::zip

extern

Referenced by pyrosetta.toolbox.atom_pair_energy::_atom_pair_energy_table(), pyrosetta.distributed.cluster.io.IO::_get_instance_and_metadata(), pyrosetta.distributed.viewer.modules::_pose_to_residue_chain_tuples(), add_rosetta_options_0(), pyrosetta.distributed.utility.log.ProgressLogger::enumerate(), pyrosetta.distributed.viewer.core::init(), dbscan_cluster_rotamer::main(), main(), DRRAFTER_util::parse_tag(), util::parse_tag(), dbscan_adaptive_kernel_density_bb_dependent_rotlib::plot_cluster(), pyrosetta.utility.array::rolling_window(), pyrosetta.tests.protocols.indexed_structure_store.test_search.TestStructureSearch::test_pair_search(), pyrosetta.tests.distributed.test_smoke.SmokeTestDistributed::test_poses_from_files_io(), and pyrosetta.tests.distributed.test_smoke.SmokeTestDistributed::test_poses_from_sequences_io().