Functions
BooleanOptionKey const	file ("in:file")

FileVectorOptionKey const	s ("in:file:s")

FileVectorOptionKey const	t ("in:file:t")

FileVectorOptionKey const	l ("in:file:l")

FileOptionKey const	job_definition_file ("in:file:job_definition_file")

FileVectorOptionKey const	list ("in:file:list")

BooleanOptionKey const	srlz ("in:file:srlz")

BooleanOptionKey const	srlz_override ("in:file:srlz_override")

FileVectorOptionKey const	screening_list ("in:file:screening_list")

FileOptionKey const	screening_job_file ("in:file:screening_job_file")

BooleanOptionKey const	shuffle_screening_jobs ("in:file:shuffle_screening_jobs")

FileOptionKey const	native ("in:file:native")

FileOptionKey const	torsion_bin_probs ("in:file:torsion_bin_probs")

FileOptionKey const	PCS_frag_cst ("in:file:PCS_frag_cst")

FileOptionKey const	talos_phi_psi ("in:file:talos_phi_psi")

FileOptionKey const	talos_cs ("in:file:talos_cs")

FileOptionKey const	ambig_talos_cs_A ("in:file:ambig_talos_cs_A")

FileOptionKey const	ambig_talos_cs_B ("in:file:ambig_talos_cs_B")

IntegerVectorOptionKey const	native_exclude_res ("in:file:native_exclude_res")

BooleanOptionKey const	no_detect_pseudobonds ("in:file:no_detect_pseudobonds")

StringVectorOptionKey const	tags ("in:file:tags")

StringVectorOptionKey const	user_tags ("in:file:user_tags")

FileOptionKey const	tagfile ("in:file:tagfile")

FileVectorOptionKey const	frag_files ("in:file:frag_files")

StringVectorOptionKey const	remap_pdb_atom_names_for ("in:file:remap_pdb_atom_names_for")

FileVectorOptionKey const	extra_res ("in:file:extra_res")

FileVectorOptionKey const	extra_res_fa ("in:file:extra_res_fa")

BooleanOptionKey const	override_database_params ("in:file:override_database_params")

FileVectorOptionKey const	extra_res_mol ("in:file:extra_res_mol")

FileVectorOptionKey const	extra_res_mmCIF ("in:file:extra_res_mmCIF")

BooleanOptionKey const	load_PDB_components ("in:file:load_PDB_components")

StringOptionKey const	PDB_components_directory ("in:file:PDB_components_directory")

StringVectorOptionKey const	PDB_components_overrides ("in:file:PDB_components_overrides")

BooleanOptionKey const	check_all_PDB_components ("in:file:check_all_PDB_components")

StringOptionKey const	extra_res_database ("in:file:extra_res_database")

StringOptionKey const	extra_res_pq_schema ("in:file:extra_res_pq_schema")

StringOptionKey const	extra_res_database_mode ("in:file:extra_res_database_mode")

FileOptionKey const	extra_res_database_resname_list ("in:file:extra_res_database_resname_list")

FileVectorOptionKey const	extra_res_cen ("in:file:extra_res_cen")

PathVectorOptionKey const	extra_res_path ("in:file:extra_res_path")

PathVectorOptionKey const	extra_rot_lib_path ("in:file:extra_rot_lib_path")

PathVectorOptionKey const	override_rot_lib_path ("in:file:override_rot_lib_path")

PathVectorOptionKey const	extra_res_batch_path ("in:file:extra_res_batch_path")

FileVectorOptionKey const	extra_patch_fa ("in:file:extra_patch_fa")

FileVectorOptionKey const	extra_patch_cen ("in:file:extra_patch_cen")

StringOptionKey const	frag3 ("in:file:frag3")

StringOptionKey const	frag9 ("in:file:frag9")

StringOptionKey const	fragA ("in:file:fragA")

StringOptionKey const	fragB ("in:file:fragB")

StringOptionKey const	surface_vectors ("in:file:surface_vectors")

StringOptionKey const	xyz ("in:file:xyz")

BooleanOptionKey const	keep_input_scores ("in:file:keep_input_scores")

BooleanOptionKey const	lazy_silent ("in:file:lazy_silent")

FileVectorOptionKey const	silent ("in:file:silent")

BooleanOptionKey const	force_silent_bitflip_on_read ("in:file:force_silent_bitflip_on_read")

FileVectorOptionKey const	atom_tree_diff ("in:file:atom_tree_diff")

StringOptionKey const	zip ("in:file:zip")

FileVectorOptionKey const	boinc_wu_zip ("in:file:boinc_wu_zip")

BooleanOptionKey const	fullatom ("in:file:fullatom")

BooleanOptionKey const	centroid_input ("in:file:centroid_input")

BooleanOptionKey const	centroid ("in:file:centroid")

BooleanOptionKey const	assign_gasteiger_atom_types ("in:file:assign_gasteiger_atom_types")

StringOptionKey const	treat_residues_in_these_chains_as_separate_chemical_entities ("in:file:treat_residues_in_these_chains_as_separate_chemical_entities")

StringOptionKey const	residue_type_set ("in:file:residue_type_set")

FileOptionKey const	pca ("in:file:pca")

RealOptionKey const	silent_energy_cut ("in:file:silent_energy_cut")

FileVectorOptionKey const	silent_list ("in:file:silent_list")

BooleanOptionKey const	silent_renumber ("in:file:silent_renumber")

StringOptionKey const	silent_struct_type ("in:file:silent_struct_type")

BooleanOptionKey const	silent_read_through_errors ("in:file:silent_read_through_errors")

StringOptionKey const	silent_score_prefix ("in:file:silent_score_prefix")

IntegerOptionKey const	silent_select_random ("in:file:silent_select_random")

IntegerOptionKey const	silent_select_range_start ("in:file:silent_select_range_start")

IntegerOptionKey const	silent_select_range_mul ("in:file:silent_select_range_mul")

IntegerOptionKey const	silent_select_range_len ("in:file:silent_select_range_len")

BooleanOptionKey const	skip_failed_simulations ("in:file:skip_failed_simulations")

StringVectorOptionKey const	silent_scores_wanted ("in:file:silent_scores_wanted")

FileVectorOptionKey const	fasta ("in:file:fasta")

FileVectorOptionKey const	pssm ("in:file:pssm")

StringVectorOptionKey const	seq ("in:file:seq")

FileOptionKey const	checkpoint ("in:file:checkpoint")

FileOptionKey const	binary_chk ("in:file:binary_chk")

FileVectorOptionKey const	alignment ("in:file:alignment")

FileVectorOptionKey const	alignment2 ("in:file:alignment2")

FileOptionKey const	rama2b_map ("in:file:rama2b_map")

FileOptionKey const	psipred_ss2 ("in:file:psipred_ss2")

FileOptionKey const	dssp ("in:file:dssp")

BooleanOptionKey const	fail_on_bad_hbond ("in:file:fail_on_bad_hbond")

FileOptionKey const	movemap ("in:file:movemap")

BooleanOptionKey const	repair_sidechains ("in:file:repair_sidechains")

BooleanOptionKey const	no_binary_dunlib ("in:file:no_binary_dunlib")

IntegerOptionKey const	extended_pose ("in:file:extended_pose")

FileVectorOptionKey const	template_pdb ("in:file:template_pdb")

FileOptionKey const	template_silent ("in:file:template_silent")

FileVectorOptionKey const	rdc ("in:file:rdc")

FileVectorOptionKey const	csa ("in:file:csa")

FileVectorOptionKey const	dc ("in:file:dc")

FileVectorOptionKey const	burial ("in:file:burial")

FileOptionKey const	hrf_ms_labeling ("in:file:hrf_ms_labeling")

FileVectorOptionKey const	vall ("in:file:vall")

BooleanOptionKey const	rescore ("in:file:rescore")

StringOptionKey const	spanfile ("in:file:spanfile")

StringOptionKey const	lipofile ("in:file:lipofile")

StringOptionKey const	HDX ("in:file:HDX")

RealOptionKey const	d2h_sa_reweight ("in:file:d2h_sa_reweight")

FileOptionKey const	sucker_params ("in:file:sucker_params")

FileOptionKey const	fold_tree ("in:file:fold_tree")

BooleanOptionKey const	obey_ENDMDL ("in:file:obey_ENDMDL")

BooleanOptionKey const	new_chain_order ("in:file:new_chain_order")

FileOptionKey const	ddg_predictions_file ("in:file:ddg_predictions_file")

ResidueChainVectorOptionKey const	input_res ("in:file:input_res")

IntegerVectorOptionKey const	minimize_res ("in:file:minimize_res")

StringOptionKey const	md_schfile ("in:file:md_schfile")

FileOptionKey const	native_contacts ("in:file:native_contacts")

Function Documentation

◆ alignment()

FileVectorOptionKey const in::file::alignment ( "in:file:alignment" )

References out::file::file().

Referenced by input_alignments(), input_alignmentsMapped(), and main().

◆ alignment2()

FileVectorOptionKey const in::file::alignment2 ( "in:file:alignment2" )

References out::file::file().

Referenced by main().

◆ ambig_talos_cs_A()

FileOptionKey const in::file::ambig_talos_cs_A ( "in:file:ambig_talos_cs_A" )

References out::file::file().

◆ ambig_talos_cs_B()

FileOptionKey const in::file::ambig_talos_cs_B ( "in:file:ambig_talos_cs_B" )

References out::file::file().

◆ assign_gasteiger_atom_types()

BooleanOptionKey const in::file::assign_gasteiger_atom_types ( "in:file:assign_gasteiger_atom_types" )

References out::file::file().

◆ atom_tree_diff()

FileVectorOptionKey const in::file::atom_tree_diff ( "in:file:atom_tree_diff" )

References out::file::file().

◆ binary_chk()

FileOptionKey const in::file::binary_chk ( "in:file:binary_chk" )

References out::file::file().

◆ boinc_wu_zip()

FileVectorOptionKey const in::file::boinc_wu_zip ( "in:file:boinc_wu_zip" )

References out::file::file().

◆ burial()

FileVectorOptionKey const in::file::burial ( "in:file:burial" )

References out::file::file().

◆ centroid()

BooleanOptionKey const in::file::centroid ( "in:file:centroid" )

References out::file::file().

Referenced by collect_residue_types(), and main().

◆ centroid_input()

BooleanOptionKey const in::file::centroid_input ( "in:file:centroid_input" )

References out::file::file().

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

◆ check_all_PDB_components()

BooleanOptionKey const in::file::check_all_PDB_components ( "in:file:check_all_PDB_components" )

References out::file::file().

◆ checkpoint()

FileOptionKey const in::file::checkpoint ( "in:file:checkpoint" )

References out::file::file().

Referenced by main(), PickSSE::PickSSE(), and register_options().

◆ csa()

FileVectorOptionKey const in::file::csa ( "in:file:csa" )

References out::file::file().

◆ d2h_sa_reweight()

RealOptionKey const in::file::d2h_sa_reweight ( "in:file:d2h_sa_reweight" )

References out::file::file().

◆ dc()

FileVectorOptionKey const in::file::dc ( "in:file:dc" )

References out::file::file().

◆ ddg_predictions_file()

FileOptionKey const in::file::ddg_predictions_file ( "in:file:ddg_predictions_file" )

References out::file::file().

◆ dssp()

FileOptionKey const in::file::dssp ( "in:file:dssp" )

References out::file::file().

◆ extended_pose()

IntegerOptionKey const in::file::extended_pose ( "in:file:extended_pose" )

References out::file::file().

◆ extra_patch_cen()

FileVectorOptionKey const in::file::extra_patch_cen ( "in:file:extra_patch_cen" )

References out::file::file().

◆ extra_patch_fa()

FileVectorOptionKey const in::file::extra_patch_fa ( "in:file:extra_patch_fa" )

References out::file::file().

◆ extra_res()

FileVectorOptionKey const in::file::extra_res ( "in:file:extra_res" )

References out::file::file().

Referenced by main().

◆ extra_res_batch_path()

PathVectorOptionKey const in::file::extra_res_batch_path ( "in:file:extra_res_batch_path" )

References out::file::file().

◆ extra_res_cen()

FileVectorOptionKey const in::file::extra_res_cen ( "in:file:extra_res_cen" )

References out::file::file().

Referenced by main().

◆ extra_res_database()

StringOptionKey const in::file::extra_res_database ( "in:file:extra_res_database" )

References out::file::file().

◆ extra_res_database_mode()

StringOptionKey const in::file::extra_res_database_mode ( "in:file:extra_res_database_mode" )

References out::file::file().

◆ extra_res_database_resname_list()

FileOptionKey const in::file::extra_res_database_resname_list ( "in:file:extra_res_database_resname_list" )

References out::file::file().

◆ extra_res_fa()

FileVectorOptionKey const in::file::extra_res_fa ( "in:file:extra_res_fa" )

References out::file::file().

Referenced by main().

◆ extra_res_mmCIF()

FileVectorOptionKey const in::file::extra_res_mmCIF ( "in:file:extra_res_mmCIF" )

References out::file::file().

◆ extra_res_mol()

FileVectorOptionKey const in::file::extra_res_mol ( "in:file:extra_res_mol" )

References out::file::file().

◆ extra_res_path()

PathVectorOptionKey const in::file::extra_res_path ( "in:file:extra_res_path" )

References out::file::file().

◆ extra_res_pq_schema()

StringOptionKey const in::file::extra_res_pq_schema ( "in:file:extra_res_pq_schema" )

References out::file::file().

◆ extra_rot_lib_path()

PathVectorOptionKey const in::file::extra_rot_lib_path ( "in:file:extra_rot_lib_path" )

References out::file::file().

◆ fail_on_bad_hbond()

BooleanOptionKey const in::file::fail_on_bad_hbond ( "in:file:fail_on_bad_hbond" )

References out::file::file().

Referenced by main().

◆ fasta()

FileVectorOptionKey const in::file::fasta ( "in:file:fasta" )

References out::file::file().

Referenced by RNA_ScoreMover::apply(), build_template(), coarse_frag_test(), coarse_rna_denovo_test(), DomainAssemblerNDocker::DomainAssemblerNDocker(), easy_loop_model_test(), easy_target_test(), general_initialize(), hermann_phase_two_minimize(), main(), my_main(), Prepare(), rebuild_centroid_test(), rebuild_test(), protocols::abinitio::ApplicationContext::register_options(), register_options(), protocols::abinitio::JumpSpecificAbrelax::register_options(), register_options_broker(), apps::pilot::SampleSecondaryStructureAlignmentMover::revert_loops_to_original(), rna_assemble_all_combinations_test(), rna_assemble_test(), rna_build_helix_test(), rna_build_helix_test_OLD(), rna_build_helix_test_precompute(), rna_thread_test(), rna_torsion_check_test(), DockFragmentsMover::run(), protocols::abinitio::JumpSpecificAbrelax::setup(), TryScoreFilter::setup_pose(), setup_rna_working_parameters(), stepwise_template_test(), SymmAbRelaxTest(), and thermal_sampler().

◆ file()

BooleanOptionKey const in::file::file ( "in:file" )

References out::file::file().

◆ fold_tree()

FileOptionKey const in::file::fold_tree ( "in:file:fold_tree" )

References out::file::file().

Referenced by do_erraser2().

◆ force_silent_bitflip_on_read()

BooleanOptionKey const in::file::force_silent_bitflip_on_read ( "in:file:force_silent_bitflip_on_read" )

References out::file::file().

◆ frag3()

StringOptionKey const in::file::frag3 ( "in:file:frag3" )

References out::file::file().

Referenced by protocols::abinitio::ApplicationContext::ApplicationContext(), DomainAssemblerNDocker::DomainAssemblerNDocker(), get_fragments(), main(), protocols::abinitio::ApplicationContext::register_options(), register_options(), protocols::abinitio::JumpSpecificAbrelax::register_options(), register_options_broker(), setup_for_folding(), protocols::abinitio::JumpSpecificAbrelax::setup_fragments(), SmoothFragRepackMover::SmoothFragRepackMover(), and TryScoreFilter::TryScoreFilter().

◆ frag9()

StringOptionKey const in::file::frag9 ( "in:file:frag9" )

References out::file::file().

Referenced by protocols::abinitio::ApplicationContext::ApplicationContext(), DomainAssemblerNDocker::DomainAssemblerNDocker(), get_fragments(), main(), protocols::abinitio::ApplicationContext::register_options(), register_options(), protocols::abinitio::JumpSpecificAbrelax::register_options(), register_options_broker(), setup_for_folding(), protocols::abinitio::JumpSpecificAbrelax::setup_fragments(), and TryScoreFilter::TryScoreFilter().

◆ frag_files()

FileVectorOptionKey const in::file::frag_files ( "in:file:frag_files" )

References out::file::file().

Referenced by rebuild_centroid_test().

◆ fragA()

StringOptionKey const in::file::fragA ( "in:file:fragA" )

References out::file::file().

Referenced by protocols::abinitio::ApplicationContext::ApplicationContext(), DomainAssemblerNDocker::DomainAssemblerNDocker(), get_fragments(), main(), register_options(), setup_for_folding(), protocols::abinitio::JumpSpecificAbrelax::setup_fragments(), and TryScoreFilter::TryScoreFilter().

◆ fragB()

StringOptionKey const in::file::fragB ( "in:file:fragB" )

References out::file::file().

Referenced by protocols::abinitio::ApplicationContext::ApplicationContext(), DomainAssemblerNDocker::DomainAssemblerNDocker(), get_fragments(), main(), register_options(), setup_for_folding(), protocols::abinitio::JumpSpecificAbrelax::setup_fragments(), and TryScoreFilter::TryScoreFilter().

◆ fullatom()

BooleanOptionKey const in::file::fullatom ( "in:file:fullatom" )

References out::file::file().

Referenced by Minimize::apply(), protocols::abinitio::JumpSpecificAbrelax::do_rerun(), main(), Minimize::Minimize(), and protocols::abinitio::JumpSpecificAbrelax::setup_fold().

◆ HDX()

StringOptionKey const in::file::HDX ( "in:file:HDX" )

References out::file::file().

Referenced by register_options().

◆ hrf_ms_labeling()

FileOptionKey const in::file::hrf_ms_labeling ( "in:file:hrf_ms_labeling" )

References out::file::file().

◆ input_res()

ResidueChainVectorOptionKey const in::file::input_res ( "in:file:input_res" )

References out::file::file().

Referenced by main(), and mg_modeler_test().

◆ job_definition_file()

FileOptionKey const in::file::job_definition_file ( "in:file:job_definition_file" )

References out::file::file().

Referenced by main().

◆ keep_input_scores()

BooleanOptionKey const in::file::keep_input_scores ( "in:file:keep_input_scores" )

References out::file::file().

◆ l()

FileVectorOptionKey const in::file::l ( "in:file:l" )

References out::file::file().

Referenced by main(), mg_pdbstats_test(), MSA_design_main(), my_main(), polar_pdbstats_test(), and rhiju_pdbstats().

◆ lazy_silent()

BooleanOptionKey const in::file::lazy_silent ( "in:file:lazy_silent" )

References out::file::file().

◆ lipofile()

StringOptionKey const in::file::lipofile ( "in:file:lipofile" )

References out::file::file().

◆ list()

FileVectorOptionKey const in::file::list ( "in:file:list" )

References out::file::file().

◆ load_PDB_components()

BooleanOptionKey const in::file::load_PDB_components ( "in:file:load_PDB_components" )

References out::file::file().

Referenced by main().

◆ md_schfile()

StringOptionKey const in::file::md_schfile ( "in:file:md_schfile" )

References out::file::file().

Referenced by main().

◆ minimize_res()

IntegerVectorOptionKey const in::file::minimize_res ( "in:file:minimize_res" )

References out::file::file().

Referenced by main(), and rna_fullatom_minimize_test().

◆ movemap()

FileOptionKey const in::file::movemap ( "in:file:movemap" )

References out::file::file().

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

◆ native()

FileOptionKey const in::file::native ( "in:file:native" )

References out::file::file().

Referenced by align_pdbs(), analyze_base_pair_test(), protocols::abinitio::ApplicationContext::ApplicationContext(), ConstraintMinimizer::apply(), DeleteSegments::apply(), LoopHashRelax_Sampler::apply(), Foldptn::apply(), MinPackMinMover::apply(), ExposedStrandMover::apply(), HDdesignMover::apply(), RescoreCenrot::apply(), CrystDesign::apply(), MPDomainAssembly::apply(), build_next_nucleotide_test(), build_template(), BuildFullModel::BuildFullModel(), byres_analysis(), calc_rms_test(), calc_rmsd_test(), calculate_pairwise_RMSD(), chi_stats_test(), coarse_rna_denovo_test(), cst_relax_test(), DeleteSegments::DeleteSegments(), DomainAssemblerNDocker::DomainAssemblerNDocker(), easy_loop_model_test(), easy_target_test(), erraser_monte_carlo(), fillPoseAndDataList(), Foldptn::Foldptn(), general_initialize(), get_info_test(), get_rmsd(), GunnTest::GunnTest(), hermann_phase_two(), hermann_phase_two_minimize(), initialize_native_pose(), lariat_modeling(), ligand_dock_main_jd1(), LocalRmsd::LocalRmsd(), loop_closure_test(), main(), minimize_test(), minimizer_test(), my_main(), MyScoreMover::MyScoreMover(), pack_phosphates(), pdb_scoring(), pep_phipsi_analysis(), pep_rmsd_analysis(), processChildren(), processChildrenIntensification(), read_native_pose(), rebuild_centroid_test(), rebuild_test(), protocols::abinitio::ApplicationContext::register_options(), register_options(), protocols::abinitio::JumpSpecificAbrelax::register_options(), protocols::abinitio::Application::register_options(), register_options_broker(), repack_test(), rna_assemble_all_combinations_test(), rna_fullatom_minimize_silent_test(), rna_fullatom_minimize_test(), rna_lores_score_silent_test(), rna_protein_rb_test(), rna_resample_test(), rna_stats_test(), RotamerAnalysis(), MPI_Refinement_Launcher::run(), MPI_LoopHash_Launcher::run(), run(), DockFragmentsMover::run(), sample_state_to_state(), sample_trp_test(), screen_phosphates(), protocols::abinitio::JumpSpecificAbrelax::setup(), protocols::abinitio::Application::setup(), setup_pose_setup_class(), spinner_test(), stepwise_template_test(), swa_rna_sample(), and test().

◆ native_contacts()

FileOptionKey const in::file::native_contacts ( "in:file:native_contacts" )

References out::file::file().

◆ native_exclude_res()

IntegerVectorOptionKey const in::file::native_exclude_res ( "in:file:native_exclude_res" )

References out::file::file().

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

◆ new_chain_order()

BooleanOptionKey const in::file::new_chain_order ( "in:file:new_chain_order" )

References out::file::file().

◆ no_binary_dunlib()

BooleanOptionKey const in::file::no_binary_dunlib ( "in:file:no_binary_dunlib" )

References out::file::file().

◆ no_detect_pseudobonds()

BooleanOptionKey const in::file::no_detect_pseudobonds ( "in:file:no_detect_pseudobonds" )

References out::file::file().

◆ obey_ENDMDL()

BooleanOptionKey const in::file::obey_ENDMDL ( "in:file:obey_ENDMDL" )

References out::file::file().

◆ override_database_params()

BooleanOptionKey const in::file::override_database_params ( "in:file:override_database_params" )

References out::file::file().

◆ override_rot_lib_path()

PathVectorOptionKey const in::file::override_rot_lib_path ( "in:file:override_rot_lib_path" )

References out::file::file().

◆ pca()

FileOptionKey const in::file::pca ( "in:file:pca" )

References out::file::file().

◆ PCS_frag_cst()

FileOptionKey const in::file::PCS_frag_cst ( "in:file:PCS_frag_cst" )

References out::file::file().

◆ PDB_components_directory()

StringOptionKey const in::file::PDB_components_directory ( "in:file:PDB_components_directory" )

References out::file::file().

◆ PDB_components_overrides()

StringVectorOptionKey const in::file::PDB_components_overrides ( "in:file:PDB_components_overrides" )

References out::file::file().

◆ psipred_ss2()

FileOptionKey const in::file::psipred_ss2 ( "in:file:psipred_ss2" )

References out::file::file().

Referenced by main(), and register_options().

◆ pssm()

FileVectorOptionKey const in::file::pssm ( "in:file:pssm" )

References out::file::file().

Referenced by main(), and register_options().

◆ rama2b_map()

FileOptionKey const in::file::rama2b_map ( "in:file:rama2b_map" )

References out::file::file().

◆ rdc()

FileVectorOptionKey const in::file::rdc ( "in:file:rdc" )

References out::file::file().

Referenced by register_options().

◆ remap_pdb_atom_names_for()

StringVectorOptionKey const in::file::remap_pdb_atom_names_for ( "in:file:remap_pdb_atom_names_for" )

References out::file::file().

◆ repair_sidechains()

BooleanOptionKey const in::file::repair_sidechains ( "in:file:repair_sidechains" )

References out::file::file().

Referenced by main().

◆ rescore()

BooleanOptionKey const in::file::rescore ( "in:file:rescore" )

References out::file::file().

Referenced by main().

◆ residue_type_set()

StringOptionKey const in::file::residue_type_set ( "in:file:residue_type_set" )

References out::file::file().

Referenced by ComputeSAXSSpectrum::ComputeSAXSSpectrum(), load_coords(), main(), register_options(), RescoreSAXS::RescoreSAXS(), and RotateSAXS::RotateSAXS().

◆ s()

FileVectorOptionKey const in::file::s ( "in:file:s" )

References out::file::file().

Referenced by align_pdbs(), analyze_base_pair_test(), protocols::abinitio::ApplicationContext::ApplicationContext(), calc_rmsd_test(), calculate_pairwise_RMSD(), calculate_sasa(), chi_stats_test(), coarse_to_full_test(), color_by_geom_sol_RNA_test(), color_by_lj_base_RNA_test(), color_by_lj_test(), convert_to_native_test(), count_contacts(), create_bp_jump_database_test(), create_rna_benchmark_test(), create_rna_vall_torsions_test(), cst_relax_test(), densityTools(), do_erraser2(), do_initial_checks(), doit(), DomainAssemblerNDocker::DomainAssemblerNDocker(), dostuff(), drrafter_error_estimation(), easy_loop_model_test(), easy_target_test(), entropy_calculate_test(), env_sugar_test(), erraser2_test(), erraser_monte_carlo(), files_for_openMM_test(), fill_input_poses_based_on_possible_checkpoints(), find_close_motifs(), ga_main(), get_info_test(), get_pose_energy_breakdown(), get_rmsd(), get_tasks_from_command_line(), graphics_main(), homolog_finder(), import_and_dump_pdb(), juke_sam_test(), loop_closure_test(), main(), mg_modeler_test(), minimize_pdb(), minimizer_test(), mismatch_test(), modeler_closure_test(), morph_pdbs_test(), MSA_design_main(), multiple_variant_type_test(), mutate_residues_wrapper(), my_main(), nucleobase_probe_score_test(), o2prime_packer(), obtain_start_pose(), OPT_KEY(), pack_phosphates(), pack_polar_hydrogens(), parse_pathway_test(), pdb_little_motif_test(), pdb_to_silent_file(), pdb_to_silent_file_simple(), posewrap_from_command_line(), predict_chem_map_test(), print_hbonds_test(), print_internal_coord_test(), pymol_struct_type_test(), rb_entropy_test(), rebuild_centroid_test(), rebuild_test(), protocols::abinitio::ApplicationContext::register_options(), register_options(), repack_test(), resample_full_model_test(), rhiju_pdbstats(), rna_backbone_rebuild_test(), rna_chain_closure_test(), rna_close_chainbreaks_test(), rna_design_gap_test(), rna_design_test(), rna_fullatom_minimize_silent_test(), rna_fullatom_minimize_test(), rna_fullatom_multiscore_test(), rna_fullatom_score_test(), rna_idealize_test(), rna_lores_score_silent_test(), rna_lores_score_test(), rna_o2prime_test(), rna_protein_pdbstats_test(), rna_protein_prepack_test(), rna_protein_rb_test(), rna_protein_repack_test(), rna_stats_test(), rna_suitename(), rna_superimpose_and_graft_test(), rna_thread_test(), run(), run_hd(), run_hh(), sample_rama_test(), sample_trp_test(), sample_trp_tyr_test(), sasa_test(), screen_phosphates(), sequence_tolerance_main(), sequence_tolerance_mf_main(), set_ideal_geometry(), set_up_pose(), setup_copy_DOF_input(), protocols::abinitio::JumpSpecificAbrelax::setup_fold(), TryScoreFilter::setup_pose(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), spinner_test(), ss_ds_ts_assign_test(), sugar_geometry_RNA_test(), tar_motif_test(), test_function(), test_kc(), test_kc2(), and thermal_sampler().

◆ screening_job_file()

FileOptionKey const in::file::screening_job_file ( "in:file:screening_job_file" )

References out::file::file().

◆ screening_list()

FileVectorOptionKey const in::file::screening_list ( "in:file:screening_list" )

References out::file::file().

◆ seq()

StringVectorOptionKey const in::file::seq ( "in:file:seq" )

References out::file::file().

◆ shuffle_screening_jobs()

BooleanOptionKey const in::file::shuffle_screening_jobs ( "in:file:shuffle_screening_jobs" )

References out::file::file().

◆ silent()

FileVectorOptionKey const in::file::silent ( "in:file:silent" )

References out::file::file().

Referenced by analyze_base_pair_test(), RNA_ScoreMover::apply(), build_full_model_test(), calc_rms_test(), calc_rmsf_and_avrg(), cluster_outfile_test(), cluster_outfile_test_OLD(), cluster_test(), coarse_rna_denovo_test(), color_by_lj_test(), connectivity_test(), count_contacts(), dist_matrix_test(), protocols::abinitio::JumpSpecificAbrelax::do_distributed_rerun(), protocols::abinitio::JumpSpecificAbrelax::do_rerun(), drrafter_error_estimation(), entropy_calculate_test(), extract_pdbs_test(), filter_combine_long_loop(), frag_extract_test(), general_initialize(), get_info_test(), get_pose_energy_breakdown(), get_rmsd(), hermann_phase_two(), hermann_phase_two_minimize(), ligand_dock_main_jd1(), main(), minimizer_test(), my_main(), peptide_plane_test(), ThisApplication::pick_frags(), post_rebuild_bulge_assembly(), read_structures(), rebuild_centroid_test(), rebuild_test(), register_options(), protocols::abinitio::JumpSpecificAbrelax::register_options(), register_options_broker(), reverse_doublet_test(), rna_assemble_all_combinations_test(), rna_assemble_test(), rna_fullatom_minimize_silent_test(), rna_fullatom_minimize_test(), rna_lores_score_silent_test(), rna_sample_virtual_sugar(), run(), ScoreFragmentSetMover::run(), FragmentAssemblyMover::run(), ConsensusFragmentMover::run(), SolutionRescoreMover::run(), save_cluster_tree_lite(), setup_copy_DOF_input(), setup_rna_working_parameters(), swa_rna_cluster(), thermal_sampler(), and write_for_resnum().

◆ silent_energy_cut()

RealOptionKey const in::file::silent_energy_cut ( "in:file:silent_energy_cut" )

References out::file::file().

Referenced by main().

◆ silent_list()

FileVectorOptionKey const in::file::silent_list ( "in:file:silent_list" )

References out::file::file().

Referenced by save_cluster_tree_lite().

◆ silent_read_through_errors()

BooleanOptionKey const in::file::silent_read_through_errors ( "in:file:silent_read_through_errors" )

References out::file::file().

Referenced by main().

◆ silent_renumber()

BooleanOptionKey const in::file::silent_renumber ( "in:file:silent_renumber" )

References out::file::file().

Referenced by main().

◆ silent_score_prefix()

StringOptionKey const in::file::silent_score_prefix ( "in:file:silent_score_prefix" )

References out::file::file().

◆ silent_scores_wanted()

StringVectorOptionKey const in::file::silent_scores_wanted ( "in:file:silent_scores_wanted" )

References out::file::file().

◆ silent_select_random()

IntegerOptionKey const in::file::silent_select_random ( "in:file:silent_select_random" )

References out::file::file().

◆ silent_select_range_len()

IntegerOptionKey const in::file::silent_select_range_len ( "in:file:silent_select_range_len" )

References out::file::file().

◆ silent_select_range_mul()

IntegerOptionKey const in::file::silent_select_range_mul ( "in:file:silent_select_range_mul" )

References out::file::file().

◆ silent_select_range_start()

IntegerOptionKey const in::file::silent_select_range_start ( "in:file:silent_select_range_start" )

References out::file::file().

◆ silent_struct_type()

StringOptionKey const in::file::silent_struct_type ( "in:file:silent_struct_type" )

References out::file::file().

Referenced by main(), and my_main().

◆ skip_failed_simulations()

BooleanOptionKey const in::file::skip_failed_simulations ( "in:file:skip_failed_simulations" )

References out::file::file().

◆ spanfile()

StringOptionKey const in::file::spanfile ( "in:file:spanfile" )

References out::file::file().

Referenced by main().

◆ srlz()

BooleanOptionKey const in::file::srlz ( "in:file:srlz" )

References out::file::file().

◆ srlz_override()

BooleanOptionKey const in::file::srlz_override ( "in:file:srlz_override" )

References out::file::file().

◆ sucker_params()

FileOptionKey const in::file::sucker_params ( "in:file:sucker_params" )

References out::file::file().

Referenced by main().

◆ surface_vectors()

StringOptionKey const in::file::surface_vectors ( "in:file:surface_vectors" )

References out::file::file().

◆ t()

FileVectorOptionKey const in::file::t ( "in:file:t" )

References out::file::file().

◆ tagfile()

FileOptionKey const in::file::tagfile ( "in:file:tagfile" )

References out::file::file().

Referenced by main().

◆ tags()

StringVectorOptionKey const in::file::tags ( "in:file:tags" )

References out::file::file().

Referenced by analyze_base_pair_test(), build_full_model_test(), color_by_lj_test(), count_contacts(), drrafter_error_estimation(), extract_pdbs_test(), get_info_test(), get_pose_energy_breakdown(), get_rmsd(), get_silent_file_tags(), ligand_dock_main_jd1(), main(), my_main(), post_rebuild_bulge_assembly(), rebuild_centroid_test(), rebuild_test(), rna_fullatom_minimize_test(), and thermal_sampler().

◆ talos_cs()

FileOptionKey const in::file::talos_cs ( "in:file:talos_cs" )

References out::file::file().

◆ talos_phi_psi()

FileOptionKey const in::file::talos_phi_psi ( "in:file:talos_phi_psi" )

References out::file::file().

Referenced by main(), and register_options().

◆ template_pdb()

FileVectorOptionKey const in::file::template_pdb ( "in:file:template_pdb" )

References out::file::file().

Referenced by calc_rmsf_and_avrg(), get_exclid(), and main().

◆ template_silent()

FileOptionKey const in::file::template_silent ( "in:file:template_silent" )

References out::file::file().

◆ torsion_bin_probs()

FileOptionKey const in::file::torsion_bin_probs ( "in:file:torsion_bin_probs" )

References out::file::file().

Referenced by attach_abego_pools(), main(), and register_options().

◆ treat_residues_in_these_chains_as_separate_chemical_entities()

StringOptionKey const in::file::treat_residues_in_these_chains_as_separate_chemical_entities ( "in:file:treat_residues_in_these_chains_as_separate_chemical_entities" )

References out::file::file().

◆ user_tags()

StringVectorOptionKey const in::file::user_tags ( "in:file:user_tags" )

References out::file::file().

Referenced by main().

◆ vall()

FileVectorOptionKey const in::file::vall ( "in:file:vall" )

References out::file::file().

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

◆ xyz()

StringOptionKey const in::file::xyz ( "in:file:xyz" )

References out::file::file().

Referenced by main(), and register_options().

◆ zip()

StringOptionKey const in::file::zip ( "in:file:zip" )

References out::file::file().

Functions

Function Documentation

◆ alignment()

◆ alignment2()

◆ ambig_talos_cs_A()

◆ ambig_talos_cs_B()

◆ assign_gasteiger_atom_types()

◆ atom_tree_diff()

◆ binary_chk()

◆ boinc_wu_zip()

◆ burial()

◆ centroid()

◆ centroid_input()

◆ check_all_PDB_components()

◆ checkpoint()

◆ csa()

◆ d2h_sa_reweight()

◆ dc()

◆ ddg_predictions_file()

◆ dssp()

◆ extended_pose()

◆ extra_patch_cen()

◆ extra_patch_fa()

◆ extra_res()

◆ extra_res_batch_path()

◆ extra_res_cen()

◆ extra_res_database()

◆ extra_res_database_mode()

◆ extra_res_database_resname_list()

◆ extra_res_fa()

◆ extra_res_mmCIF()

◆ extra_res_mol()

◆ extra_res_path()

◆ extra_res_pq_schema()

◆ extra_rot_lib_path()

◆ fail_on_bad_hbond()

◆ fasta()

◆ file()

◆ fold_tree()

◆ force_silent_bitflip_on_read()

◆ frag3()

◆ frag9()

◆ frag_files()

◆ fragA()

◆ fragB()

◆ fullatom()

◆ HDX()

◆ hrf_ms_labeling()

◆ input_res()

◆ job_definition_file()

◆ keep_input_scores()

◆ l()

◆ lazy_silent()

◆ lipofile()

◆ list()

◆ load_PDB_components()

◆ md_schfile()

◆ minimize_res()

◆ movemap()

◆ native()

◆ native_contacts()

◆ native_exclude_res()

◆ new_chain_order()

◆ no_binary_dunlib()

◆ no_detect_pseudobonds()

◆ obey_ENDMDL()

◆ override_database_params()

◆ override_rot_lib_path()

◆ pca()

◆ PCS_frag_cst()

◆ PDB_components_directory()

◆ PDB_components_overrides()

◆ psipred_ss2()

◆ pssm()

◆ rama2b_map()

◆ rdc()

◆ remap_pdb_atom_names_for()

◆ repair_sidechains()

◆ rescore()

◆ residue_type_set()