out::file Namespace Reference

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

Function Documentation

alignment()

StringOptionKey const out::file::alignment

(

"out:file:alignment"

)

References file().

Referenced by main().

atom_tree_diff()

StringOptionKey const out::file::atom_tree_diff

(

"out:file:atom_tree_diff"

)

References file().

atom_tree_diff_bb()

IntegerOptionKey const out::file::atom_tree_diff_bb

(

"out:file:atom_tree_diff_bb"

)

References file().

atom_tree_diff_bl()

IntegerOptionKey const out::file::atom_tree_diff_bl

(

"out:file:atom_tree_diff_bl"

)

References file().

atom_tree_diff_sc()

IntegerOptionKey const out::file::atom_tree_diff_sc

(

"out:file:atom_tree_diff_sc"

)

References file().

cif_extra_data_separate_file()

BooleanOptionKey const out::file::cif_extra_data_separate_file

(

"out:file:cif_extra_data_separate_file"

)

References file().

design_contrast()

FileOptionKey const out::file::design_contrast

(

"out:file:design_contrast"

)

References file().

Referenced by main().

do_not_autoassign_SS()

BooleanOptionKey const out::file::do_not_autoassign_SS

(

"out:file:do_not_autoassign_SS"

)

References file().

dont_rewrite_dunbrack_database()

BooleanOptionKey const out::file::dont_rewrite_dunbrack_database

(

"out:file:dont_rewrite_dunbrack_database"

)

References file().

file()

BooleanOptionKey const out::file::file

(

"out:file"

)

Referenced by in::file::alignment(), alignment(), in::file::alignment2(), in::file::ambig_talos_cs_A(), in::file::ambig_talos_cs_B(), in::file::assign_gasteiger_atom_types(), in::file::atom_tree_diff(), atom_tree_diff(), atom_tree_diff_bb(), atom_tree_diff_bl(), atom_tree_diff_sc(), in::file::binary_chk(), in::file::boinc_wu_zip(), in::file::burial(), in::file::centroid(), in::file::centroid_input(), in::file::check_all_PDB_components(), in::file::checkpoint(), cif_extra_data_separate_file(), in::file::csa(), in::file::d2h_sa_reweight(), in::file::dc(), in::file::ddg_predictions_file(), design_contrast(), do_not_autoassign_SS(), dont_rewrite_dunbrack_database(), in::file::dssp(), in::file::extended_pose(), in::file::extra_patch_cen(), in::file::extra_patch_fa(), in::file::extra_res(), in::file::extra_res_batch_path(), in::file::extra_res_cen(), in::file::extra_res_database(), in::file::extra_res_database_mode(), in::file::extra_res_database_resname_list(), in::file::extra_res_fa(), in::file::extra_res_mmCIF(), in::file::extra_res_mol(), in::file::extra_res_path(), in::file::extra_res_pq_schema(), in::file::extra_rot_lib_path(), in::file::fail_on_bad_hbond(), in::file::fasta(), in::file::file(), in::file::fold_tree(), force_nonideal_structure(), in::file::force_silent_bitflip_on_read(), in::file::frag3(), in::file::frag9(), in::file::frag_files(), frag_prefix(), in::file::fragA(), in::file::fragB(), in::file::fullatom(), fullatom(), in::file::HDX(), in::file::hrf_ms_labeling(), in::file::input_res(), in::file::job_definition_file(), in::file::keep_input_scores(), in::file::l(), in::file::lazy_silent(), in::file::lipofile(), in::file::list(), in::file::load_PDB_components(), in::file::md_schfile(), in::file::minimize_res(), in::file::movemap(), in::file::native(), in::file::native_contacts(), in::file::native_exclude_res(), in::file::new_chain_order(), in::file::no_binary_dunlib(), no_chainend_ter(), in::file::no_detect_pseudobonds(), no_extra_sdf_data(), no_output_cen(), no_scores_in_pdb(), o(), in::file::obey_ENDMDL(), output_ligands_as_separate_chains(), output_only_asymmetric_unit(), output_orbitals(), output_pose_cache_data(), output_pose_energies_table(), output_pose_fold_tree(), output_secondary_structure(), output_torsions(), output_virtual(), output_virtual_zero_occ(), in::file::override_database_params(), in::file::override_rot_lib_path(), in::file::pca(), in::file::PCS_frag_cst(), pdb_comments(), in::file::PDB_components_directory(), in::file::PDB_components_overrides(), pdb_parents(), per_chain_renumbering(), in::file::psipred_ss2(), in::file::pssm(), in::file::rama2b_map(), raw(), in::file::rdc(), in::file::remap_pdb_atom_names_for(), renumber_pdb(), in::file::repair_sidechains(), in::file::rescore(), in::file::residue_type_set(), residue_type_set(), in::file::s(), score_only(), scorefile(), scorefile_format(), in::file::screening_job_file(), in::file::screening_list(), in::file::seq(), set_pdb_author(), in::file::shuffle_screening_jobs(), in::file::silent(), silent(), in::file::silent_energy_cut(), in::file::silent_list(), silent_preserve_H(), silent_print_all_score_headers(), in::file::silent_read_through_errors(), in::file::silent_renumber(), in::file::silent_score_prefix(), in::file::silent_scores_wanted(), in::file::silent_select_random(), in::file::silent_select_range_len(), in::file::silent_select_range_mul(), in::file::silent_select_range_start(), in::file::silent_struct_type(), silent_struct_type(), in::file::skip_failed_simulations(), in::file::spanfile(), in::file::srlz(), srlz(), in::file::srlz_override(), in::file::sucker_params(), suppress_zero_occ_pdb_output(), in::file::surface_vectors(), in::file::t(), in::file::tagfile(), in::file::tags(), in::file::talos_cs(), in::file::talos_phi_psi(), in::file::template_pdb(), in::file::template_silent(), in::file::torsion_bin_probs(), in::file::treat_residues_in_these_chains_as_separate_chemical_entities(), use_occurrence_data(), use_pdb_format_HETNAM_records(), in::file::user_tags(), in::file::vall(), weight_silent_scores(), write_glycan_pdb_codes(), write_pdb_link_records(), write_pdb_parametric_info(), write_pdb_title_section_records(), write_seqres_records(), in::file::xyz(), and in::file::zip().

force_nonideal_structure()

BooleanOptionKey const out::file::force_nonideal_structure

(

"out:file:force_nonideal_structure"

)

References file().

frag_prefix()

StringOptionKey const out::file::frag_prefix

(

"out:file:frag_prefix"

)

References file().

Referenced by main(), and register_options().

fullatom()

BooleanOptionKey const out::file::fullatom

(

"out:file:fullatom"

)

References file().

Referenced by main().

no_chainend_ter()

BooleanOptionKey const out::file::no_chainend_ter

(

"out:file:no_chainend_ter"

)

References file().

Referenced by main().

no_extra_sdf_data()

BooleanOptionKey const out::file::no_extra_sdf_data

(

"out:file:no_extra_sdf_data"

)

References file().

no_output_cen()

BooleanOptionKey const out::file::no_output_cen

(

"out:file:no_output_cen"

)

References file().

no_scores_in_pdb()

BooleanOptionKey const out::file::no_scores_in_pdb

(

"out:file:no_scores_in_pdb"

)

References file().

o()

StringOptionKey const out::file::o

(

"out:file:o"

)

References file().

Referenced by assign_rigid_body_settings_to_clusters_test(), chi_stats_test(), cluster_rigid_body_settings_test(), coarse_to_full_test(), connectivity_test(), create_bp_jump_database_test(), create_rna_vall_torsions_test(), define_states_test(), delta_chi_correction_test(), design_test(), dinucleotide_test(), dist_matrix_test(), doit(), dostuff(), double_helix_test(), TCDock::dump_onecomp(), TCDock::dump_pdb(), entropy_calculate_test(), frag_extract_test(), get_info_test(), graft_pdb(), helix_ST(), homolog_finder(), luxr_setup(), main(), mg_modeler_test(), mg_pdbstats_test(), one_chain_MC_sampling(), one_chain_ST_MC(), output_results(), output_stuff(), pack_polar_hydrogens(), polar_pdbstats_test(), print_pep_csts(), Bola::random_nonclashing_move(), read_write(), reverse_rbs_test(), rhiju_pdbstats(), rna_build_helix_test(), rna_protein_pdbstats_test(), rna_thread_test(), run_pep_prep(), RunPepSpec(), swa_rna_sample(), tar_motif_test(), TCDock::TCDock(), two_base_pairs_test(), and two_base_pairs_via_loop_closure_test().

output_ligands_as_separate_chains()

BooleanOptionKey const out::file::output_ligands_as_separate_chains

(

"out:file:output_ligands_as_separate_chains"

)

References file().

output_only_asymmetric_unit()

BooleanOptionKey const out::file::output_only_asymmetric_unit

(

"out:file:output_only_asymmetric_unit"

)

References file().

output_orbitals()

BooleanOptionKey const out::file::output_orbitals

(

"out:file:output_orbitals"

)

References file().

output_pose_cache_data()

BooleanOptionKey const out::file::output_pose_cache_data

(

"out:file:output_pose_cache_data"

)

References file().

output_pose_energies_table()

BooleanOptionKey const out::file::output_pose_energies_table

(

"out:file:output_pose_energies_table"

)

References file().

output_pose_fold_tree()

BooleanOptionKey const out::file::output_pose_fold_tree

(

"out:file:output_pose_fold_tree"

)

References file().

output_secondary_structure()

BooleanOptionKey const out::file::output_secondary_structure

(

"out:file:output_secondary_structure"

)

References file().

output_torsions()

BooleanOptionKey const out::file::output_torsions

(

"out:file:output_torsions"

)

References file().

output_virtual()

BooleanOptionKey const out::file::output_virtual

(

"out:file:output_virtual"

)

References file().

output_virtual_zero_occ()

BooleanOptionKey const out::file::output_virtual_zero_occ

(

"out:file:output_virtual_zero_occ"

)

References file().

pdb_comments()

BooleanOptionKey const out::file::pdb_comments

(

"out:file:pdb_comments"

)

References file().

pdb_parents()

BooleanOptionKey const out::file::pdb_parents

(

"out:file:pdb_parents"

)

References file().

per_chain_renumbering()

BooleanOptionKey const out::file::per_chain_renumbering

(

"out:file:per_chain_renumbering"

)

References file().

raw()

BooleanOptionKey const out::file::raw

(

"out:file:raw"

)

References file().

Referenced by distribute_jobs().

renumber_pdb()

BooleanOptionKey const out::file::renumber_pdb

(

"out:file:renumber_pdb"

)

References file().

residue_type_set()

StringOptionKey const out::file::residue_type_set

(

"out:file:residue_type_set"

)

References file().

Referenced by frag_extract_test(), get_info_test(), main(), register_options(), and run().

score_only()

StringOptionKey const out::file::score_only

(

"out:file:score_only"

)

References file().

scorefile()

StringOptionKey const out::file::scorefile

(

"out:file:scorefile"

)

References file().

Referenced by distribute_jobs(), and main().

scorefile_format()

StringOptionKey const out::file::scorefile_format

(

"out:file:scorefile_format"

)

References file().

set_pdb_author()

StringOptionKey const out::file::set_pdb_author

(

"out:file:set_pdb_author"

)

References file().

silent()

StringOptionKey const out::file::silent

(

"out:file:silent"

)

References file().

Referenced by analyze_base_pair_test(), RNA_ScoreMover::apply(), base_pair_to_base_pair_test(), benzene_pair_score_test(), build_full_model_test(), build_next_nucleotide_test(), BuildFullModel::BuildFullModel(), calc_rms_test(), cluster_outfile_test(), cluster_outfile_test_OLD(), cluster_rigid_body_settings_test(), cluster_silent_file_data(), cluster_test(), coarse_rna_denovo_test(), StepWiseJobQueen::complete_larval_job_maturation(), cst_relax_test(), define_states_test(), dinucleotide_test(), distribute_jobs(), protocols::abinitio::JumpSpecificAbrelax::do_rerun(), doit(), dostuff(), BuildFullModel::fill_and_sample_full_model(), finely_sample_base_pair_test(), get_rmsd(), hermann_phase_two_minimize(), initialize_rigid_body_sampler(), lariat_modeling(), ligand_dock_main_jd1(), main(), mg_modeler_test(), minimize_with_constraints(), modeler_closure_test(), modeler_map_test(), my_main(), nucleobase_probe_score_test(), parse_pathway_test(), post_rebuild_bulge_assembly(), rebuild_centroid_test(), rebuild_test(), protocols::abinitio::ApplicationContext::register_options(), protocols::abinitio::JumpSpecificAbrelax::register_options(), register_options(), register_options_broker(), 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_fullatom_minimize_silent_test(), rna_fullatom_minimize_test(), rna_fullatom_score_test(), rna_lores_score_silent_test(), rna_o2prime_test(), rna_protein_rb_test(), rna_resample_test(), rna_sample_virtual_sugar(), rna_stats_test(), DomainAssemblerNDocker::run(), DockFragmentsMover::run(), FragmentAssemblyMover::run(), run_mc(), sample_rama_test(), sample_state_to_state(), sample_trp_test(), save_cluster_tree_lite(), spinner_test(), stepwise_monte_carlo_legacy(), stepwise_template_test(), swa_rna_cluster(), swa_rna_sample(), and two_base_pairs_test().

silent_preserve_H()

BooleanOptionKey const out::file::silent_preserve_H

(

"out:file:silent_preserve_H"

)

References file().

silent_print_all_score_headers()

BooleanOptionKey const out::file::silent_print_all_score_headers

(

"out:file:silent_print_all_score_headers"

)

References file().

silent_struct_type()

StringOptionKey const out::file::silent_struct_type

(

"out:file:silent_struct_type"

)

References file().

Referenced by my_main().

srlz()

BooleanOptionKey const out::file::srlz

(

"out:file:srlz"

)

References file().

suppress_zero_occ_pdb_output()

BooleanOptionKey const out::file::suppress_zero_occ_pdb_output

(

"out:file:suppress_zero_occ_pdb_output"

)

References file().

Referenced by main().

use_occurrence_data()

BooleanOptionKey const out::file::use_occurrence_data

(

"out:file:use_occurrence_data"

)

References file().

use_pdb_format_HETNAM_records()

BooleanOptionKey const out::file::use_pdb_format_HETNAM_records

(

"out:file:use_pdb_format_HETNAM_records"

)

References file().

weight_silent_scores()

BooleanOptionKey const out::file::weight_silent_scores

(

"out:file:weight_silent_scores"

)

References file().

write_glycan_pdb_codes()

BooleanOptionKey const out::file::write_glycan_pdb_codes

(

"out:file:write_glycan_pdb_codes"

)

References file().

write_pdb_link_records()

BooleanOptionKey const out::file::write_pdb_link_records

(

"out:file:write_pdb_link_records"

)

References file().

write_pdb_parametric_info()

BooleanOptionKey const out::file::write_pdb_parametric_info

(

"out:file:write_pdb_parametric_info"

)

References file().

write_pdb_title_section_records()

BooleanOptionKey const out::file::write_pdb_title_section_records

(

"out:file:write_pdb_title_section_records"

)

References file().

write_seqres_records()

BooleanOptionKey const out::file::write_seqres_records

(

"out:file:write_seqres_records"

)

References file().