Rosetta  2019.47
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Functions
in::file Namespace Reference

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")
 
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

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

Referenced by main().

FileVectorOptionKey const in::file::alignment2 ( "in:file:alignment2"  )
FileOptionKey const in::file::ambig_talos_cs_A ( "in:file:ambig_talos_cs_A"  )
FileOptionKey const in::file::ambig_talos_cs_B ( "in:file:ambig_talos_cs_B"  )
BooleanOptionKey const in::file::assign_gasteiger_atom_types ( "in:file:assign_gasteiger_atom_types"  )
FileVectorOptionKey const in::file::atom_tree_diff ( "in:file:atom_tree_diff"  )
FileOptionKey const in::file::binary_chk ( "in:file:binary_chk"  )
FileVectorOptionKey const in::file::boinc_wu_zip ( "in:file:boinc_wu_zip"  )
FileVectorOptionKey const in::file::burial ( "in:file:burial"  )
BooleanOptionKey const in::file::centroid ( "in:file:centroid"  )

Referenced by main().

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

Referenced by main().

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

Referenced by register_options().

FileVectorOptionKey const in::file::csa ( "in:file:csa"  )
RealOptionKey const in::file::d2h_sa_reweight ( "in:file:d2h_sa_reweight"  )
FileVectorOptionKey const in::file::dc ( "in:file:dc"  )
FileOptionKey const in::file::ddg_predictions_file ( "in:file:ddg_predictions_file"  )
FileOptionKey const in::file::dssp ( "in:file:dssp"  )
IntegerOptionKey const in::file::extended_pose ( "in:file:extended_pose"  )
FileVectorOptionKey const in::file::extra_patch_cen ( "in:file:extra_patch_cen"  )
FileVectorOptionKey const in::file::extra_patch_fa ( "in:file:extra_patch_fa"  )
FileVectorOptionKey const in::file::extra_res ( "in:file:extra_res"  )

Referenced by main().

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

Referenced by main().

StringOptionKey const in::file::extra_res_database ( "in:file:extra_res_database"  )
StringOptionKey const in::file::extra_res_database_mode ( "in:file:extra_res_database_mode"  )
FileOptionKey const in::file::extra_res_database_resname_list ( "in:file:extra_res_database_resname_list"  )
FileVectorOptionKey const in::file::extra_res_fa ( "in:file:extra_res_fa"  )

Referenced by main().

FileVectorOptionKey const in::file::extra_res_mmCIF ( "in:file:extra_res_mmCIF"  )
FileVectorOptionKey const in::file::extra_res_mol ( "in:file:extra_res_mol"  )
PathVectorOptionKey const in::file::extra_res_path ( "in:file:extra_res_path"  )
StringOptionKey const in::file::extra_res_pq_schema ( "in:file:extra_res_pq_schema"  )
PathVectorOptionKey const in::file::extra_rot_lib_path ( "in:file:extra_rot_lib_path"  )
BooleanOptionKey const in::file::fail_on_bad_hbond ( "in:file:fail_on_bad_hbond"  )
FileVectorOptionKey const in::file::fasta ( "in:file:fasta"  )
BooleanOptionKey const in::file::file ( "in:file"  )
FileOptionKey const in::file::fold_tree ( "in:file:fold_tree"  )

Referenced by do_erraser2().

BooleanOptionKey const in::file::force_silent_bitflip_on_read ( "in:file:force_silent_bitflip_on_read"  )
StringOptionKey const in::file::frag3 ( "in:file:frag3"  )
StringOptionKey const in::file::frag9 ( "in:file:frag9"  )
FileVectorOptionKey const in::file::frag_files ( "in:file:frag_files"  )
StringOptionKey const in::file::fragA ( "in:file:fragA"  )
StringOptionKey const in::file::fragB ( "in:file:fragB"  )
BooleanOptionKey const in::file::fullatom ( "in:file:fullatom"  )
StringOptionKey const in::file::HDX ( "in:file:HDX"  )
FileOptionKey const in::file::hrf_ms_labeling ( "in:file:hrf_ms_labeling"  )
ResidueChainVectorOptionKey const in::file::input_res ( "in:file:input_res"  )

Referenced by main(), and mg_modeler_test().

FileOptionKey const in::file::job_definition_file ( "in:file:job_definition_file"  )
BooleanOptionKey const in::file::keep_input_scores ( "in:file:keep_input_scores"  )
FileVectorOptionKey const in::file::l ( "in:file:l"  )

Referenced by main(), and rhiju_pdbstats().

BooleanOptionKey const in::file::lazy_silent ( "in:file:lazy_silent"  )
StringOptionKey const in::file::lipofile ( "in:file:lipofile"  )
FileVectorOptionKey const in::file::list ( "in:file:list"  )
BooleanOptionKey const in::file::load_PDB_components ( "in:file:load_PDB_components"  )
StringOptionKey const in::file::md_schfile ( "in:file:md_schfile"  )
IntegerVectorOptionKey const in::file::minimize_res ( "in:file:minimize_res"  )
FileOptionKey const in::file::movemap ( "in:file:movemap"  )

Referenced by main().

FileOptionKey const in::file::native ( "in:file:native"  )
FileOptionKey const in::file::native_contacts ( "in:file:native_contacts"  )
IntegerVectorOptionKey const in::file::native_exclude_res ( "in:file:native_exclude_res"  )
BooleanOptionKey const in::file::new_chain_order ( "in:file:new_chain_order"  )
BooleanOptionKey const in::file::no_binary_dunlib ( "in:file:no_binary_dunlib"  )
BooleanOptionKey const in::file::no_detect_pseudobonds ( "in:file:no_detect_pseudobonds"  )
BooleanOptionKey const in::file::obey_ENDMDL ( "in:file:obey_ENDMDL"  )
PathVectorOptionKey const in::file::override_rot_lib_path ( "in:file:override_rot_lib_path"  )
FileOptionKey const in::file::pca ( "in:file:pca"  )
FileOptionKey const in::file::PCS_frag_cst ( "in:file:PCS_frag_cst"  )
StringOptionKey const in::file::PDB_components_directory ( "in:file:PDB_components_directory"  )
StringVectorOptionKey const in::file::PDB_components_overrides ( "in:file:PDB_components_overrides"  )
FileOptionKey const in::file::psipred_ss2 ( "in:file:psipred_ss2"  )
FileVectorOptionKey const in::file::pssm ( "in:file:pssm"  )

Referenced by main(), and register_options().

FileOptionKey const in::file::rama2b_map ( "in:file:rama2b_map"  )
FileVectorOptionKey const in::file::rdc ( "in:file:rdc"  )
StringVectorOptionKey const in::file::remap_pdb_atom_names_for ( "in:file:remap_pdb_atom_names_for"  )
BooleanOptionKey const in::file::repair_sidechains ( "in:file:repair_sidechains"  )

Referenced by main().

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

Referenced by main().

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

Referenced by main().

FileVectorOptionKey const in::file::s ( "in:file:s"  )
FileOptionKey const in::file::screening_job_file ( "in:file:screening_job_file"  )
FileVectorOptionKey const in::file::screening_list ( "in:file:screening_list"  )
StringVectorOptionKey const in::file::seq ( "in:file:seq"  )
BooleanOptionKey const in::file::shuffle_screening_jobs ( "in:file:shuffle_screening_jobs"  )
FileVectorOptionKey const in::file::silent ( "in:file:silent"  )
RealOptionKey const in::file::silent_energy_cut ( "in:file:silent_energy_cut"  )
FileVectorOptionKey const in::file::silent_list ( "in:file:silent_list"  )
BooleanOptionKey const in::file::silent_read_through_errors ( "in:file:silent_read_through_errors"  )

Referenced by main().

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

Referenced by main().

StringOptionKey const in::file::silent_score_prefix ( "in:file:silent_score_prefix"  )
StringVectorOptionKey const in::file::silent_scores_wanted ( "in:file:silent_scores_wanted"  )
IntegerOptionKey const in::file::silent_select_random ( "in:file:silent_select_random"  )
IntegerOptionKey const in::file::silent_select_range_len ( "in:file:silent_select_range_len"  )
IntegerOptionKey const in::file::silent_select_range_mul ( "in:file:silent_select_range_mul"  )
IntegerOptionKey const in::file::silent_select_range_start ( "in:file:silent_select_range_start"  )
StringOptionKey const in::file::silent_struct_type ( "in:file:silent_struct_type"  )

Referenced by main().

BooleanOptionKey const in::file::skip_failed_simulations ( "in:file:skip_failed_simulations"  )
StringOptionKey const in::file::spanfile ( "in:file:spanfile"  )
BooleanOptionKey const in::file::srlz ( "in:file:srlz"  )
BooleanOptionKey const in::file::srlz_override ( "in:file:srlz_override"  )
FileOptionKey const in::file::sucker_params ( "in:file:sucker_params"  )
StringOptionKey const in::file::surface_vectors ( "in:file:surface_vectors"  )
FileVectorOptionKey const in::file::t ( "in:file:t"  )
FileOptionKey const in::file::tagfile ( "in:file:tagfile"  )

Referenced by main().

StringVectorOptionKey const in::file::tags ( "in:file:tags"  )
FileOptionKey const in::file::talos_cs ( "in:file:talos_cs"  )
FileOptionKey const in::file::talos_phi_psi ( "in:file:talos_phi_psi"  )

Referenced by register_options().

FileVectorOptionKey const in::file::template_pdb ( "in:file:template_pdb"  )
FileOptionKey const in::file::template_silent ( "in:file:template_silent"  )
FileOptionKey const in::file::torsion_bin_probs ( "in:file:torsion_bin_probs"  )

Referenced by register_options().

StringOptionKey const in::file::treat_residues_in_these_chains_as_separate_chemical_entities ( "in:file:treat_residues_in_these_chains_as_separate_chemical_entities"  )
StringVectorOptionKey const in::file::user_tags ( "in:file:user_tags"  )
FileVectorOptionKey const in::file::vall ( "in:file:vall"  )
StringOptionKey const in::file::xyz ( "in:file:xyz"  )

Referenced by register_options().

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