Rosetta Utilities  2014.35
Functions | Variables
basic::options::OptionKeys::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")
 
FileVectorOptionKey const list ("in:file:list")
 
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")
 
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")
 
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 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")
 
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")
 
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")
 
BooleanOptionKey const read_pdb_link_records ("in:file:read_pdb_link_records")
 
FileOptionKey const native_contacts ("in:file:native_contacts")
 

Variables

BooleanOptionKey const file
 
FileVectorOptionKey const s
 
FileVectorOptionKey const t
 
FileVectorOptionKey const l
 
FileVectorOptionKey const list
 
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
 
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
 
FileVectorOptionKey const extra_res_mol
 
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 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
 
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
 
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
 
BooleanOptionKey const read_pdb_link_records
 
FileOptionKey const native_contacts
 

Function Documentation

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

Variable Documentation

FileVectorOptionKey const basic::options::OptionKeys::in::file::alignment("in:file:alignment")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::alignment2("in:file:alignment2")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::ambig_talos_cs_A("in:file:ambig_talos_cs_A")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::ambig_talos_cs_B("in:file:ambig_talos_cs_B")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::atom_tree_diff("in:file:atom_tree_diff")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::binary_chk("in:file:binary_chk")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::boinc_wu_zip("in:file:boinc_wu_zip")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::burial("in:file:burial")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::centroid("in:file:centroid")
BooleanOptionKey const basic::options::OptionKeys::in::file::centroid_input("in:file:centroid_input")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::checkpoint("in:file:checkpoint")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::csa("in:file:csa")

Referenced by add_rosetta_options_0().

RealOptionKey const basic::options::OptionKeys::in::file::d2h_sa_reweight("in:file:d2h_sa_reweight")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::dc("in:file:dc")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::ddg_predictions_file("in:file:ddg_predictions_file")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::dssp("in:file:dssp")

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::in::file::extended_pose("in:file:extended_pose")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_patch_cen("in:file:extra_patch_cen")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_patch_fa("in:file:extra_patch_fa")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res("in:file:extra_res")

Referenced by add_rosetta_options_0().

PathVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_batch_path("in:file:extra_res_batch_path")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_cen("in:file:extra_res_cen")

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::extra_res_database("in:file:extra_res_database")

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::extra_res_database_mode("in:file:extra_res_database_mode")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::extra_res_database_resname_list("in:file:extra_res_database_resname_list")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_fa("in:file:extra_res_fa")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_mol("in:file:extra_res_mol")

Referenced by add_rosetta_options_0().

PathVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_path("in:file:extra_res_path")

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::extra_res_pq_schema("in:file:extra_res_pq_schema")

Referenced by add_rosetta_options_0().

PathVectorOptionKey const basic::options::OptionKeys::in::file::extra_rot_lib_path("in:file:extra_rot_lib_path")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::fail_on_bad_hbond("in:file:fail_on_bad_hbond")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::fasta("in:file:fasta")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::file("in:file")
FileOptionKey const basic::options::OptionKeys::in::file::fold_tree("in:file:fold_tree")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::force_silent_bitflip_on_read("in:file:force_silent_bitflip_on_read")

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::frag3("in:file:frag3")

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::frag9("in:file:frag9")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::frag_files("in:file:frag_files")

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::fragA("in:file:fragA")

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::fragB("in:file:fragB")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::fullatom("in:file:fullatom")

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::HDX("in:file:HDX")

Referenced by add_rosetta_options_0().

ResidueChainVectorOptionKey const basic::options::OptionKeys::in::file::input_res("in:file:input_res")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::keep_input_scores("in:file:keep_input_scores")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::l("in:file:l")
BooleanOptionKey const basic::options::OptionKeys::in::file::lazy_silent("in:file:lazy_silent")

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::lipofile("in:file:lipofile")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::list("in:file:list")
StringOptionKey const basic::options::OptionKeys::in::file::md_schfile("in:file:md_schfile")

Referenced by add_rosetta_options_0().

IntegerVectorOptionKey const basic::options::OptionKeys::in::file::minimize_res("in:file:minimize_res")
FileOptionKey const basic::options::OptionKeys::in::file::movemap("in:file:movemap")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::native("in:file:native")
FileOptionKey const basic::options::OptionKeys::in::file::native_contacts("in:file:native_contacts")

Referenced by add_rosetta_options_0().

IntegerVectorOptionKey const basic::options::OptionKeys::in::file::native_exclude_res("in:file:native_exclude_res")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::new_chain_order("in:file:new_chain_order")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::no_binary_dunlib("in:file:no_binary_dunlib")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::obey_ENDMDL("in:file:obey_ENDMDL")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::pca("in:file:pca")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::PCS_frag_cst("in:file:PCS_frag_cst")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::psipred_ss2("in:file:psipred_ss2")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::pssm("in:file:pssm")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::rama2b_map("in:file:rama2b_map")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::rdc("in:file:rdc")
BooleanOptionKey const basic::options::OptionKeys::in::file::read_pdb_link_records("in:file:read_pdb_link_records")

Referenced by add_rosetta_options_0().

StringVectorOptionKey const basic::options::OptionKeys::in::file::remap_pdb_atom_names_for("in:file:remap_pdb_atom_names_for")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::repair_sidechains("in:file:repair_sidechains")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::rescore("in:file:rescore")

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::residue_type_set("in:file:residue_type_set")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::s("in:file:s")

Referenced by add_rosetta_options_0(), basic::Tracer::calculate_tracer_level(), utility::options::VectorOption_T_< BooleanVectorOptionKey, bool >::can_hold_another(), numeric::kinematic_closure::chainXYZ(), numeric::kinematic_closure::radians::chainXYZ(), utility::query::Filter_And< T >::description(), utility::query::Filter_Or< T >::description(), utility::query::Filter_Not< T >::description(), utility::query::Metric_Neg< T >::description(), utility::down_cast(), basic::Emitter::escape_string(), fastsin(), utility::sql_database::DatabaseSessionManager::get_session_mysql(), utility::sql_database::DatabaseSessionManager::get_session_postgres(), utility::sql_database::DatabaseSessionManager::get_session_sqlite3(), basic::Tracer::in(), numeric::jacobi(), numeric::jacobi_rotation(), utility::options::ScalarOption_T_< PathOptionKey, file::PathName >::legal_string(), utility::options::VectorOption_T_< BooleanVectorOptionKey, bool >::legal_string(), numeric::kinematic_closure::numchanges(), numeric::kinematic_closure::numroots(), utility::options::operator+(), utility::operator+(), utility::operator-(), utility::operator|(), utility::options::OptionCollection::prefix(), basic::Tracer::prepend_channel_name(), basic::database::schema_generator::Index::print(), numeric::BodyPosition< typename >::q_refresh(), numeric::linear_algebra::qzhes(), numeric::linear_algebra::qzit(), numeric::linear_algebra::qzval(), numeric::linear_algebra::qzvec(), numeric::remainder_conversion(), utility::signals::SignalHub< ReturnType, Signal >::send(), basic::Emitter::set_indent(), utility::options::ScalarOption_T_< PathOptionKey, file::PathName >::shortd(), utility::options::VectorOption_T_< BooleanVectorOptionKey, bool >::shortd(), solve_c_svc(), solve_epsilon_svr(), solve_nu_svc(), solve_nu_svr(), solve_one_class(), utility::keys::ClassKeyVector< K, T, C >::sort(), utility::options::OptionCollection::space_prefixed(), basic::options::start_files(), utility::options::OptionCollection::suffix(), basic::svd::SVD_Solver::svbksb(), basic::svd::SVD_Solver::svdcmp(), basic::TracerToFile::t_flush(), basic::ComparingTracer::t_flush(), basic::Tracer::TracerProxy::t_flush(), utility::options::OptionCollection::tab_prefixed(), numeric::kinematic_closure::torsion(), numeric::kinematic_closure::radians::torsion(), utility::options::OptionCollection::trim(), utility::options::OptionCollection::trimmed(), and utility::options::OptionCollection::wrapped().

FileOptionKey const basic::options::OptionKeys::in::file::screening_job_file("in:file:screening_job_file")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::screening_list("in:file:screening_list")
StringVectorOptionKey const basic::options::OptionKeys::in::file::seq("in:file:seq")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::shuffle_screening_jobs("in:file:shuffle_screening_jobs")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::silent("in:file:silent")

Referenced by add_rosetta_options_0().

RealOptionKey const basic::options::OptionKeys::in::file::silent_energy_cut("in:file:silent_energy_cut")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::silent_list("in:file:silent_list")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::silent_read_through_errors("in:file:silent_read_through_errors")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::silent_renumber("in:file:silent_renumber")

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::silent_score_prefix("in:file:silent_score_prefix")

Referenced by add_rosetta_options_0().

StringVectorOptionKey const basic::options::OptionKeys::in::file::silent_scores_wanted("in:file:silent_scores_wanted")

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::in::file::silent_select_random("in:file:silent_select_random")

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::in::file::silent_select_range_len("in:file:silent_select_range_len")

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::in::file::silent_select_range_mul("in:file:silent_select_range_mul")

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::in::file::silent_select_range_start("in:file:silent_select_range_start")

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::silent_struct_type("in:file:silent_struct_type")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::skip_failed_simulations("in:file:skip_failed_simulations")

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::spanfile("in:file:spanfile")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::sucker_params("in:file:sucker_params")

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::surface_vectors("in:file:surface_vectors")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::t("in:file:t")

Referenced by add_rosetta_options_0(), utility::options::OptionCollection::cleaned(), numeric::model_quality::erfcc(), numeric::statistics::erfcx_y100(), basic::sampling::orientations::Quaternion::euler(), utility::from_string(), numeric::hsv_to_rgb(), numeric::jacobi(), numeric::jacobi_rotation(), numeric::fourier::kf_bfly2(), numeric::fourier::kf_bfly_generic(), numeric::model_quality::maxsub(), utility::options::OptionCollection::merged(), multiclass_probability(), basic::sampling::orientations::Quaternion::Normalize(), utility::json_spirit::Value_impl< Config >::Variant_converter_visitor::operator()(), numeric::sphericalVector< typename >::operator*=(), numeric::xyzTriple< typename >::operator*=(), numeric::xyzVector< T >::operator*=(), numeric::xyzMatrix< T >::operator*=(), numeric::sphericalVector< typename >::operator+=(), numeric::xyzTriple< typename >::operator+=(), numeric::xyzVector< T >::operator+=(), numeric::xyzMatrix< T >::operator+=(), numeric::sphericalVector< typename >::operator-=(), numeric::xyzTriple< typename >::operator-=(), numeric::xyzVector< T >::operator-=(), numeric::xyzMatrix< T >::operator-=(), numeric::operator<<(), utility::io::ocstream::operator<<(), utility::io::orstream::operator<<(), utility::io::ozstream::operator<<(), utility::io::mpi_stream::basic_mpi_ostream< Elem, Tr, ElemA, ByteT, ByteAT >::operator<<(), numeric::sphericalVector< typename >::operator=(), numeric::xyzTriple< typename >::operator=(), numeric::xyzVector< T >::operator=(), numeric::xyzMatrix< T >::operator=(), numeric::operator>>(), utility::io::icstream::operator>>(), utility::io::irstream::operator>>(), utility::io::izstream::operator>>(), powi(), basic::prof_show(), basic::sampling::orientations::QuaternionGrid::QuaternionGrid(), basic::YamlEmitter::quote_string(), basic::JsonEmitter::quote_string(), numeric::linear_algebra::qzhes(), numeric::linear_algebra::qzit(), numeric::linear_algebra::qzval(), numeric::linear_algebra::qzvec(), numeric::read_row(), numeric::model_quality::rmsfitca2(), numeric::model_quality::rmsfitca3(), Solver::select_working_set(), Solver_NU::select_working_set(), sigmoid_train(), numeric::xyzTriple< typename >::square(), numeric::xyzVector< T >::square(), utility::string_split(), swap(), numeric::Quaternion< T >::swap(), basic::T(), numeric::kinematic_closure::test_point_value2(), basic::gpu::Timer::Timer(), utility::lua::LuaObject::to(), utility::to_string(), numeric::geometry::BoundingBox< Vector >::translate(), and numeric::statistics::w_im_y100().

FileOptionKey const basic::options::OptionKeys::in::file::tagfile("in:file:tagfile")

Referenced by add_rosetta_options_0().

StringVectorOptionKey const basic::options::OptionKeys::in::file::tags("in:file:tags")
FileOptionKey const basic::options::OptionKeys::in::file::talos_cs("in:file:talos_cs")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::talos_phi_psi("in:file:talos_phi_psi")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::template_pdb("in:file:template_pdb")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::template_silent("in:file:template_silent")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::torsion_bin_probs("in:file:torsion_bin_probs")

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::treat_residues_in_these_chains_as_separate_chemical_entities("in:file:treat_residues_in_these_chains_as_separate_chemical_entities")

Referenced by add_rosetta_options_0().

StringVectorOptionKey const basic::options::OptionKeys::in::file::user_tags("in:file:user_tags")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::vall("in:file:vall")

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::xyz("in:file:xyz")
StringOptionKey const basic::options::OptionKeys::in::file::zip("in:file:zip")

Referenced by add_rosetta_options_0().