Rosetta 3.3
Variables
basic::options::OptionKeys::in::file Namespace Reference

Variables

BooleanOptionKey const file
 gzipped
FileVectorOptionKey const s
FileVectorOptionKey const l
FileVectorOptionKey const list
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
IntegerVectorOptionKey const frag_sizes
FileVectorOptionKey const extra_res_fa
FileVectorOptionKey const extra_res_mol
FileVectorOptionKey const extra_res_cen
PathVectorOptionKey const extra_res_path
StringOptionKey const frag3
StringOptionKey const frag9
StringOptionKey const fragA
StringOptionKey const fragB
StringOptionKey const xyz
IntegerOptionKey const fragA_size
BooleanOptionKey const keep_input_scores
BooleanOptionKey const lazy_silent
FileVectorOptionKey const silent
FileVectorOptionKey const atom_tree_diff
StringOptionKey const zip
FileVectorOptionKey const boinc_wu_zip
BooleanOptionKey const fullatom
StringOptionKey const residue_type_set
FileOptionKey const pca
RealOptionKey const silent_energy_cut
FileVectorOptionKey const silent_list
BooleanOptionKey const silent_renumber
BooleanOptionKey const silent_optH
StringOptionKey const silent_struct_type
BooleanOptionKey const silent_read_through_errors
StringOptionKey const silent_score_prefix
IntegerOptionKey const silent_select_random
StringVectorOptionKey const silent_scores_wanted
BooleanOptionKey const centroid_input
FileVectorOptionKey const fasta
FileVectorOptionKey const pssm
StringVectorOptionKey const seq
FileOptionKey const checkpoint
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 vall
BooleanOptionKey const rescore
StringOptionKey const spanfile
StringOptionKey const lipofile
FileOptionKey const sucker_params
FileOptionKey const fold_tree
BooleanOptionKey const obey_ENDMDL
BooleanOptionKey const new_chain_order
FileOptionKey const ddg_predictions_file

Variable Documentation

Referenced by add_rosetta_options_0(), and main().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0(), and main().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0(), and main().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by ObjexxFCL::fmt::A(), add_rosetta_options_0(), utility::options::VectorOption_T_< BooleanVectorOptionKey, bool >::can_hold_another(), ObjexxFCL::center(), ObjexxFCL::centered(), ObjexxFCL::char_of(), create_bp_jump_database_test(), create_rna_vall_torsions_test(), ObjexxFCL::date(), utility::query::Metric_Neg< T >::description(), utility::query::Filter_Not< T >::description(), utility::query::Filter_Or< T >::description(), utility::query::Filter_And< T >::description(), ObjexxFCL::double_of(), utility::down_cast(), ObjexxFCL::equali(), basic::Emitter::escape_string(), ObjexxFCL::float_of(), ObjexxFCL::get(), utility::sql_database::DatabaseSessionManager::get_session(), ObjexxFCL::head(), ObjexxFCL::IACHAR(), ObjexxFCL::ICHAR(), ObjexxFCL::int_of(), ObjexxFCL::is_bool(), ObjexxFCL::is_char(), ObjexxFCL::is_double(), ObjexxFCL::is_float(), ObjexxFCL::is_int(), ObjexxFCL::is_long(), ObjexxFCL::is_longdouble(), ObjexxFCL::is_short(), ObjexxFCL::is_type< char >(), ObjexxFCL::is_uint(), ObjexxFCL::is_ulong(), ObjexxFCL::is_ushort(), numeric::jacobi(), numeric::jacobi_rotation(), ObjexxFCL::left_justified(), ObjexxFCL::left_justify(), utility::options::VectorOption_T_< BooleanVectorOptionKey, bool >::legal_string(), utility::options::ScalarOption_T_< PathOptionKey, file::PathName >::legal_string(), ObjexxFCL::long_of(), ObjexxFCL::longdouble_of(), ObjexxFCL::lowercase(), ObjexxFCL::lpad(), ObjexxFCL::lpadded(), ObjexxFCL::lstrip(), ObjexxFCL::lstrip_whitespace(), ObjexxFCL::lstripped(), ObjexxFCL::lstripped_whitespace(), main(), minimize_with_constraints(), utility::options::operator+(), utility::operator+(), utility::operator-(), ObjexxFCL::operator==(), ObjexxFCL::operator>>(), utility::operator|(), ObjexxFCL::overlay(), ObjexxFCL::pad(), ObjexxFCL::padded(), utility::options::OptionCollection::prefix(), reduce_fa_rep(), ObjexxFCL::remainder_conversion(), numeric::remainder_conversion(), ObjexxFCL::right_justified(), ObjexxFCL::right_justify(), rna_denovo_test(), rna_design_test(), ObjexxFCL::rpad(), ObjexxFCL::rpadded(), ObjexxFCL::rstrip(), ObjexxFCL::rstrip_whitespace(), ObjexxFCL::rstripped(), ObjexxFCL::rstripped_whitespace(), utility::signals::SignalHub< ReturnType, Signal >::send(), sequence_tolerance_main(), basic::Emitter::set_indent(), LigandDockBenchmark::setUp(), ObjexxFCL::short_of(), utility::options::VectorOption_T_< BooleanVectorOptionKey, bool >::shortd(), utility::options::ScalarOption_T_< PathOptionKey, file::PathName >::shortd(), ObjexxFCL::size(), ObjexxFCL::sized(), utility::keys::ClassKeyVector< K, T, C >::sort(), utility::options::OptionCollection::space_prefixed(), ss_ds_ts_assign_test(), basic::options::start_files(), store_energies(), ObjexxFCL::strip(), ObjexxFCL::strip_whitespace(), ObjexxFCL::stripped(), ObjexxFCL::stripped_whitespace(), utility::options::OptionCollection::suffix(), ObjexxFCL::fmt::SW(), basic::TracerToFile::t_flush(), basic::Tracer::TracerProxy::t_flush(), basic::ComparingTracer::t_flush(), utility::options::OptionCollection::tab_prefixed(), utility::options::OptionCollection::trim(), ObjexxFCL::trim(), ObjexxFCL::trim_whitespace(), utility::options::OptionCollection::trimmed(), ObjexxFCL::trimmed(), ObjexxFCL::trimmed_whitespace(), ObjexxFCL::type_of< char >(), ObjexxFCL::type_of< std::string >(), ObjexxFCL::uint_of(), ObjexxFCL::ulong_of(), ObjexxFCL::unique(), ObjexxFCL::uppercase(), ObjexxFCL::ushort_of(), vector1_str(), and utility::options::OptionCollection::wrapped().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0(), and main().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0().

Referenced by add_rosetta_options_0(), and main().

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