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

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Variable Documentation

FileVectorOptionKey const basic::options::OptionKeys::in::file::alignment

Referenced by add_rosetta_options_0(), and main().

FileVectorOptionKey const basic::options::OptionKeys::in::file::alignment2

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::ambig_talos_cs_A

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::ambig_talos_cs_B

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::atom_tree_diff

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::boinc_wu_zip

Referenced by add_rosetta_options_0(), and main().

BooleanOptionKey const basic::options::OptionKeys::in::file::centroid_input

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::checkpoint

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::ddg_predictions_file

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::dssp

Referenced by add_rosetta_options_0(), and AnchorFinderMover::apply().

IntegerOptionKey const basic::options::OptionKeys::in::file::extended_pose

Referenced by add_rosetta_options_0(), and rna_denovo_test().

FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_cen

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_fa

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_mol

Referenced by add_rosetta_options_0().

PathVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_path

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::fail_on_bad_hbond

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::fasta

Referenced by add_rosetta_options_0(), and rna_denovo_test().

BooleanOptionKey const basic::options::OptionKeys::in::file::file

gzipped

plain text

Referenced by add_rosetta_options_0(), MRMover::apply_makefrags(), ca_to_allatom_main(), main(), and basic::options::start_files().

FileOptionKey const basic::options::OptionKeys::in::file::fold_tree

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::frag3

Referenced by add_rosetta_options_0(), and FloppyTailMover::FloppyTailMover().

StringOptionKey const basic::options::OptionKeys::in::file::frag9

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::frag_files

Referenced by add_rosetta_options_0().

IntegerVectorOptionKey const basic::options::OptionKeys::in::file::frag_sizes

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::fragA

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::in::file::fragA_size

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::fragB

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::fullatom

Referenced by add_rosetta_options_0(), and main().

BooleanOptionKey const basic::options::OptionKeys::in::file::keep_input_scores

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::l

Referenced by add_rosetta_options_0(), utility::BitVector< B >::BitVector(), utility::signals::SignalHub< ReturnType, Signal >::current_links(), ObjexxFCL::fmt::F(), utility::file::file_size(), ObjexxFCL::fmt::G(), numeric::interpolation::periodic_range::periodic_value::half::interpolated(), numeric::interpolation::periodic_range::periodic_value::full::interpolated(), numeric::interpolation::periodic_range::half::interpolated(), numeric::interpolation::periodic_range::full::interpolated(), main(), numeric::model_quality::maxsub(), ObjexxFCL::mod(), ObjexxFCL::operator>>(), ObjexxFCL::RemainderSelector< T, true >::remainder(), numeric::RemainderSelector< T, true >::remainder(), utility::options::OptionCollection::show_all_hier(), utility::options::OptionCollection::show_table_text(), basic::options::start_files(), utility::options::OptionCollection::wrapped(), and basic::Emitter::write_raw().

BooleanOptionKey const basic::options::OptionKeys::in::file::lazy_silent

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::lipofile

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::list

Referenced by add_rosetta_options_0(), main(), make_1mer_frags(), make_frags(), and basic::options::start_files().

FileOptionKey const basic::options::OptionKeys::in::file::movemap

Referenced by add_rosetta_options_0(), LigandRepackMinimizeProtocol::apply(), MRMover::apply_relax(), main(), my_main(), SmallMoverBenchmark::setUp(), and ShearMoverBenchmark::setUp().

FileOptionKey const basic::options::OptionKeys::in::file::native

Referenced by add_rosetta_options_0(), main(), and rna_denovo_test().

IntegerVectorOptionKey const basic::options::OptionKeys::in::file::native_exclude_res

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::new_chain_order

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::no_binary_dunlib

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::obey_ENDMDL

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::pca

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::PCS_frag_cst

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::psipred_ss2

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::pssm

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::rama2b_map

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::rdc

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::repair_sidechains

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::rescore

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::residue_type_set

Referenced by add_rosetta_options_0(), UBQ_E2Mover::init_on_new_input(), main(), match_main(), and basic::options::process().

FileVectorOptionKey const basic::options::OptionKeys::in::file::s

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().

StringVectorOptionKey const basic::options::OptionKeys::in::file::seq

Referenced by add_rosetta_options_0(), composite_sequences_from_cmd_line(), main(), and my_main().

FileVectorOptionKey const basic::options::OptionKeys::in::file::silent

Referenced by add_rosetta_options_0(), ca_to_allatom_main(), distribute_jobs(), extract_pdbs_test(), main(), minimize_with_constraints(), and rna_denovo_test().

RealOptionKey const basic::options::OptionKeys::in::file::silent_energy_cut

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::silent_list

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::silent_optH

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::silent_read_through_errors

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::in::file::silent_renumber

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::silent_score_prefix

Referenced by add_rosetta_options_0().

StringVectorOptionKey const basic::options::OptionKeys::in::file::silent_scores_wanted

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::in::file::silent_select_random

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::silent_struct_type

Referenced by add_rosetta_options_0(), and ca_to_allatom_main().

StringOptionKey const basic::options::OptionKeys::in::file::spanfile

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::sucker_params

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::tagfile

Referenced by add_rosetta_options_0().

StringVectorOptionKey const basic::options::OptionKeys::in::file::tags

Referenced by add_rosetta_options_0(), and main().

FileOptionKey const basic::options::OptionKeys::in::file::talos_cs

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::talos_phi_psi

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::template_pdb

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::template_silent

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::in::file::torsion_bin_probs

Referenced by add_rosetta_options_0().

StringVectorOptionKey const basic::options::OptionKeys::in::file::user_tags

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::in::file::vall

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::in::file::xyz

Referenced by add_rosetta_options_0(), main(), and numeric::spherical_to_xyz().

StringOptionKey const basic::options::OptionKeys::in::file::zip

Referenced by add_rosetta_options_0(), and main().