basic::options::OptionKeys::rna::denovo Namespace Reference

Namespaces
	db
	minimize
	out

Variables
BooleanOptionKey const	denovo
IntegerOptionKey const	cycles
RealOptionKey const	rna_protein_docking_freq
IntegerOptionKey const	rounds
RealOptionKey const	temperature
BooleanOptionKey const	minimize_rna
StringVectorOptionKey const	sequence
StringOptionKey const	secstruct
StringOptionKey const	secstruct_general
StringOptionKey const	secstruct_file
StringOptionKey const	secstruct_general_file
StringOptionKey const	secstruct_legacy
StringOptionKey const	lores_scorefxn
StringVectorOptionKey const	set_lores_weights
IntegerOptionKey const	symm_hack_arity
IntegerOptionKey const	exhaustive_fragment_insertion
BooleanOptionKey const	filter_lores_base_pairs
BooleanOptionKey const	filter_lores_base_pairs_early
BooleanOptionKey const	filter_chain_closure
BooleanOptionKey const	filter_chain_closure_halfway
RealOptionKey const	filter_chain_closure_distance
BooleanOptionKey const	relax_rna
BooleanOptionKey const	simple_relax
BooleanOptionKey const	ignore_secstruct
RealOptionKey const	jump_change_frequency
BooleanOptionKey const	close_loops
BooleanOptionKey const	close_loops_after_each_move
BooleanOptionKey const	heat
BooleanOptionKey const	staged_constraints
StringOptionKey const	jump_library_file
StringOptionKey const	vall_torsions
BooleanOptionKey const	use_1jj2_torsions
RealOptionKey const	fuzz_fragments
RealOptionKey const	rna_lores_chainbreak_weight
RealOptionKey const	rna_lores_linear_chainbreak_weight
BooleanOptionKey const	fixed_stems
BooleanOptionKey const	allow_bulge
IntegerVectorOptionKey const	allowed_bulge_res
BooleanOptionKey const	allow_consecutive_bulges
BooleanOptionKey const	move_first_rigid_body
BooleanOptionKey const	root_at_first_rigid_body
BooleanOptionKey const	dock_each_chunk
BooleanOptionKey const	dock_each_chunk_per_chain
FileVectorOptionKey const	dock_chunks
BooleanOptionKey const	center_jumps_in_single_stranded
FileVectorOptionKey const	initial_structures
BooleanOptionKey const	ft_close_chains
FileVectorOptionKey const	helical_substructs
RealOptionKey const	suppress_bp_constraint
BooleanOptionKey const	output_filters
BooleanOptionKey const	autofilter
BooleanOptionKey const	no_filters
ResidueChainVectorOptionKey const	output_res_num
IntegerOptionKey const	offset
ResidueChainVectorOptionKey const	input_silent_res
ResidueChainVectorOptionKey const	virtual_anchor
ResidueChainVectorOptionKey const	obligate_pair
StringVectorOptionKey const	obligate_pair_explicit
StringVectorOptionKey const	chain_connection
ResidueChainVectorOptionKey const	remove_pair
ResidueChainVectorOptionKey const	remove_obligate_pair
StringOptionKey const	refine_silent_file
StringVectorOptionKey const	refine_silent_tags
IntegerOptionKey const	refine_silent_number_of_poses
StringOptionKey const	get_fold_tree_from_silent_file
StringVectorOptionKey const	fold_tree_from_silent_file_tag
BooleanOptionKey const	refine_native_get_good_FT
BooleanOptionKey const	refine_native
BooleanOptionKey const	override_refine_pose_rounds
BooleanOptionKey const	bps_moves
BooleanOptionKey const	disallow_bps_at_extra_min_res
BooleanOptionKey const	allow_fragment_moves_in_bps
IntegerOptionKey const	frag_size
BooleanOptionKey const	VDW_rep_screen_include_sidechains
BooleanOptionKey const	gradual_constraints
BooleanOptionKey const	ramp_rnp_vdw
RealOptionKey const	grid_vdw_weight
StringOptionKey const	tag
StringOptionKey const	working_native
BooleanOptionKey const	use_legacy_setup
BooleanOptionKey const	cst_gap
BooleanOptionKey const	convert_protein_CEN
BooleanOptionKey const	rna_protein_docking
BooleanOptionKey const	small_docking_moves
RealOptionKey const	docking_move_size
BooleanOptionKey const	rna_protein_docking_legacy
BooleanOptionKey const	rnp_high_res_relax
IntegerOptionKey const	rnp_high_res_cycles
BooleanOptionKey const	rnp_pack_first
BooleanOptionKey const	rnp_min_first
BooleanOptionKey const	rnp_ramp_rep
BooleanOptionKey const	new_fold_tree_initializer
BooleanOptionKey const	randomize_init_rnp
BooleanOptionKey const	dock_into_density
BooleanOptionKey const	dock_into_density_legacy
IntegerVectorOptionKey const	exclude_fragments
StringOptionKey const	exclusion_match_type
RealOptionKey const	fragment_homology_rmsd
BooleanOptionKey const	exclude_native_fragments
StringVectorOptionKey const	exclude_fragment_files
BooleanOptionKey const	dump_stems

Variable Documentation

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::allow_bulge

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::allow_consecutive_bulges

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::allow_fragment_moves_in_bps

Referenced by add_rosetta_options_13().

IntegerVectorOptionKey const basic::options::OptionKeys::rna::denovo::allowed_bulge_res

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::autofilter

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::bps_moves

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::center_jumps_in_single_stranded

Referenced by add_rosetta_options_13().

StringVectorOptionKey const basic::options::OptionKeys::rna::denovo::chain_connection

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::close_loops

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::close_loops_after_each_move

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::convert_protein_CEN

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::cst_gap

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::rna::denovo::cycles

Referenced by add_rosetta_options_12().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::denovo

Referenced by add_rosetta_options_12(), align_pdbs(), calculate_pairwise_RMSD(), create_base_pair_step_database_test(), create_bp_jump_database_test(), get_pose_and_numbering(), graft_pdb(), mutate_residues_wrapper(), my_main(), prepare_threaded_model(), rna_denovo_legacy(), rna_design_test(), rna_features_from_pose(), rna_fullatom_minimize_test(), and rna_suitename().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::disallow_bps_at_extra_min_res

Referenced by add_rosetta_options_13().

FileVectorOptionKey const basic::options::OptionKeys::rna::denovo::dock_chunks

Referenced by add_rosetta_options_13(), and rna_denovo().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::dock_each_chunk

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::dock_each_chunk_per_chain

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::dock_into_density

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::dock_into_density_legacy

Referenced by add_rosetta_options_13().

RealOptionKey const basic::options::OptionKeys::rna::denovo::docking_move_size

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::dump_stems

Referenced by add_rosetta_options_13().

StringVectorOptionKey const basic::options::OptionKeys::rna::denovo::exclude_fragment_files

Referenced by add_rosetta_options_13().

IntegerVectorOptionKey const basic::options::OptionKeys::rna::denovo::exclude_fragments

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::exclude_native_fragments

Referenced by add_rosetta_options_13().

StringOptionKey const basic::options::OptionKeys::rna::denovo::exclusion_match_type

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::rna::denovo::exhaustive_fragment_insertion

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::filter_chain_closure

Referenced by add_rosetta_options_13().

RealOptionKey const basic::options::OptionKeys::rna::denovo::filter_chain_closure_distance

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::filter_chain_closure_halfway

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::filter_lores_base_pairs

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::filter_lores_base_pairs_early

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::fixed_stems

Referenced by add_rosetta_options_13().

StringVectorOptionKey const basic::options::OptionKeys::rna::denovo::fold_tree_from_silent_file_tag

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::rna::denovo::frag_size

Referenced by add_rosetta_options_13(), and main().

RealOptionKey const basic::options::OptionKeys::rna::denovo::fragment_homology_rmsd

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::ft_close_chains

Referenced by add_rosetta_options_13().

RealOptionKey const basic::options::OptionKeys::rna::denovo::fuzz_fragments

Referenced by add_rosetta_options_13().

StringOptionKey const basic::options::OptionKeys::rna::denovo::get_fold_tree_from_silent_file

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::gradual_constraints

Referenced by add_rosetta_options_13().

RealOptionKey const basic::options::OptionKeys::rna::denovo::grid_vdw_weight

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::heat

Referenced by add_rosetta_options_13().

FileVectorOptionKey const basic::options::OptionKeys::rna::denovo::helical_substructs

Referenced by add_rosetta_options_13(), and rna_denovo().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::ignore_secstruct

Referenced by add_rosetta_options_13().

FileVectorOptionKey const basic::options::OptionKeys::rna::denovo::initial_structures

Referenced by add_rosetta_options_13(), and rna_denovo().

ResidueChainVectorOptionKey const basic::options::OptionKeys::rna::denovo::input_silent_res

Referenced by add_rosetta_options_13().

RealOptionKey const basic::options::OptionKeys::rna::denovo::jump_change_frequency

Referenced by add_rosetta_options_13().

StringOptionKey const basic::options::OptionKeys::rna::denovo::jump_library_file

Referenced by add_rosetta_options_13().

StringOptionKey const basic::options::OptionKeys::rna::denovo::lores_scorefxn

Referenced by add_rosetta_options_13(), and create_bp_jump_database_test().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::minimize_rna

Referenced by add_rosetta_options_12(), get_stepwise_score_function(), rna_denovo(), and StepWiseJobQueen::StepWiseJobQueen().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::move_first_rigid_body

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::new_fold_tree_initializer

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::no_filters

Referenced by add_rosetta_options_13().

ResidueChainVectorOptionKey const basic::options::OptionKeys::rna::denovo::obligate_pair

Referenced by add_rosetta_options_13().

StringVectorOptionKey const basic::options::OptionKeys::rna::denovo::obligate_pair_explicit

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::rna::denovo::offset

Referenced by ObjexxFCL::FArray3< T >::a(), ObjexxFCL::FArray4< T >::a(), ObjexxFCL::FArray5< T >::a(), ObjexxFCL::FArray6< T >::a(), ObjexxFCL::FArray2< T >::a(), ObjexxFCL::FArray3D< typename >::a(), ObjexxFCL::KeyFArray3D< typename >::a(), ObjexxFCL::FArray4D< typename >::a(), ObjexxFCL::KeyFArray4D< typename >::a(), ObjexxFCL::KeyFArray2D< typename >::a(), ObjexxFCL::FArray5D< typename >::a(), ObjexxFCL::KeyFArray5D< typename >::a(), ObjexxFCL::FArray2D< double >::a(), ObjexxFCL::FArray6D< typename >::a(), ObjexxFCL::KeyFArray6D< typename >::a(), ObjexxFCL::FArray2A< typename >::a(), ObjexxFCL::FArray2P< typename >::a(), ObjexxFCL::FArray3A< typename >::a(), ObjexxFCL::FArray3P< typename >::a(), ObjexxFCL::FArray4A< typename >::a(), ObjexxFCL::FArray4P< typename >::a(), ObjexxFCL::FArray5P< typename >::a(), ObjexxFCL::FArray5A< typename >::a(), ObjexxFCL::FArray6P< typename >::a(), ObjexxFCL::FArray6A< typename >::a(), add_rosetta_options_13(), MPDomainAssembly::apply(), utility::graph::LowMemGraph< _Node, _Edge >::delete_edge(), delete_protein_from_pose(), delete_RNA_from_pose(), utility::graph::LowMemGraph< _Node, _Edge >::drop_all_edges_for_node(), utility::graph::LowMemNode::find_edge(), utility::graph::LowMemGraph< _Node, _Edge >::internal_create_new_edge(), utility::graph::LowMemNode::internal_find_edge(), utility::graph::LowMemGraph< _Node, _Edge >::internal_get_edge(), numeric::interpolation::multilinear_interpolation(), ScoreFragmentSetMover::overlap_score(), prepare_threaded_model(), numeric::geometry::hashing::SixDCoordinateBinner::radial_bin_index(), utility::json_spirit::remove_trailing(), numeric::MathNTensor< double, 2 >::replace_layer(), ScoreFragmentSetMover::run(), SolutionRescoreMover::run(), setup_mask(), and fmt::BasicWriter< Char >::write_double().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::output_filters

Referenced by add_rosetta_options_13().

ResidueChainVectorOptionKey const basic::options::OptionKeys::rna::denovo::output_res_num

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::override_refine_pose_rounds

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::ramp_rnp_vdw

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::randomize_init_rnp

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::refine_native

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::refine_native_get_good_FT

Referenced by add_rosetta_options_13().

StringOptionKey const basic::options::OptionKeys::rna::denovo::refine_silent_file

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::rna::denovo::refine_silent_number_of_poses

Referenced by add_rosetta_options_13().

StringVectorOptionKey const basic::options::OptionKeys::rna::denovo::refine_silent_tags

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::relax_rna

Referenced by add_rosetta_options_13().

ResidueChainVectorOptionKey const basic::options::OptionKeys::rna::denovo::remove_obligate_pair

Referenced by add_rosetta_options_13().

ResidueChainVectorOptionKey const basic::options::OptionKeys::rna::denovo::remove_pair

Referenced by add_rosetta_options_13().

RealOptionKey const basic::options::OptionKeys::rna::denovo::rna_lores_chainbreak_weight

Referenced by add_rosetta_options_13().

RealOptionKey const basic::options::OptionKeys::rna::denovo::rna_lores_linear_chainbreak_weight

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::rna_protein_docking

Referenced by add_rosetta_options_13().

RealOptionKey const basic::options::OptionKeys::rna::denovo::rna_protein_docking_freq

Referenced by add_rosetta_options_12().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::rna_protein_docking_legacy

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::rna::denovo::rnp_high_res_cycles

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::rnp_high_res_relax

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::rnp_min_first

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::rnp_pack_first

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::rnp_ramp_rep

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::root_at_first_rigid_body

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::rna::denovo::rounds

Referenced by add_rosetta_options_12().

StringOptionKey const basic::options::OptionKeys::rna::denovo::secstruct

Referenced by add_rosetta_options_13(), MetalSiteFinderMover::apply(), MPDomainAssembly::apply(), zinc_stats::ZincStatisticGenerator::initialize_from_options(), zinc_stats::ZincStatisticGenerator::iterate_over_residues(), main(), rebuild_test(), rna_fullatom_minimize_test(), and spanfile_from_pdb().

StringOptionKey const basic::options::OptionKeys::rna::denovo::secstruct_file

Referenced by add_rosetta_options_13(), and rna_fullatom_minimize_test().

StringOptionKey const basic::options::OptionKeys::rna::denovo::secstruct_general

Referenced by add_rosetta_options_13().

StringOptionKey const basic::options::OptionKeys::rna::denovo::secstruct_general_file

Referenced by add_rosetta_options_13().

StringOptionKey const basic::options::OptionKeys::rna::denovo::secstruct_legacy

Referenced by add_rosetta_options_13().

StringVectorOptionKey const basic::options::OptionKeys::rna::denovo::sequence

Referenced by add_rosetta_options_13().

StringVectorOptionKey const basic::options::OptionKeys::rna::denovo::set_lores_weights

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::simple_relax

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::small_docking_moves

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::staged_constraints

Referenced by add_rosetta_options_13().

RealOptionKey const basic::options::OptionKeys::rna::denovo::suppress_bp_constraint

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::rna::denovo::symm_hack_arity

Referenced by add_rosetta_options_13().

StringOptionKey const basic::options::OptionKeys::rna::denovo::tag

Referenced by add_rosetta_options_13().

RealOptionKey const basic::options::OptionKeys::rna::denovo::temperature

Referenced by add_rosetta_options_12().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::use_1jj2_torsions

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::use_legacy_setup

Referenced by add_rosetta_options_13().

StringOptionKey const basic::options::OptionKeys::rna::denovo::vall_torsions

Referenced by add_rosetta_options_13(), create_rna_vall_torsions_test(), main(), and my_main().

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::VDW_rep_screen_include_sidechains

Referenced by add_rosetta_options_13().

ResidueChainVectorOptionKey const basic::options::OptionKeys::rna::denovo::virtual_anchor

Referenced by add_rosetta_options_13().

StringOptionKey const basic::options::OptionKeys::rna::denovo::working_native

Referenced by add_rosetta_options_13().