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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_13().

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

Referenced by add_rosetta_options_13().

FileVectorOptionKey const basic::options::OptionKeys::rna::denovo::initial_structures
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
BooleanOptionKey const basic::options::OptionKeys::rna::denovo::minimize_rna
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_13().

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_13().

StringOptionKey const basic::options::OptionKeys::rna::denovo::secstruct
StringOptionKey const basic::options::OptionKeys::rna::denovo::secstruct_file
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_13().

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
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().