rna.OptionKeys.gen.hh File Reference

basic::options::OptionKeys collection More...

#include <basic/options/keys/OptionKeys.hh>

Namespaces
	basic
	Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input.
	basic::options
	basic::options::OptionKeys
	basic::options::OptionKeys::rna
	basic::options::OptionKeys::rna::denovo
	basic::options::OptionKeys::rna::denovo::out
	basic::options::OptionKeys::rna::denovo::db
	basic::options::OptionKeys::rna::denovo::minimize
	basic::options::OptionKeys::rna::erraser

Variables
BooleanOptionKey const	basic::options::OptionKeys::rna::rna
BooleanOptionKey const	basic::options::OptionKeys::rna::corrected_geo
BooleanOptionKey const	basic::options::OptionKeys::rna::vary_geometry
StringOptionKey const	basic::options::OptionKeys::rna::data_file
BooleanOptionKey const	basic::options::OptionKeys::rna::cut_at_rna_chainbreak
BooleanOptionKey const	basic::options::OptionKeys::rna::evaluate_base_pairs
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::denovo
IntegerOptionKey const	basic::options::OptionKeys::rna::denovo::cycles
RealOptionKey const	basic::options::OptionKeys::rna::denovo::rna_protein_docking_freq
IntegerOptionKey const	basic::options::OptionKeys::rna::denovo::rounds
RealOptionKey const	basic::options::OptionKeys::rna::denovo::temperature
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::minimize_rna
StringVectorOptionKey const	basic::options::OptionKeys::rna::denovo::sequence
StringOptionKey const	basic::options::OptionKeys::rna::denovo::secstruct
StringOptionKey const	basic::options::OptionKeys::rna::denovo::secstruct_general
StringOptionKey const	basic::options::OptionKeys::rna::denovo::secstruct_file
StringOptionKey const	basic::options::OptionKeys::rna::denovo::secstruct_general_file
StringOptionKey const	basic::options::OptionKeys::rna::denovo::secstruct_legacy
StringOptionKey const	basic::options::OptionKeys::rna::denovo::lores_scorefxn
StringVectorOptionKey const	basic::options::OptionKeys::rna::denovo::set_lores_weights
IntegerOptionKey const	basic::options::OptionKeys::rna::denovo::symm_hack_arity
IntegerOptionKey const	basic::options::OptionKeys::rna::denovo::exhaustive_fragment_insertion
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::filter_lores_base_pairs
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::filter_lores_base_pairs_early
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::filter_chain_closure
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::filter_chain_closure_halfway
RealOptionKey const	basic::options::OptionKeys::rna::denovo::filter_chain_closure_distance
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::relax_rna
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::simple_relax
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::ignore_secstruct
RealOptionKey const	basic::options::OptionKeys::rna::denovo::jump_change_frequency
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::close_loops
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::close_loops_after_each_move
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::heat
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::staged_constraints
StringOptionKey const	basic::options::OptionKeys::rna::denovo::jump_library_file
StringOptionKey const	basic::options::OptionKeys::rna::denovo::vall_torsions
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::use_1jj2_torsions
RealOptionKey const	basic::options::OptionKeys::rna::denovo::fuzz_fragments
RealOptionKey const	basic::options::OptionKeys::rna::denovo::rna_lores_chainbreak_weight
RealOptionKey const	basic::options::OptionKeys::rna::denovo::rna_lores_linear_chainbreak_weight
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::fixed_stems
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::allow_bulge
IntegerVectorOptionKey const	basic::options::OptionKeys::rna::denovo::allowed_bulge_res
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::allow_consecutive_bulges
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::move_first_rigid_body
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::root_at_first_rigid_body
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::dock_each_chunk
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::dock_each_chunk_per_chain
FileVectorOptionKey const	basic::options::OptionKeys::rna::denovo::dock_chunks
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::center_jumps_in_single_stranded
FileVectorOptionKey const	basic::options::OptionKeys::rna::denovo::initial_structures
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::ft_close_chains
FileVectorOptionKey const	basic::options::OptionKeys::rna::denovo::helical_substructs
RealOptionKey const	basic::options::OptionKeys::rna::denovo::suppress_bp_constraint
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::output_filters
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::autofilter
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::no_filters
ResidueChainVectorOptionKey const	basic::options::OptionKeys::rna::denovo::output_res_num
IntegerOptionKey const	basic::options::OptionKeys::rna::denovo::offset
ResidueChainVectorOptionKey const	basic::options::OptionKeys::rna::denovo::input_silent_res
ResidueChainVectorOptionKey const	basic::options::OptionKeys::rna::denovo::virtual_anchor
ResidueChainVectorOptionKey const	basic::options::OptionKeys::rna::denovo::obligate_pair
StringVectorOptionKey const	basic::options::OptionKeys::rna::denovo::obligate_pair_explicit
StringVectorOptionKey const	basic::options::OptionKeys::rna::denovo::chain_connection
ResidueChainVectorOptionKey const	basic::options::OptionKeys::rna::denovo::remove_pair
ResidueChainVectorOptionKey const	basic::options::OptionKeys::rna::denovo::remove_obligate_pair
StringOptionKey const	basic::options::OptionKeys::rna::denovo::refine_silent_file
StringVectorOptionKey const	basic::options::OptionKeys::rna::denovo::refine_silent_tags
IntegerOptionKey const	basic::options::OptionKeys::rna::denovo::refine_silent_number_of_poses
StringOptionKey const	basic::options::OptionKeys::rna::denovo::get_fold_tree_from_silent_file
StringVectorOptionKey const	basic::options::OptionKeys::rna::denovo::fold_tree_from_silent_file_tag
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::refine_native_get_good_FT
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::refine_native
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::override_refine_pose_rounds
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::bps_moves
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::disallow_bps_at_extra_min_res
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::allow_fragment_moves_in_bps
IntegerOptionKey const	basic::options::OptionKeys::rna::denovo::frag_size
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::VDW_rep_screen_include_sidechains
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::gradual_constraints
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::ramp_rnp_vdw
RealOptionKey const	basic::options::OptionKeys::rna::denovo::grid_vdw_weight
StringOptionKey const	basic::options::OptionKeys::rna::denovo::tag
StringOptionKey const	basic::options::OptionKeys::rna::denovo::working_native
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::use_legacy_setup
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::cst_gap
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::convert_protein_CEN
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::rna_protein_docking
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::small_docking_moves
RealOptionKey const	basic::options::OptionKeys::rna::denovo::docking_move_size
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::rna_protein_docking_legacy
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::rnp_high_res_relax
IntegerOptionKey const	basic::options::OptionKeys::rna::denovo::rnp_high_res_cycles
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::rnp_pack_first
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::rnp_min_first
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::rnp_ramp_rep
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::new_fold_tree_initializer
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::randomize_init_rnp
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::dock_into_density
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::dock_into_density_legacy
IntegerVectorOptionKey const	basic::options::OptionKeys::rna::denovo::exclude_fragments
StringOptionKey const	basic::options::OptionKeys::rna::denovo::exclusion_match_type
RealOptionKey const	basic::options::OptionKeys::rna::denovo::fragment_homology_rmsd
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::exclude_native_fragments
StringVectorOptionKey const	basic::options::OptionKeys::rna::denovo::exclude_fragment_files
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::dump_stems
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::out::out
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::out::output_lores_silent_file
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::out::dump
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::out::binary_output
StringOptionKey const	basic::options::OptionKeys::rna::denovo::out::output_score_file
IntegerOptionKey const	basic::options::OptionKeys::rna::denovo::out::output_score_frequency
ResidueChainVectorOptionKey const	basic::options::OptionKeys::rna::denovo::out::output_jump_res
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::out::output_jump_o3p_to_o5p
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::out::output_jump_chainbreak
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::out::output_rotation_vector
StringOptionKey const	basic::options::OptionKeys::rna::denovo::out::output_jump_reference_RT
RealVectorOptionKey const	basic::options::OptionKeys::rna::denovo::out::target_xyz
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::out::save_jump_histogram
StringOptionKey const	basic::options::OptionKeys::rna::denovo::out::output_histogram_file
RealOptionKey const	basic::options::OptionKeys::rna::denovo::out::jump_histogram_boxsize
RealOptionKey const	basic::options::OptionKeys::rna::denovo::out::jump_histogram_binwidth
RealOptionKey const	basic::options::OptionKeys::rna::denovo::out::jump_histogram_binwidth_rotvector
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::db::db
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::db::jump_database
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::db::bps_database
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::minimize::minimize
IntegerOptionKey const	basic::options::OptionKeys::rna::denovo::minimize::minimize_rounds
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::minimize::skip_coord_constraints
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::minimize::skip_o2prime_trials
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::minimize::deriv_check
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::minimize::minimizer_use_coordinate_constraints
StringOptionKey const	basic::options::OptionKeys::rna::denovo::minimize::min_type
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::minimize::minimize_bps
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::minimize::minimize_all_protein
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::minimize::minimize_protein_sc
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::minimize::protein_packing
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::minimize::protein_pack_all
RealOptionKey const	basic::options::OptionKeys::rna::denovo::minimize::protein_packing_distance
ResidueChainVectorOptionKey const	basic::options::OptionKeys::rna::denovo::minimize::extra_minimize_res
ResidueChainVectorOptionKey const	basic::options::OptionKeys::rna::denovo::minimize::extra_minimize_chi_res
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::minimize::minimize_use_nblist
BooleanOptionKey const	basic::options::OptionKeys::rna::denovo::minimize::minimize_nblist_auto_update
IntegerOptionKey const	basic::options::OptionKeys::rna::denovo::minimize::minimize_max_iter
BooleanOptionKey const	basic::options::OptionKeys::rna::erraser::erraser
BooleanOptionKey const	basic::options::OptionKeys::rna::erraser::rna_prot_erraser
BooleanOptionKey const	basic::options::OptionKeys::rna::erraser::constrain_P
ResidueChainVectorOptionKey const	basic::options::OptionKeys::rna::erraser::fixed_res
BooleanOptionKey const	basic::options::OptionKeys::rna::erraser::ready_set_only
BooleanOptionKey const	basic::options::OptionKeys::rna::erraser::skip_minimize
BooleanOptionKey const	basic::options::OptionKeys::rna::erraser::attempt_pyrimidine_flip

Detailed Description

basic::options::OptionKeys collection

Author

Stuart G. Mentzer (Stuar.nosp@m.t_Me.nosp@m.ntzer.nosp@m.@obj.nosp@m.exx.c.nosp@m.om)

James M. Thompson (tex@u.nosp@m..was.nosp@m.hingt.nosp@m.on.e.nosp@m.du)