stepwise.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::stepwise
	basic::options::OptionKeys::stepwise::monte_carlo
	basic::options::OptionKeys::stepwise::monte_carlo::csa
	basic::options::OptionKeys::stepwise::polar_hydrogens
	basic::options::OptionKeys::stepwise::rna
	basic::options::OptionKeys::stepwise::protein

Variables
BooleanOptionKey const	basic::options::OptionKeys::stepwise::stepwise
StringVectorOptionKey const	basic::options::OptionKeys::stepwise::s1
StringVectorOptionKey const	basic::options::OptionKeys::stepwise::s2
StringVectorOptionKey const	basic::options::OptionKeys::stepwise::silent1
StringVectorOptionKey const	basic::options::OptionKeys::stepwise::silent2
StringVectorOptionKey const	basic::options::OptionKeys::stepwise::tags1
StringVectorOptionKey const	basic::options::OptionKeys::stepwise::tags2
IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::slice_res1
IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::slice_res2
IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::input_res1
IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::input_res2
BooleanOptionKey const	basic::options::OptionKeys::stepwise::backbone_only1
BooleanOptionKey const	basic::options::OptionKeys::stepwise::backbone_only2
IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::fixed_res
BooleanOptionKey const	basic::options::OptionKeys::stepwise::test_encapsulation
BooleanOptionKey const	basic::options::OptionKeys::stepwise::choose_random
IntegerOptionKey const	basic::options::OptionKeys::stepwise::num_random_samples
IntegerOptionKey const	basic::options::OptionKeys::stepwise::max_tries_multiplier_for_ccd
IntegerOptionKey const	basic::options::OptionKeys::stepwise::num_pose_minimize
BooleanOptionKey const	basic::options::OptionKeys::stepwise::atr_rep_screen
BooleanOptionKey const	basic::options::OptionKeys::stepwise::atr_rep_screen_for_docking
StringOptionKey const	basic::options::OptionKeys::stepwise::align_pdb
StringOptionKey const	basic::options::OptionKeys::stepwise::new_align_pdb
BooleanOptionKey const	basic::options::OptionKeys::stepwise::enumerate
BooleanOptionKey const	basic::options::OptionKeys::stepwise::preminimize
BooleanOptionKey const	basic::options::OptionKeys::stepwise::skip_preminimize
BooleanOptionKey const	basic::options::OptionKeys::stepwise::minimize_waters
BooleanOptionKey const	basic::options::OptionKeys::stepwise::test_all_moves
BooleanOptionKey const	basic::options::OptionKeys::stepwise::new_move_selector
BooleanOptionKey const	basic::options::OptionKeys::stepwise::dump
BooleanOptionKey const	basic::options::OptionKeys::stepwise::VERBOSE
BooleanOptionKey const	basic::options::OptionKeys::stepwise::use_green_packer
RealOptionKey const	basic::options::OptionKeys::stepwise::rmsd_screen
BooleanOptionKey const	basic::options::OptionKeys::stepwise::skip_minimize
BooleanOptionKey const	basic::options::OptionKeys::stepwise::virtualize_packable_moieties_in_screening_pose
StringOptionKey const	basic::options::OptionKeys::stepwise::minimizer_mode
StringOptionKey const	basic::options::OptionKeys::stepwise::sampler_silent_file
BooleanOptionKey const	basic::options::OptionKeys::stepwise::superimpose_over_all
ResidueChainVectorOptionKey const	basic::options::OptionKeys::stepwise::alignment_anchor_res
StringVectorOptionKey const	basic::options::OptionKeys::stepwise::move
StringOptionKey const	basic::options::OptionKeys::stepwise::min_type
RealOptionKey const	basic::options::OptionKeys::stepwise::min_tolerance
BooleanOptionKey const	basic::options::OptionKeys::stepwise::output_minimized_pose_list
BooleanOptionKey const	basic::options::OptionKeys::stepwise::virtualize_free_moieties_in_native
BooleanOptionKey const	basic::options::OptionKeys::stepwise::output_cluster_size
BooleanOptionKey const	basic::options::OptionKeys::stepwise::lores
BooleanOptionKey const	basic::options::OptionKeys::stepwise::verbose_sampler
BooleanOptionKey const	basic::options::OptionKeys::stepwise::pack_protein_side_chains
IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::definitely_virtualize
BooleanOptionKey const	basic::options::OptionKeys::stepwise::force_moving_res_for_erraser
BooleanOptionKey const	basic::options::OptionKeys::stepwise::boltzmann_choice_post_enumerated_minimize
BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::monte_carlo
BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::verbose_scores
BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::skip_deletions
BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::allow_internal_hinge_moves
BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::allow_internal_local_moves
BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::allow_skip_bulge
RealOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::skip_bulge_frequency
RealOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::from_scratch_frequency
BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::allow_split_off
IntegerOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::cycles
RealOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::temperature
RealOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::add_proposal_density_factor
RealOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::add_delete_frequency
RealOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::docking_frequency
RealOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::submotif_frequency
RealOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::intermolecular_frequency
RealOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::minimize_single_res_frequency
BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::allow_variable_bond_geometry
RealOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::switch_focus_frequency
RealOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::just_min_after_mutation_frequency
BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::local_redock_only
BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::make_movie
BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::recover_low
BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::use_precomputed_library
BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::allow_submotif_split
BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::force_submotif_without_intervening_bulge
BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::use_first_jump_for_submotif
StringVectorOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::exclude_submotifs
RealOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::vary_loop_length_frequency
BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::designing_with_noncanonicals
IntegerOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::checkpointing_frequency
BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::continue_until_none_missing
FileVectorOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::full_model_constraints
BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::csa::csa
IntegerOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::csa::csa_bank_size
RealOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::csa::csa_rmsd
BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::csa::csa_output_rounds
BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::csa::annealing
BooleanOptionKey const	basic::options::OptionKeys::stepwise::polar_hydrogens::polar_hydrogens
BooleanOptionKey const	basic::options::OptionKeys::stepwise::polar_hydrogens::vary_polar_hydrogen_geometry
RealOptionKey const	basic::options::OptionKeys::stepwise::polar_hydrogens::bond_angle_sd_polar_hydrogen
RealOptionKey const	basic::options::OptionKeys::stepwise::polar_hydrogens::bond_torsion_sd_polar_hydrogen
BooleanOptionKey const	basic::options::OptionKeys::stepwise::polar_hydrogens::fix_lengths
BooleanOptionKey const	basic::options::OptionKeys::stepwise::polar_hydrogens::fix_angles
BooleanOptionKey const	basic::options::OptionKeys::stepwise::polar_hydrogens::fix_torsions
BooleanOptionKey const	basic::options::OptionKeys::stepwise::polar_hydrogens::disallow_pack_polar_hydrogens
BooleanOptionKey const	basic::options::OptionKeys::stepwise::polar_hydrogens::disallow_vary_geometry_proton_chi
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::rna
IntegerOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_num_pose_kept
RealOptionKey const	basic::options::OptionKeys::stepwise::rna::native_edensity_score_cutoff
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::o2prime_legacy_mode
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::allow_virtual_o2prime_hydrogens
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_perform_phosphate_pack
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::force_phosphate_instantiation
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::distinguish_pucker
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::finer_sampling_at_chain_closure
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::PBP_clustering_at_chain_closure
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::sample_all_chi
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_allow_syn_pyrimidine
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_extra_chi_rotamer
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_extra_beta_rotamer
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_extra_epsilon_rotamer
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::force_centroid_interaction
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::virtual_sugar_legacy_mode
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::VDW_rep_optimize_memory_usage
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::erraser
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::centroid_screen
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::VDW_atr_rep_screen
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::minimize_and_score_native_pose
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::rm_virt_phosphate
StringVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::VDW_rep_screen_info
RealOptionKey const	basic::options::OptionKeys::stepwise::rna::VDW_rep_alignment_RMSD_CUTOFF
StringVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::VDW_rep_delete_matching_res
RealOptionKey const	basic::options::OptionKeys::stepwise::rna::VDW_rep_screen_physical_pose_clash_dist_cutoff
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::integration_test
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::allow_bulge_at_chainbreak
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::parin_favorite_output
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::reinitialize_CCD_torsions
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::sample_both_sugar_base_rotamer
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_include_torsion_value_in_tag
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_assert_no_virt_sugar_sampling
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_try_sugar_instantiation
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::do_not_sample_multiple_virtual_sugar
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::sample_ONLY_multiple_virtual_sugar
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::allow_base_pair_only_centroid_screen
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::minimizer_rename_tag
IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::minimize_res
StringVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::alignment_res
IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::native_alignment_res
IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::rmsd_res
IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::missing_res
IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::missing_res2
IntegerOptionKey const	basic::options::OptionKeys::stepwise::rna::job_queue_ID
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::minimize_and_score_sugar
IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::global_sample_res_list
FileOptionKey const	basic::options::OptionKeys::stepwise::rna::filter_output_filename
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::combine_long_loop_mode
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::combine_helical_silent_file
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::output_extra_RMSDs
IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::protonated_H1_adenosine_list
IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::native_virtual_res
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::simple_append_map
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::allow_fixed_res_at_moving_res
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::force_user_defined_jumps
StringVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::jump_point_pairs
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::add_virt_root
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::floating_base
IntegerOptionKey const	basic::options::OptionKeys::stepwise::rna::floating_base_anchor_res
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::allow_chain_boundary_jump_partner_right_at_fixed_BP
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::rebuild_bulge_mode
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::virtual_sugar_keep_base_fixed
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::virtual_sugar_do_minimize
RealOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_max_centroid_distance
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::filter_user_alignment_res
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::tether_jump
BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::turn_off_rna_chem_map_during_optimize
BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::protein
BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::global_optimize
BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::disable_sampling_of_loop_takeoff
BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::sample_beta
BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::ghost_loops
BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::centroid_screen
RealOptionKey const	basic::options::OptionKeys::stepwise::protein::centroid_score_diff_cut
StringOptionKey const	basic::options::OptionKeys::stepwise::protein::centroid_weights
RealOptionKey const	basic::options::OptionKeys::stepwise::protein::score_diff_cut
BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::filter_native_big_bins
BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::cluster_by_all_atom_rmsd
BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::centroid_output
IntegerOptionKey const	basic::options::OptionKeys::stepwise::protein::n_sample
IntegerOptionKey const	basic::options::OptionKeys::stepwise::protein::nstruct_centroid
BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::ccd_close
IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::protein::bridge_res
BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::cart_min
BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::move_jumps_between_chains
BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::use_packer_instead_of_rotamer_trials
BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::expand_loop_takeoff
BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::skip_coord_constraints
BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::allow_virtual_side_chains
BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::protein_prepack
StringOptionKey const	basic::options::OptionKeys::stepwise::protein::disulfide_file

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)