#include <RNA_FragmentMonteCarloOptions.hh>
Public Member Functions | |
| RNA_FragmentMonteCarloOptions () | |
| RNA_FragmentMonteCarloOptionsOP | clone () const |
| clone the options More... | |
| void | initialize_from_command_line () |
| void | initialize_from_options (utility::options::OptionCollection const &opts) |
| void | initialize_from_tag (utility::tag::TagCOP const &tag) |
| void | initialize_for_farna_optimizer (core::Size const &cycles) |
| void | parse_my_tag (utility::tag::TagCOP) override |
| Initialize from the recursive "tag" structure. More... | |
| std::string | type () const override |
| The class name (its type) for a particular instance. This function allows for better error message delivery. More... | |
| void | set_rounds (core::Size const &setting) |
| core::Size | rounds () const |
| void | set_close_loops_after_each_move (bool const &setting) |
| bool | close_loops_after_each_move () const |
| void | set_refine_pose (bool const &setting) |
| bool | refine_pose () const |
| void | set_override_refine_pose_rounds (bool const &setting) |
| bool | override_refine_pose_rounds () const |
| void | set_refine_native_get_good_FT (bool const &setting) |
| bool | refine_native_get_good_FT () const |
| void | set_temperature (core::Real const setting) |
| core::Real | temperature () const |
| void | set_autofilter (bool const &setting) |
| bool | autofilter () const |
| void | set_autofilter_score_quantile (core::Real const &setting) |
| core::Real | autofilter_score_quantile () const |
| void | set_minimize_structure (bool const &setting) |
| bool | minimize_structure () const |
| void | set_relax_structure (bool const &setting) |
| bool | relax_structure () const |
| void | set_use_chem_shift_data (bool const &setting) |
| bool | use_chem_shift_data () const |
| void | set_superimpose_over_all (bool const &setting) |
| bool | superimpose_over_all () const |
| void | set_fixed_stems (bool const &setting) |
| bool | fixed_stems () const |
| void | set_ft_close_chains (bool const &setting) |
| bool | ft_close_chains () const |
| void | set_jump_change_frequency (core::Real const &setting) |
| core::Real | jump_change_frequency () const |
| void | set_close_loops (bool const setting) |
| bool | close_loops () const |
| void | set_allow_bulge (bool const &setting) |
| bool | allow_bulge () const |
| void | set_allow_consecutive_bulges (bool const &setting) |
| bool | allow_consecutive_bulges () const |
| void | set_simple_rmsd_cutoff_relax (bool const &setting) |
| bool | simple_rmsd_cutoff_relax () const |
| void | set_filter_lores_base_pairs (bool const setting) |
| bool | filter_lores_base_pairs () const |
| void | set_filter_lores_base_pairs_early (bool const setting) |
| bool | filter_lores_base_pairs_early () const |
| void | set_filter_chain_closure (bool const setting) |
| bool | filter_chain_closure () const |
| void | set_filter_chain_closure_distance (core::Real const setting) |
| core::Real | filter_chain_closure_distance () const |
| void | set_filter_chain_closure_halfway (bool const setting) |
| bool | filter_chain_closure_halfway () const |
| void | set_chainbreak_weight (core::Real const &setting) |
| core::Real | chainbreak_weight () const |
| void | set_linear_chainbreak_weight (core::Real const &setting) |
| core::Real | linear_chainbreak_weight () const |
| void | set_allowed_bulge_res (utility::vector1< core::Size > const &setting) |
| utility::vector1< core::Size > const & | allowed_bulge_res () const |
| void | set_filter_vdw (bool const setting) |
| bool | filter_vdw () const |
| void | set_VDW_rep_screen_info (utility::vector1< std::string > const &setting) |
| utility::vector1< std::string > | VDW_rep_screen_info () const |
| void | set_vdw_rep_screen_include_sidechains (bool const setting) |
| bool | vdw_rep_screen_include_sidechains () const |
| void | set_gradual_constraints (bool const setting) |
| bool | gradual_constraints () const |
| void | set_ramp_rnp_vdw (bool const &setting) |
| bool | ramp_rnp_vdw () const |
| void | set_grid_vdw_weight (core::Real const &setting) |
| core::Real | grid_vdw_weight () const |
| void | set_convert_protein_centroid (bool const &setting) |
| bool | convert_protein_centroid () const |
| void | set_rna_protein_docking (bool const &setting) |
| bool | rna_protein_docking () const |
| void | set_small_docking_moves (bool const &setting) |
| bool | small_docking_moves () const |
| void | set_docking_move_size (core::Real const &setting) |
| core::Real | docking_move_size () const |
| void | set_rna_protein_docking_legacy (bool const &setting) |
| bool | rna_protein_docking_legacy () const |
| void | set_rna_protein_docking_freq (core::Real const &setting) |
| core::Real | rna_protein_docking_freq () const |
| void | set_docking (bool const &setting) |
| bool | docking () const |
| void | set_randomize_init_rnp (bool const &setting) |
| bool | randomize_init_rnp () const |
| void | set_rnp_high_res_relax (bool const &setting) |
| bool | rnp_high_res_relax () const |
| void | set_rnp_high_res_cycles (core::Real const &setting) |
| core::Real | rnp_high_res_cycles () const |
| void | set_rnp_pack_first (bool const &setting) |
| bool | rnp_pack_first () const |
| void | set_rnp_ramp_rep (bool const &setting) |
| bool | rnp_ramp_rep () const |
| void | set_rnp_min_first (bool const &setting) |
| bool | rnp_min_first () const |
| void | set_dock_into_density_legacy (bool const &setting) |
| bool | dock_into_density_legacy () const |
| void | set_new_fold_tree_initializer (bool const &setting) |
| bool | new_fold_tree_initializer () const |
| void | set_initial_structures_provided (bool const &setting) |
| bool | initial_structures_provided () const |
| void | set_monte_carlo_cycles (core::Size const setting) |
| core::Size | monte_carlo_cycles () const |
| void | set_user_defined_cycles (bool const &setting) |
| bool | user_defined_cycles () const |
| void | set_ignore_secstruct (bool const &setting) |
| bool | ignore_secstruct () const |
| void | set_titrate_stack_bonus (bool const &setting) |
| bool | titrate_stack_bonus () const |
| void | set_staged_constraints (bool const &setting) |
| bool | staged_constraints () const |
| void | set_root_at_first_rigid_body (bool const &setting) |
| bool | root_at_first_rigid_body () const |
| void | set_dock_each_chunk (bool const &setting) |
| bool | dock_each_chunk () const |
| void | set_dock_each_chunk_per_chain (bool const &setting) |
| bool | dock_each_chunk_per_chain () const |
| void | set_dock_chunks (utility::vector1< std::string > const &dock_chunks) |
| utility::vector1< std::string > const & | dock_chunks () const |
| void | set_center_jumps_in_single_stranded (bool const &setting) |
| bool | center_jumps_in_single_stranded () const |
| void | set_suppress_bp_constraint (core::Real const &setting) |
| core::Real | suppress_bp_constraint () const |
| void | set_bps_moves (bool const &setting) |
| bool | bps_moves () const |
| void | set_disallow_bps_at_extra_min_res (bool const &setting) |
| bool | disallow_bps_at_extra_min_res () const |
| void | set_allow_fragment_moves_in_bps (bool const &setting) |
| bool | allow_fragment_moves_in_bps () const |
| void | set_frag_size (core::Size const &setting) |
| core::Size | frag_size () const |
| void | set_jump_library_file (std::string const &setting) |
| std::string | jump_library_file () const |
| void | set_all_rna_fragments_file (std::string const &setting) |
| std::string | all_rna_fragments_file () const |
| void | set_vall_torsions_file (std::string const &setting) |
| std::string | vall_torsions_file () const |
| void | set_chunk_pdb_files (utility::vector1< std::string > const &chunk_pdb_files) |
| utility::vector1< std::string > const & | chunk_pdb_files () const |
| void | set_helical_substructs (utility::vector1< std::string > const &setting) |
| utility::vector1< std::string > const & | helical_substructs () const |
| void | set_helical_substruct_res (utility::vector1< utility::vector1< core::Size > > const &setting) |
| utility::vector1< utility::vector1< core::Size > > const & | helical_substruct_res () const |
| void | set_dock_chunks_res (utility::vector1< core::Size > const &setting) |
| utility::vector1< core::Size > const & | dock_chunks_res () const |
| void | set_chunk_initialization_pdb_files (utility::vector1< std::string > const &input_files) |
| utility::vector1< std::string > const & | chunk_initialization_pdb_files () const |
| void | set_chunk_silent_files (utility::vector1< std::string > const &chunk_silent_files) |
| utility::vector1< std::string > const & | chunk_silent_files () const |
| void | set_input_res (utility::vector1< Size > const &input_res) |
| utility::vector1< Size > const & | input_res () const |
| void | set_input_res_initialize (utility::vector1< Size > const &input_res) |
| utility::vector1< Size > const & | input_res_initialize () const |
| void | set_output_score_frequency (core::Size const &setting) |
| core::Size | output_score_frequency () const |
| void | set_output_score_file (std::string const &setting) |
| std::string | output_score_file () const |
| void | set_output_lores_silent_file (bool const setting) |
| bool | output_lores_silent_file () const |
| void | set_output_jump_res (utility::vector1< Size > const &output_jump_res) |
| utility::vector1< Size > const & | output_jump_res () const |
| void | set_output_jump_o3p_to_o5p (bool const &setting) |
| bool | output_jump_o3p_to_o5p () const |
| void | set_output_jump_chainbreak (bool const &setting) |
| bool | output_jump_chainbreak () const |
| void | set_save_jump_histogram (bool const &setting) |
| bool | save_jump_histogram () const |
| void | set_output_histogram_file (std::string const &setting) |
| std::string | output_histogram_file () const |
| void | set_output_rotation_vector (bool const &setting) |
| bool | output_rotation_vector () const |
| void | set_output_jump_target_xyz (core::Vector const &setting) |
| core::Vector | output_jump_target_xyz () const |
| void | set_output_jump_reference_RT_string (std::string const &setting) |
| std::string | output_jump_reference_RT_string () const |
| void | set_jump_histogram_boxsize (core::Real const &setting) |
| core::Real | jump_histogram_boxsize () const |
| void | set_jump_histogram_binwidth (core::Real const &setting) |
| core::Real | jump_histogram_binwidth () const |
| void | set_jump_histogram_binwidth_rotvector (core::Real const &setting) |
| core::Real | jump_histogram_binwidth_rotvector () const |
| void | set_rmsd_screen (core::Real const setting) |
| core::Real | rmsd_screen () const |
| void | set_disallow_realign (bool const setting) |
| bool | disallow_realign () const |
| void | set_align_pdb (std::string const &setting) |
| std::string | align_pdb () const |
| void | set_symm_hack_arity (Size const setting) |
| Size | symm_hack_arity () const |
| void | set_exhaustive_fragment_insertion (Size const setting) |
| Size | exhaustive_fragment_insertion () const |
| void | set_output_filters (bool const setting) |
| bool | output_filters () const |
| void | set_save_times (bool const setting) |
| bool | save_times () const |
 Public Member Functions inherited from core::import_pose::options::RNA_MinimizerOptions | |
| RNA_MinimizerOptions () | |
| RNA_MinimizerOptionsOP | clone () const |
| clone the options More... | |
| void | initialize_from_command_line () |
| void | initialize_from_options (utility::options::OptionCollection const &opts) |
| void | initialize_from_tag (utility::tag::TagCOP const &tag) |
| void | parse_my_tag (utility::tag::TagCOP) override |
| Initialize from the recursive "tag" structure. More... | |
| std::string | type () const override |
| The class name (its type) for a particular instance. This function allows for better error message delivery. More... | |
| void | set_vary_bond_geometry (bool const &setting) |
| bool | vary_bond_geometry () const |
| void | set_extra_minimize_res (utility::vector1< Size > const &extra_minimize_res) |
| utility::vector1< Size > const & | extra_minimize_res () const |
| void | set_extra_minimize_chi_res (utility::vector1< Size > const &extra_minimize_chi_res) |
| utility::vector1< Size > const & | extra_minimize_chi_res () const |
| void | set_minimizer_use_coordinate_constraints (bool const &setting) |
| bool | minimizer_use_coordinate_constraints () const |
| void | set_min_type (std::string const &setting) |
| std::string | min_type () const |
| void | set_minimize_bps (bool const &setting) |
| bool | minimize_bps () const |
| void | set_minimize_all_protein (bool const &setting) |
| bool | minimize_all_protein () const |
| void | set_minimize_protein_sc (bool const &setting) |
| bool | minimize_protein_sc () const |
| void | set_protein_packing (bool const &setting) |
| bool | protein_packing () const |
| void | set_protein_pack_all (bool const &setting) |
| bool | protein_pack_all () const |
| void | set_protein_packing_distance (core::Real const &setting) |
| core::Real | protein_packing_distance () const |
| void | set_deriv_check (bool const &setting) |
| bool | deriv_check () const |
| void | set_skip_o2prime_trials (bool const &setting) |
| bool | skip_o2prime_trials () const |
| void | set_minimize_rounds (core::Size const &setting) |
| core::Size | minimize_rounds () const |
| void | set_use_nblist (bool const &setting) |
| bool | use_nblist () const |
| void | set_nblist_auto_update (bool const &setting) |
| bool | nblist_auto_update () const |
| void | set_max_iter (core::Size const &setting) |
| core::Size | max_iter () const |
| Public Member Functions inherited from core::import_pose::options::RNA_BasicOptions | |
| RNA_BasicOptions () | |
| RNA_BasicOptionsOP | clone () const |
| clone the options More... | |
| void | initialize_from_command_line () |
| void | initialize_from_options (utility::options::OptionCollection const &opts) |
| void | initialize_from_tag (utility::tag::TagCOP const &tag) |
| void | set_dump_pdb (bool const setting) |
| bool | dump_pdb () const |
| void | set_move_first_rigid_body (bool const &setting) |
| bool | move_first_rigid_body () const |
| void | set_dock_into_density (bool const &setting) |
| bool | dock_into_density () const |
| void | set_model_with_density (bool const &setting) |
| bool | model_with_density () const |
| void | set_verbose (bool const &setting) |
| bool | verbose () const |
Static Public Member Functions | |
| static void | list_attributes (utility::tag::AttributeList &attlist) |
| static void | list_options_read (utility::options::OptionKeyList &opts) |
| Static Public Member Functions inherited from core::import_pose::options::RNA_MinimizerOptions | |
| static void | list_attributes (utility::tag::AttributeList &attlist) |
| static void | list_options_read (utility::options::OptionKeyList &opts) |
| Static Public Member Functions inherited from core::import_pose::options::RNA_BasicOptions | |
| static void | list_attributes (utility::tag::AttributeList &attlist) |
| static void | list_options_read (utility::options::OptionKeyList &opts) |
Constructor & Destructor Documentation
◆ RNA_FragmentMonteCarloOptions()
| core::import_pose::options::RNA_FragmentMonteCarloOptions::RNA_FragmentMonteCarloOptions | ( | ) |
Member Function Documentation
◆ align_pdb()
|
inline |
References align_pdb_.
◆ all_rna_fragments_file()
|
inline |
References all_rna_fragments_file_.
◆ allow_bulge()
|
inline |
References allow_bulge_.
◆ allow_consecutive_bulges()
|
inline |
References allow_consecutive_bulges_.
◆ allow_fragment_moves_in_bps()
|
inline |
References allow_fragment_moves_in_bps_.
◆ allowed_bulge_res()
|
inline |
References allowed_bulge_res_.
◆ autofilter()
|
inline |
References autofilter_.
◆ autofilter_score_quantile()
|
inline |
References autofilter_score_quantile_.
◆ bps_moves()
|
inline |
References bps_moves_.
◆ center_jumps_in_single_stranded()
|
inline |
References center_jumps_in_single_stranded_.
◆ chainbreak_weight()
|
inline |
References chainbreak_weight_.
◆ chunk_initialization_pdb_files()
|
inline |
References chunk_initialization_pdb_files_.
◆ chunk_pdb_files()
|
inline |
References chunk_pdb_files_.
Referenced by set_chunk_pdb_files().
◆ chunk_silent_files()
|
inline |
References chunk_silent_files_.
Referenced by set_chunk_silent_files().
◆ clone()
| RNA_FragmentMonteCarloOptionsOP core::import_pose::options::RNA_FragmentMonteCarloOptions::clone | ( | ) | const |
clone the options
◆ close_loops()
|
inline |
References close_loops_.
Referenced by core::import_pose::options::RNA_DeNovoProtocolOptions::initialize_from_options().
◆ close_loops_after_each_move()
|
inline |
References close_loops_after_each_move_.
◆ convert_protein_centroid()
|
inline |
References convert_protein_centroid_.
◆ disallow_bps_at_extra_min_res()
|
inline |
References disallow_bps_at_extra_min_res_.
◆ disallow_realign()
|
inline |
References disallow_realign_.
◆ dock_chunks()
|
inline |
References dock_chunks_.
Referenced by set_dock_chunks().
◆ dock_chunks_res()
|
inline |
References dock_chunks_res_.
◆ dock_each_chunk()
|
inline |
References dock_each_chunk_.
◆ dock_each_chunk_per_chain()
|
inline |
References dock_each_chunk_per_chain_.
◆ dock_into_density_legacy()
|
inline |
References dock_into_density_legacy_.
◆ docking()
|
inline |
References docking_.
◆ docking_move_size()
|
inline |
References docking_move_size_.
◆ exhaustive_fragment_insertion()
|
inline |
References exhaustive_fragment_insertion_.
◆ filter_chain_closure()
|
inline |
References filter_chain_closure_.
◆ filter_chain_closure_distance()
|
inline |
References filter_chain_closure_distance_.
◆ filter_chain_closure_halfway()
|
inline |
References filter_chain_closure_halfway_.
◆ filter_lores_base_pairs()
|
inline |
References filter_lores_base_pairs_.
◆ filter_lores_base_pairs_early()
|
inline |
References filter_lores_base_pairs_early_.
◆ filter_vdw()
|
inline |
References filter_vdw_.
◆ fixed_stems()
|
inline |
References fixed_stems_.
◆ frag_size()
|
inline |
References frag_size_.
◆ ft_close_chains()
|
inline |
References ft_close_chains_.
◆ gradual_constraints()
|
inline |
References gradual_constraints_.
◆ grid_vdw_weight()
|
inline |
References grid_vdw_weight_.
◆ helical_substruct_res()
|
inline |
References helical_substruct_res_.
◆ helical_substructs()
|
inline |
References helical_substructs_.
◆ ignore_secstruct()
|
inline |
References ignore_secstruct_.
◆ initial_structures_provided()
|
inline |
References initial_structures_provided_.
◆ initialize_for_farna_optimizer()
| void core::import_pose::options::RNA_FragmentMonteCarloOptions::initialize_for_farna_optimizer | ( | core::Size const & | cycles | ) |
◆ initialize_from_command_line()
| void core::import_pose::options::RNA_FragmentMonteCarloOptions::initialize_from_command_line | ( | ) |
◆ initialize_from_options()
| void core::import_pose::options::RNA_FragmentMonteCarloOptions::initialize_from_options | ( | utility::options::OptionCollection const & | opts | ) |
References protocols::hybridization::path.
Referenced by core::import_pose::options::RNA_DeNovoProtocolOptions::initialize_from_command_line(), core::import_pose::options::RNA_DeNovoProtocolOptions::initialize_from_options(), and core::import_pose::libraries::RNA_LibraryManager::rna_jump_library_cop().
◆ initialize_from_tag()
| void core::import_pose::options::RNA_FragmentMonteCarloOptions::initialize_from_tag | ( | utility::tag::TagCOP const & | tag | ) |
References core::pose::motif::a(), and protocols::match::upstream::b.
Referenced by core::import_pose::options::RNA_DeNovoProtocolOptions::initialize_from_tag().
◆ input_res()
|
inline |
References input_res_.
Referenced by set_input_res(), and set_input_res_initialize().
◆ input_res_initialize()
|
inline |
References input_res_initialize_.
◆ jump_change_frequency()
|
inline |
References jump_change_frequency_.
◆ jump_histogram_binwidth()
|
inline |
References jump_histogram_binwidth_.
◆ jump_histogram_binwidth_rotvector()
|
inline |
References jump_histogram_binwidth_rotvector_.
◆ jump_histogram_boxsize()
|
inline |
References jump_histogram_boxsize_.
◆ jump_library_file()
|
inline |
References jump_library_file_.
Referenced by core::import_pose::libraries::RNA_LibraryManager::rna_jump_library_cop().
◆ linear_chainbreak_weight()
|
inline |
References linear_chainbreak_weight_.
◆ list_attributes()
|
static |
◆ list_options_read()
|
static |
References protocols::hybridization::path.
Referenced by core::import_pose::options::RNA_DeNovoProtocolOptions::list_options_read().
◆ minimize_structure()
|
inline |
References minimize_structure_.
◆ monte_carlo_cycles()
|
inline |
References monte_carlo_cycles_.
◆ new_fold_tree_initializer()
|
inline |
References new_fold_tree_initializer_.
◆ output_filters()
|
inline |
References output_filters_.
◆ output_histogram_file()
|
inline |
References output_histogram_file_.
◆ output_jump_chainbreak()
|
inline |
References output_jump_chainbreak_.
◆ output_jump_o3p_to_o5p()
|
inline |
References output_jump_o3p_to_o5p_.
◆ output_jump_reference_RT_string()
|
inline |
References output_jump_reference_RT_string_.
◆ output_jump_res()
|
inline |
References output_jump_res_.
Referenced by set_output_jump_res().
◆ output_jump_target_xyz()
|
inline |
References output_jump_target_xyz_.
◆ output_lores_silent_file()
|
inline |
References output_lores_silent_file_.
◆ output_rotation_vector()
|
inline |
References output_rotation_vector_.
◆ output_score_file()
|
inline |
References output_score_file_.
◆ output_score_frequency()
|
inline |
References output_score_frequency_.
◆ override_refine_pose_rounds()
|
inline |
References override_refine_pose_rounds_.
◆ parse_my_tag()
|
inlineoverridevirtual |
Initialize from the recursive "tag" structure.
Reimplemented from core::import_pose::options::RNA_BasicOptions.
◆ ramp_rnp_vdw()
|
inline |
References ramp_rnp_vdw_.
◆ randomize_init_rnp()
|
inline |
References randomize_init_rnp_.
◆ refine_native_get_good_FT()
|
inline |
References refine_native_get_good_FT_.
◆ refine_pose()
|
inline |
References refine_pose_.
◆ relax_structure()
|
inline |
References relax_structure_.
◆ rmsd_screen()
|
inline |
References rmsd_screen_.
◆ rna_protein_docking()
|
inline |
References rna_protein_docking_.
◆ rna_protein_docking_freq()
|
inline |
References rna_protein_docking_freq_.
◆ rna_protein_docking_legacy()
|
inline |
References rna_protein_docking_legacy_.
◆ rnp_high_res_cycles()
|
inline |
References rnp_high_res_cycles_.
◆ rnp_high_res_relax()
|
inline |
References rnp_high_res_relax_.
◆ rnp_min_first()
|
inline |
References rnp_min_first_.
◆ rnp_pack_first()
|
inline |
References rnp_pack_first_.
◆ rnp_ramp_rep()
|
inline |
References rnp_ramp_rep_.
◆ root_at_first_rigid_body()
|
inline |
References root_at_first_rigid_body_.
◆ rounds()
|
inline |
References rounds_.
◆ save_jump_histogram()
|
inline |
References save_jump_histogram_.
◆ save_times()
|
inline |
References save_times_.
◆ set_align_pdb()
|
inline |
References align_pdb_.
◆ set_all_rna_fragments_file()
|
inline |
References all_rna_fragments_file_.
◆ set_allow_bulge()
|
inline |
References allow_bulge_.
◆ set_allow_consecutive_bulges()
|
inline |
References allow_consecutive_bulges_.
◆ set_allow_fragment_moves_in_bps()
|
inline |
References allow_fragment_moves_in_bps_.
◆ set_allowed_bulge_res()
|
inline |
References allowed_bulge_res_.
◆ set_autofilter()
|
inline |
References autofilter_.
◆ set_autofilter_score_quantile()
|
inline |
References autofilter_score_quantile_.
◆ set_bps_moves()
|
inline |
References bps_moves_.
◆ set_center_jumps_in_single_stranded()
|
inline |
References center_jumps_in_single_stranded_.
◆ set_chainbreak_weight()
|
inline |
References chainbreak_weight_.
◆ set_chunk_initialization_pdb_files()
|
inline |
References chunk_initialization_pdb_files_.
Referenced by core::import_pose::options::RNA_DeNovoProtocolOptions::initialize_from_options().
◆ set_chunk_pdb_files()
|
inline |
References chunk_pdb_files(), and chunk_pdb_files_.
Referenced by core::import_pose::options::RNA_DeNovoProtocolOptions::initialize_from_options().
◆ set_chunk_silent_files()
|
inline |
References chunk_silent_files(), and chunk_silent_files_.
Referenced by core::import_pose::options::RNA_DeNovoProtocolOptions::initialize_from_options().
◆ set_close_loops()
|
inline |
References close_loops_.
◆ set_close_loops_after_each_move()
|
inline |
References close_loops_after_each_move_.
◆ set_convert_protein_centroid()
|
inline |
References convert_protein_centroid_.
◆ set_disallow_bps_at_extra_min_res()
|
inline |
References disallow_bps_at_extra_min_res_.
◆ set_disallow_realign()
|
inline |
References disallow_realign_.
◆ set_dock_chunks()
|
inline |
References dock_chunks(), and dock_chunks_.
◆ set_dock_chunks_res()
|
inline |
References dock_chunks_res_.
◆ set_dock_each_chunk()
|
inline |
References dock_each_chunk_.
◆ set_dock_each_chunk_per_chain()
|
inline |
References dock_each_chunk_per_chain_.
◆ set_dock_into_density_legacy()
|
inline |
References dock_into_density_legacy_.
◆ set_docking()
|
inline |
References docking_.
◆ set_docking_move_size()
|
inline |
References docking_move_size_.
◆ set_exhaustive_fragment_insertion()
|
inline |
References exhaustive_fragment_insertion_.
◆ set_filter_chain_closure()
|
inline |
References filter_chain_closure_.
◆ set_filter_chain_closure_distance()
|
inline |
References filter_chain_closure_distance_.
◆ set_filter_chain_closure_halfway()
|
inline |
References filter_chain_closure_halfway_.
◆ set_filter_lores_base_pairs()
|
inline |
References filter_lores_base_pairs_.
◆ set_filter_lores_base_pairs_early()
|
inline |
References filter_lores_base_pairs_early_.
◆ set_filter_vdw()
|
inline |
References filter_vdw_.
◆ set_fixed_stems()
|
inline |
References fixed_stems_.
◆ set_frag_size()
|
inline |
References frag_size_.
◆ set_ft_close_chains()
|
inline |
References ft_close_chains_.
◆ set_gradual_constraints()
|
inline |
References gradual_constraints_.
◆ set_grid_vdw_weight()
|
inline |
References grid_vdw_weight_.
◆ set_helical_substruct_res()
|
inline |
References helical_substruct_res_.
◆ set_helical_substructs()
|
inline |
References helical_substructs_.
◆ set_ignore_secstruct()
|
inline |
References ignore_secstruct_.
◆ set_initial_structures_provided()
|
inline |
References initial_structures_provided_.
◆ set_input_res()
|
inline |
References input_res(), and input_res_.
Referenced by core::import_pose::options::RNA_DeNovoProtocolOptions::initialize_from_options().
◆ set_input_res_initialize()
|
inline |
References input_res(), and input_res_initialize_.
◆ set_jump_change_frequency()
|
inline |
References jump_change_frequency_.
◆ set_jump_histogram_binwidth()
|
inline |
References jump_histogram_binwidth_.
◆ set_jump_histogram_binwidth_rotvector()
|
inline |
References jump_histogram_binwidth_rotvector_.
◆ set_jump_histogram_boxsize()
|
inline |
References jump_histogram_boxsize_.
◆ set_jump_library_file()
|
inline |
References jump_library_file_.
◆ set_linear_chainbreak_weight()
|
inline |
References linear_chainbreak_weight_.
◆ set_minimize_structure()
|
inline |
References minimize_structure_.
◆ set_monte_carlo_cycles()
|
inline |
References monte_carlo_cycles_.
◆ set_new_fold_tree_initializer()
|
inline |
References new_fold_tree_initializer_.
◆ set_output_filters()
|
inline |
References output_filters_.
◆ set_output_histogram_file()
|
inline |
References output_histogram_file_.
◆ set_output_jump_chainbreak()
|
inline |
References output_jump_chainbreak_.
◆ set_output_jump_o3p_to_o5p()
|
inline |
References output_jump_o3p_to_o5p_.
◆ set_output_jump_reference_RT_string()
|
inline |
References output_jump_reference_RT_string_.
◆ set_output_jump_res()
|
inline |
References output_jump_res(), and output_jump_res_.
◆ set_output_jump_target_xyz()
|
inline |
References output_jump_target_xyz_.
◆ set_output_lores_silent_file()
|
inline |
References output_lores_silent_file_.
◆ set_output_rotation_vector()
|
inline |
References output_rotation_vector_.
◆ set_output_score_file()
|
inline |
References output_score_file_.
◆ set_output_score_frequency()
|
inline |
References output_score_frequency_.
◆ set_override_refine_pose_rounds()
|
inline |
References override_refine_pose_rounds_.
◆ set_ramp_rnp_vdw()
|
inline |
References ramp_rnp_vdw_.
◆ set_randomize_init_rnp()
|
inline |
References randomize_init_rnp_.
◆ set_refine_native_get_good_FT()
|
inline |
References refine_native_get_good_FT_.
◆ set_refine_pose()
|
inline |
References refine_pose_.
◆ set_relax_structure()
|
inline |
References relax_structure_.
◆ set_rmsd_screen()
|
inline |
References rmsd_screen_.
◆ set_rna_protein_docking()
|
inline |
References rna_protein_docking_.
◆ set_rna_protein_docking_freq()
|
inline |
References rna_protein_docking_freq_.
◆ set_rna_protein_docking_legacy()
|
inline |
References rna_protein_docking_legacy_.
◆ set_rnp_high_res_cycles()
|
inline |
References rnp_high_res_cycles_.
◆ set_rnp_high_res_relax()
|
inline |
References rnp_high_res_relax_.
◆ set_rnp_min_first()
|
inline |
References rnp_min_first_.
◆ set_rnp_pack_first()
|
inline |
References rnp_pack_first_.
◆ set_rnp_ramp_rep()
|
inline |
References rnp_ramp_rep_.
◆ set_root_at_first_rigid_body()
|
inline |
References root_at_first_rigid_body_.
◆ set_rounds()
|
inline |
References rounds_.
◆ set_save_jump_histogram()
|
inline |
References save_jump_histogram_.
◆ set_save_times()
|
inline |
References save_times_.
◆ set_simple_rmsd_cutoff_relax()
|
inline |
References simple_rmsd_cutoff_relax_.
◆ set_small_docking_moves()
|
inline |
References small_docking_moves_.
◆ set_staged_constraints()
|
inline |
References staged_constraints_.
◆ set_superimpose_over_all()
|
inline |
References superimpose_over_all_.
◆ set_suppress_bp_constraint()
|
inline |
References suppress_bp_constraint_.
◆ set_symm_hack_arity()
|
inline |
References symm_hack_arity_.
◆ set_temperature()
|
inline |
References temperature_.
◆ set_titrate_stack_bonus()
|
inline |
References titrate_stack_bonus_.
◆ set_use_chem_shift_data()
|
inline |
References use_chem_shift_data_.
◆ set_user_defined_cycles()
|
inline |
References user_defined_cycles_.
◆ set_vall_torsions_file()
|
inline |
References all_rna_fragments_file_.
◆ set_vdw_rep_screen_include_sidechains()
|
inline |
References vdw_rep_screen_include_sidechains_.
◆ set_VDW_rep_screen_info()
|
inline |
References VDW_rep_screen_info_.
◆ simple_rmsd_cutoff_relax()
|
inline |
References simple_rmsd_cutoff_relax_.
◆ small_docking_moves()
|
inline |
References small_docking_moves_.
◆ staged_constraints()
|
inline |
References staged_constraints_.
◆ superimpose_over_all()
|
inline |
References superimpose_over_all_.
◆ suppress_bp_constraint()
|
inline |
References suppress_bp_constraint_.
◆ symm_hack_arity()
|
inline |
References symm_hack_arity_.
◆ temperature()
|
inline |
References temperature_.
◆ titrate_stack_bonus()
|
inline |
References titrate_stack_bonus_.
◆ type()
|
inlineoverridevirtual |
The class name (its type) for a particular instance. This function allows for better error message delivery.
Reimplemented from core::import_pose::options::RNA_BasicOptions.
◆ use_chem_shift_data()
|
inline |
References use_chem_shift_data_.
◆ user_defined_cycles()
|
inline |
References user_defined_cycles_.
◆ vall_torsions_file()
|
inline |
References all_rna_fragments_file_.
◆ vdw_rep_screen_include_sidechains()
|
inline |
References vdw_rep_screen_include_sidechains_.
◆ VDW_rep_screen_info()
|
inline |
References VDW_rep_screen_info_.
Member Data Documentation
◆ align_pdb_
|
private |
Referenced by align_pdb(), and set_align_pdb().
◆ all_rna_fragments_file_
|
private |
Referenced by all_rna_fragments_file(), set_all_rna_fragments_file(), set_vall_torsions_file(), and vall_torsions_file().
◆ allow_bulge_
|
private |
Referenced by allow_bulge(), and set_allow_bulge().
◆ allow_consecutive_bulges_
|
private |
Referenced by allow_consecutive_bulges(), and set_allow_consecutive_bulges().
◆ allow_fragment_moves_in_bps_
|
private |
Referenced by allow_fragment_moves_in_bps(), and set_allow_fragment_moves_in_bps().
◆ allowed_bulge_res_
|
private |
Referenced by allowed_bulge_res(), and set_allowed_bulge_res().
◆ autofilter_
|
private |
Referenced by autofilter(), and set_autofilter().
◆ autofilter_score_quantile_
|
private |
Referenced by autofilter_score_quantile(), and set_autofilter_score_quantile().
◆ bps_moves_
|
private |
Referenced by bps_moves(), and set_bps_moves().
◆ center_jumps_in_single_stranded_
|
private |
Referenced by center_jumps_in_single_stranded(), and set_center_jumps_in_single_stranded().
◆ chainbreak_weight_
|
private |
Referenced by chainbreak_weight(), and set_chainbreak_weight().
◆ chunk_initialization_pdb_files_
|
private |
Referenced by chunk_initialization_pdb_files(), and set_chunk_initialization_pdb_files().
◆ chunk_pdb_files_
|
private |
Referenced by chunk_pdb_files(), and set_chunk_pdb_files().
◆ chunk_silent_files_
|
private |
Referenced by chunk_silent_files(), and set_chunk_silent_files().
◆ close_loops_
|
private |
Referenced by close_loops(), and set_close_loops().
◆ close_loops_after_each_move_
|
private |
Referenced by close_loops_after_each_move(), and set_close_loops_after_each_move().
◆ convert_protein_centroid_
|
private |
Referenced by convert_protein_centroid(), and set_convert_protein_centroid().
◆ disallow_bps_at_extra_min_res_
|
private |
Referenced by disallow_bps_at_extra_min_res(), and set_disallow_bps_at_extra_min_res().
◆ disallow_realign_
|
private |
Referenced by disallow_realign(), and set_disallow_realign().
◆ dock_chunks_
|
private |
Referenced by dock_chunks(), and set_dock_chunks().
◆ dock_chunks_res_
|
private |
Referenced by dock_chunks_res(), and set_dock_chunks_res().
◆ dock_each_chunk_
|
private |
Referenced by dock_each_chunk(), and set_dock_each_chunk().
◆ dock_each_chunk_per_chain_
|
private |
Referenced by dock_each_chunk_per_chain(), and set_dock_each_chunk_per_chain().
◆ dock_into_density_legacy_
|
private |
Referenced by dock_into_density_legacy(), and set_dock_into_density_legacy().
◆ docking_
|
private |
Referenced by docking(), and set_docking().
◆ docking_move_size_
|
private |
Referenced by docking_move_size(), and set_docking_move_size().
◆ exhaustive_fragment_insertion_
|
private |
Referenced by exhaustive_fragment_insertion(), and set_exhaustive_fragment_insertion().
◆ filter_chain_closure_
|
private |
Referenced by filter_chain_closure(), and set_filter_chain_closure().
◆ filter_chain_closure_distance_
|
private |
Referenced by filter_chain_closure_distance(), and set_filter_chain_closure_distance().
◆ filter_chain_closure_halfway_
|
private |
Referenced by filter_chain_closure_halfway(), and set_filter_chain_closure_halfway().
◆ filter_lores_base_pairs_
|
private |
Referenced by filter_lores_base_pairs(), and set_filter_lores_base_pairs().
◆ filter_lores_base_pairs_early_
|
private |
Referenced by filter_lores_base_pairs_early(), and set_filter_lores_base_pairs_early().
◆ filter_vdw_
|
private |
Referenced by filter_vdw(), and set_filter_vdw().
◆ fixed_stems_
|
private |
Referenced by fixed_stems(), and set_fixed_stems().
◆ frag_size_
|
private |
Referenced by frag_size(), and set_frag_size().
◆ ft_close_chains_
|
private |
Referenced by ft_close_chains(), and set_ft_close_chains().
◆ gradual_constraints_
|
private |
Referenced by gradual_constraints(), and set_gradual_constraints().
◆ grid_vdw_weight_
|
private |
Referenced by grid_vdw_weight(), and set_grid_vdw_weight().
◆ helical_substruct_res_
|
private |
Referenced by helical_substruct_res(), and set_helical_substruct_res().
◆ helical_substructs_
|
private |
Referenced by helical_substructs(), and set_helical_substructs().
◆ ignore_secstruct_
|
private |
Referenced by ignore_secstruct(), and set_ignore_secstruct().
◆ initial_structures_provided_
|
private |
Referenced by initial_structures_provided(), and set_initial_structures_provided().
◆ input_res_
|
private |
Referenced by input_res(), and set_input_res().
◆ input_res_initialize_
|
private |
Referenced by input_res_initialize(), and set_input_res_initialize().
◆ jump_change_frequency_
|
private |
Referenced by jump_change_frequency(), and set_jump_change_frequency().
◆ jump_histogram_binwidth_
|
private |
Referenced by jump_histogram_binwidth(), and set_jump_histogram_binwidth().
◆ jump_histogram_binwidth_rotvector_
|
private |
Referenced by jump_histogram_binwidth_rotvector(), and set_jump_histogram_binwidth_rotvector().
◆ jump_histogram_boxsize_
|
private |
Referenced by jump_histogram_boxsize(), and set_jump_histogram_boxsize().
◆ jump_library_file_
|
private |
Referenced by jump_library_file(), and set_jump_library_file().
◆ linear_chainbreak_weight_
|
private |
Referenced by linear_chainbreak_weight(), and set_linear_chainbreak_weight().
◆ minimize_structure_
|
private |
Referenced by minimize_structure(), and set_minimize_structure().
◆ monte_carlo_cycles_
|
private |
Referenced by monte_carlo_cycles(), and set_monte_carlo_cycles().
◆ new_fold_tree_initializer_
|
private |
Referenced by new_fold_tree_initializer(), and set_new_fold_tree_initializer().
◆ output_filters_
|
private |
Referenced by output_filters(), and set_output_filters().
◆ output_histogram_file_
|
private |
Referenced by output_histogram_file(), and set_output_histogram_file().
◆ output_jump_chainbreak_
|
private |
Referenced by output_jump_chainbreak(), and set_output_jump_chainbreak().
◆ output_jump_o3p_to_o5p_
|
private |
Referenced by output_jump_o3p_to_o5p(), and set_output_jump_o3p_to_o5p().
◆ output_jump_reference_RT_string_
|
private |
Referenced by output_jump_reference_RT_string(), and set_output_jump_reference_RT_string().
◆ output_jump_res_
|
private |
Referenced by output_jump_res(), and set_output_jump_res().
◆ output_jump_target_xyz_
|
private |
Referenced by output_jump_target_xyz(), and set_output_jump_target_xyz().
◆ output_lores_silent_file_
|
private |
Referenced by output_lores_silent_file(), and set_output_lores_silent_file().
◆ output_rotation_vector_
|
private |
Referenced by output_rotation_vector(), and set_output_rotation_vector().
◆ output_score_file_
|
private |
Referenced by output_score_file(), and set_output_score_file().
◆ output_score_frequency_
|
private |
Referenced by output_score_frequency(), and set_output_score_frequency().
◆ override_refine_pose_rounds_
|
private |
Referenced by override_refine_pose_rounds(), and set_override_refine_pose_rounds().
◆ ramp_rnp_vdw_
|
private |
Referenced by ramp_rnp_vdw(), and set_ramp_rnp_vdw().
◆ randomize_init_rnp_
|
private |
Referenced by randomize_init_rnp(), and set_randomize_init_rnp().
◆ refine_native_get_good_FT_
|
private |
Referenced by refine_native_get_good_FT(), and set_refine_native_get_good_FT().
◆ refine_pose_
|
private |
Referenced by refine_pose(), and set_refine_pose().
◆ relax_structure_
|
private |
Referenced by relax_structure(), and set_relax_structure().
◆ rmsd_screen_
|
private |
Referenced by rmsd_screen(), and set_rmsd_screen().
◆ rna_protein_docking_
|
private |
Referenced by rna_protein_docking(), and set_rna_protein_docking().
◆ rna_protein_docking_freq_
|
private |
Referenced by rna_protein_docking_freq(), and set_rna_protein_docking_freq().
◆ rna_protein_docking_legacy_
|
private |
Referenced by rna_protein_docking_legacy(), and set_rna_protein_docking_legacy().
◆ rnp_high_res_cycles_
|
private |
Referenced by rnp_high_res_cycles(), and set_rnp_high_res_cycles().
◆ rnp_high_res_relax_
|
private |
Referenced by rnp_high_res_relax(), and set_rnp_high_res_relax().
◆ rnp_min_first_
|
private |
Referenced by rnp_min_first(), and set_rnp_min_first().
◆ rnp_pack_first_
|
private |
Referenced by rnp_pack_first(), and set_rnp_pack_first().
◆ rnp_ramp_rep_
|
private |
Referenced by rnp_ramp_rep(), and set_rnp_ramp_rep().
◆ root_at_first_rigid_body_
|
private |
Referenced by root_at_first_rigid_body(), and set_root_at_first_rigid_body().
◆ rounds_
|
private |
Referenced by rounds(), and set_rounds().
◆ save_jump_histogram_
|
private |
Referenced by save_jump_histogram(), and set_save_jump_histogram().
◆ save_times_
|
private |
Referenced by save_times(), and set_save_times().
◆ simple_rmsd_cutoff_relax_
|
private |
Referenced by set_simple_rmsd_cutoff_relax(), and simple_rmsd_cutoff_relax().
◆ small_docking_moves_
|
private |
Referenced by set_small_docking_moves(), and small_docking_moves().
◆ staged_constraints_
|
private |
Referenced by set_staged_constraints(), and staged_constraints().
◆ superimpose_over_all_
|
private |
Referenced by set_superimpose_over_all(), and superimpose_over_all().
◆ suppress_bp_constraint_
|
private |
Referenced by set_suppress_bp_constraint(), and suppress_bp_constraint().
◆ symm_hack_arity_
|
private |
Referenced by set_symm_hack_arity(), and symm_hack_arity().
◆ temperature_
|
private |
Referenced by set_temperature(), and temperature().
◆ titrate_stack_bonus_
|
private |
Referenced by set_titrate_stack_bonus(), and titrate_stack_bonus().
◆ use_chem_shift_data_
|
private |
Referenced by set_use_chem_shift_data(), and use_chem_shift_data().
◆ user_defined_cycles_
|
private |
Referenced by set_user_defined_cycles(), and user_defined_cycles().
◆ vdw_rep_screen_include_sidechains_
|
private |
Referenced by set_vdw_rep_screen_include_sidechains(), and vdw_rep_screen_include_sidechains().
◆ VDW_rep_screen_info_
|
private |
Referenced by set_VDW_rep_screen_info(), and VDW_rep_screen_info().
The documentation for this class was generated from the following files:
- src/core/import_pose/options/RNA_FragmentMonteCarloOptions.hh
- src/core/import_pose/options/RNA_FragmentMonteCarloOptions.cc
