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protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions Class Reference

#include <StepWiseMonteCarloOptions.hh>

Inheritance diagram for protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions:
Inheritance graph
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Public Member Functions

 StepWiseMonteCarloOptions ()
 
virtual void show (std::ostream &) const
 Describe this instance to a given output stream. More...
 
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...
 
StepWiseMonteCarloOptionsOP clone () const
 clone the options More...
 
void initialize_from_command_line ()
 
void initialize_from_options_collection (utility::options::OptionCollection const &options)
 
protocols::stepwise::modeler::options::StepWiseModelerOptionsOP setup_modeler_options () const
 
bool const & verbose_scores () const
 
void set_verbose_scores (bool const &setting)
 
bool const & integration_test_mode () const
 
void set_integration_test_mode (bool const &setting)
 
bool const & force_centroid_interaction () const
 
void set_force_centroid_interaction (bool const &setting)
 
core::Real const & sampler_max_centroid_distance () const
 
void set_sampler_max_centroid_distance (core::Real const &setting)
 
bool const & use_phenix_geo () const
 
void set_use_phenix_geo (bool const &setting)
 
bool const & skip_deletions () const
 
void set_skip_deletions (bool const &setting)
 
bool const & erraser () const
 
void set_erraser (bool const &setting)
 
core::Size const & cycles () const
 
void set_cycles (core::Size const &setting)
 
core::Real const & add_proposal_density_factor () const
 
void set_add_proposal_density_factor (core::Real const &setting)
 
core::Real const & minimize_single_res_frequency () const
 
void set_minimize_single_res_frequency (core::Real const &setting)
 
core::Real const & just_min_after_mutation_frequency () const
 
void set_just_min_after_mutation_frequency (core::Real const &setting)
 
core::Real const & temperature () const
 
void set_temperature (core::Real const &setting)
 
core::Real const & max_missing_weight () const
 
void set_max_missing_weight (core::Real const &setting)
 
core::Real const & chainbreak_weight () const
 
void set_chainbreak_weight (core::Real const &setting)
 
bool const & allow_split_off () const
 
void set_allow_split_off (bool const &setting)
 
bool const & virtual_sugar_keep_base_fixed () const
 
void set_virtual_sugar_keep_base_fixed (bool const &setting)
 
bool const & virtual_sugar_do_minimize () const
 
void set_virtual_sugar_do_minimize (bool const &setting)
 
bool const & make_movie () const
 
void set_make_movie (bool const &setting)
 
bool const & sampler_perform_phosphate_pack () const
 
void set_sampler_perform_phosphate_pack (bool const &setting)
 
bool const & force_phosphate_instantiation () const
 
void set_force_phosphate_instantiation (bool const &setting)
 
bool const & virtualize_packable_moieties_in_screening_pose () const
 
void set_virtualize_packable_moieties_in_screening_pose (bool const &setting)
 
bool const & rebuild_bulge_mode () const
 
void set_rebuild_bulge_mode (bool const &setting)
 
bool const & tether_jump () const
 
void set_tether_jump (bool const &setting)
 
bool const & local_redock_only () const
 
void set_local_redock_only (bool const &setting)
 
bool const & skip_coord_constraints () const
 
void set_skip_coord_constraints (bool const &setting)
 
bool const & filter_native_big_bins () const
 
void set_filter_native_big_bins (bool const &setting)
 
bool const & allow_virtual_o2prime_hydrogens () const
 
void set_allow_virtual_o2prime_hydrogens (bool const &setting)
 
bool const & allow_virtual_side_chains () const
 
void set_allow_virtual_side_chains (bool const &setting)
 
core::Size const & n_sample () const
 
void set_n_sample (core::Size const &setting)
 
bool const & protein_prepack () const
 
void set_protein_prepack (bool const &setting)
 
bool const & o2prime_legacy_mode () const
 
void set_o2prime_legacy_mode (bool const &setting)
 
bool const & recover_low () const
 
void set_recover_low (bool const &setting)
 
bool const & enumerate () const
 
void set_enumerate (bool const &setting)
 
bool const & preminimize () const
 
void set_preminimize (bool const &setting)
 
bool const & skip_preminimize () const
 
void set_skip_preminimize (bool const &setting)
 
bool const & new_move_selector () const
 
void set_new_move_selector (bool const &setting)
 
bool const & test_all_moves () const
 
void set_test_all_moves (bool const &setting)
 
bool const & save_times () const
 
void set_save_times (bool const &setting)
 
bool const & use_precomputed_library () const
 
void set_use_precomputed_library (bool const &setting)
 
bool const & minimize_after_delete () const
 
void set_minimize_after_delete (bool const &setting)
 
bool const & use_first_jump_for_submotif () const
 
void set_use_first_jump_for_submotif (bool const &setting)
 
void set_exclude_submotifs (utility::vector1< std::string > const &setting)
 
utility::vector1< std::string > exclude_submotifs () const
 
bool designing_with_noncanonicals () const
 
void set_designing_with_noncanonicals (bool const &setting)
 
bool checkpoint () const
 
void set_checkpoint (bool const setting)
 
core::Size checkpointing_frequency () const
 
void set_checkpointing_frequency (core::Size const setting)
 
bool continue_until_none_missing () const
 
void set_continue_until_none_missing (bool const setting)
 
bool eval_base_pairs () const
 
void set_eval_base_pairs (bool const setting)
 
bool superimpose_over_all () const
 
void set_superimpose_over_all (bool const setting)
 
bool force_moving_res_for_erraser () const
 
void set_force_moving_res_for_erraser (bool const setting)
 
bool const & pack_protein_side_chains () const
 
void set_pack_protein_side_chains (bool const &setting)
 
- Public Member Functions inherited from protocols::stepwise::options::StepWiseBasicOptions
 StepWiseBasicOptions ()
 
StepWiseBasicOptionsOP clone () const
 clone the options More...
 
std::string const & silent_file () const
 
void set_silent_file (std::string const &setting)
 
std::string const & sampler_silent_file () const
 
void set_sampler_silent_file (std::string const &setting)
 
core::Size sampler_num_pose_kept () const
 
void set_sampler_num_pose_kept (core::Size const &setting)
 
core::Real cluster_rmsd () const
 
void set_cluster_rmsd (core::Real const &setting)
 
core::Size num_pose_minimize () const
 
void set_num_pose_minimize (core::Size const &setting)
 
core::Size num_random_samples () const
 
void set_num_random_samples (core::Size const &setting)
 
core::Size max_tries_multiplier_for_ccd () const
 
void set_max_tries_multiplier_for_ccd (core::Size const &setting)
 
void set_atr_rep_screen (bool const &setting)
 
bool atr_rep_screen () const
 
void set_atr_rep_screen_for_docking (bool const &setting)
 
bool atr_rep_screen_for_docking () const
 
utility::vector1< std::string >
const & 
VDW_rep_screen_info () const
 
void set_VDW_rep_screen_info (utility::vector1< std::string > const &setting)
 
void set_rmsd_screen (core::Real const &setting)
 
core::Real rmsd_screen () const
 
bool output_minimized_pose_list () const
 
void set_output_minimized_pose_list (bool const &setting)
 
bool output_cluster_size () const
 
void set_output_cluster_size (bool const &setting)
 
void set_min_type (std::string const &setting)
 
std::string min_type () const
 
void set_min_tolerance (core::Real const &setting)
 
core::Real min_tolerance () const
 
bool vary_rna_bond_geometry () const
 
void set_vary_rna_bond_geometry (bool const &setting)
 
bool vary_polar_hydrogen_geometry () const
 
void set_vary_polar_hydrogen_geometry (bool const &setting)
 
void set_disallow_pack_polar_hydrogens (bool const &setting)
 
bool disallow_pack_polar_hydrogens () const
 
void set_use_packer_instead_of_rotamer_trials (bool const &setting)
 
bool use_packer_instead_of_rotamer_trials () const
 
bool mapfile_activated () const
 
void set_mapfile_activated (bool const &setting)
 
void set_lores (bool const &setting)
 
bool lores () const
 
void set_verbose_sampler (bool const &setting)
 
bool verbose_sampler () const
 
void set_minimize_waters (bool const &setting)
 
bool minimize_waters () const
 
void set_hydrate_magnesiums (bool const &setting)
 
bool hydrate_magnesiums () const
 
void set_test_all_mg_hydration_frames (bool const &setting)
 
bool test_all_mg_hydration_frames () const
 
modeler::MinimizerMode const & minimizer_mode () const
 
void set_minimizer_mode (modeler::MinimizerMode const &setting)
 
core::Size n_cycles () const
 
void set_n_cycles (core::Size const setting)
 
core::Real thermal_sampler_temperature () const
 
void set_thermal_sampler_output_min_pose (bool const setting)
 
bool thermal_sampler_output_min_pose () const
 
void set_sample_pH (bool const setting)
 
bool sample_pH () const
 
bool boltzmann_choice_post_enumerated_minimize () const
 
void set_boltzmann_choice_post_enumerated_minimize (bool const setting)
 
- Public Member Functions inherited from protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
 StepWiseMoveSelectorOptions ()
 
StepWiseMoveSelectorOptionsOP clone () const
 clone the options More...
 
void initialize_from_command_line ()
 
void initialize_from_options_collection (utility::options::OptionCollection const &options)
 
void set_allow_internal_hinge_moves (bool const &setting)
 
bool allow_internal_hinge_moves () const
 
void set_allow_internal_local_moves (bool const &setting)
 
bool allow_internal_local_moves () const
 
void set_add_delete_frequency (core::Real const &setting)
 
core::Real add_delete_frequency () const
 
void set_from_scratch_frequency (core::Real const &setting)
 
core::Real from_scratch_frequency () const
 
void set_docking_frequency (core::Real const &setting)
 
core::Real docking_frequency () const
 
void set_submotif_frequency (core::Real const &setting)
 
core::Real submotif_frequency () const
 
void set_switch_focus_frequency (core::Real const &setting)
 
core::Real switch_focus_frequency () const
 
bool const & skip_deletions () const
 
void set_skip_deletions (bool const &setting)
 
void set_skip_bulge_frequency (core::Real const &setting)
 
core::Real skip_bulge_frequency () const
 
void set_vary_loop_length_frequency (core::Real const &setting)
 
core::Real vary_loop_length_frequency () const
 
void set_allow_submotif_split (bool const &setting)
 
bool allow_submotif_split () const
 
void set_force_submotif_without_intervening_bulge (bool const &setting)
 
bool force_submotif_without_intervening_bulge () const
 
void set_filter_complex_cycles (bool const &setting)
 
bool filter_complex_cycles () const
 

Static Public Member Functions

static void list_options_read (utility::options::OptionKeyList &opts)
 
- Static Public Member Functions inherited from protocols::stepwise::options::StepWiseBasicOptions
static void list_options_read (utility::options::OptionKeyList &opt)
 
- Static Public Member Functions inherited from protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
static void list_options_read (utility::options::OptionKeyList &opts)
 

Private Attributes

bool verbose_scores_
 
bool integration_test_mode_
 
bool force_centroid_interaction_
 
core::Real sampler_max_centroid_distance_
 
bool use_phenix_geo_
 
bool skip_deletions_
 
bool erraser_
 
core::Size cycles_
 
core::Real add_proposal_density_factor_
 
core::Real minimize_single_res_frequency_
 
core::Real just_min_after_mutation_frequency_
 
core::Real temperature_
 
core::Real max_missing_weight_
 
core::Real chainbreak_weight_
 
bool allow_split_off_
 
bool virtual_sugar_keep_base_fixed_
 
bool virtual_sugar_do_minimize_
 
bool make_movie_
 
bool sampler_perform_phosphate_pack_
 
bool force_phosphate_instantiation_
 
bool virtualize_packable_moieties_in_screening_pose_
 
bool rebuild_bulge_mode_
 
bool tether_jump_
 
bool local_redock_only_
 
bool skip_coord_constraints_
 
bool filter_native_big_bins_
 
bool allow_virtual_o2prime_hydrogens_
 
bool allow_virtual_side_chains_
 
core::Size n_sample_
 
bool protein_prepack_
 
bool o2prime_legacy_mode_
 
bool recover_low_
 
bool enumerate_
 
bool preminimize_
 
bool skip_preminimize_
 
bool new_move_selector_
 
bool test_all_moves_
 
bool save_times_
 
bool use_precomputed_library_
 
bool minimize_after_delete_
 
bool force_submotif_without_intervening_bulge_
 
bool pack_protein_side_chains_
 
bool use_first_jump_for_submotif_
 
utility::vector1< std::string > exclude_submotifs_
 
bool designing_with_noncanonicals_
 
bool checkpoint_
 
core::Size checkpointing_frequency_
 
bool continue_until_none_missing_
 
bool eval_base_pairs_
 
bool superimpose_over_all_
 
bool force_moving_res_for_erraser_ = false
 

Additional Inherited Members

- Protected Member Functions inherited from protocols::stepwise::options::StepWiseBasicOptions
void initialize_from_command_line ()
 
void initialize_from_options_collection (utility::options::OptionCollection const &options)
 
void initialize_variables ()
 

Constructor & Destructor Documentation

protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::StepWiseMonteCarloOptions ( )

Member Function Documentation

core::Real const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::add_proposal_density_factor ( ) const
inline
bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::allow_split_off ( ) const
inline

References allow_split_off_.

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::allow_virtual_o2prime_hydrogens ( ) const
inline
bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::allow_virtual_side_chains ( ) const
inline
core::Real const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::chainbreak_weight ( ) const
inline

References chainbreak_weight_.

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::checkpoint ( ) const
inline

References checkpoint_.

core::Size protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::checkpointing_frequency ( ) const
inline
StepWiseMonteCarloOptionsOP protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::clone ( ) const

clone the options

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::continue_until_none_missing ( ) const
inline
core::Size const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::cycles ( ) const
inline

References cycles_.

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::designing_with_noncanonicals ( ) const
inline
bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::enumerate ( ) const
inline

References enumerate_.

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::erraser ( ) const
inline

References erraser_.

Referenced by setup_modeler_options().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::eval_base_pairs ( ) const
inline

References eval_base_pairs_.

utility::vector1< std::string > protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::exclude_submotifs ( ) const
inline

References exclude_submotifs_.

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::filter_native_big_bins ( ) const
inline
bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::force_centroid_interaction ( ) const
inline
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::force_moving_res_for_erraser ( ) const
inline
bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::force_phosphate_instantiation ( ) const
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::initialize_from_command_line ( )
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::initialize_from_options_collection ( utility::options::OptionCollection const &  options)

References allow_virtual_o2prime_hydrogens_, allow_virtual_side_chains_, checkpoint_, checkpointing_frequency_, continue_until_none_missing_, designing_with_noncanonicals_, enumerate_, eval_base_pairs_, exclude_submotifs_, filter_native_big_bins_, force_centroid_interaction_, force_moving_res_for_erraser_, force_phosphate_instantiation_, force_submotif_without_intervening_bulge_, local_redock_only_, n_sample_, new_move_selector_, o2prime_legacy_mode_, pack_protein_side_chains_, preminimize_, protein_prepack_, rebuild_bulge_mode_, recover_low_, sampler_max_centroid_distance_, sampler_perform_phosphate_pack_, save_times_, set_add_proposal_density_factor(), set_allow_split_off(), set_cycles(), set_erraser(), set_force_centroid_interaction(), set_integration_test_mode(), set_just_min_after_mutation_frequency(), set_make_movie(), set_minimize_after_delete(), set_minimize_single_res_frequency(), protocols::stepwise::options::StepWiseBasicOptions::set_num_pose_minimize(), protocols::stepwise::options::StepWiseBasicOptions::set_num_random_samples(), protocols::stepwise::options::StepWiseBasicOptions::set_silent_file(), set_temperature(), set_use_phenix_geo(), set_verbose_scores(), set_virtual_sugar_do_minimize(), set_virtual_sugar_keep_base_fixed(), skip_coord_constraints_, skip_preminimize_, superimpose_over_all_, test_all_moves_, tether_jump_, use_first_jump_for_submotif_, use_precomputed_library_, and virtualize_packable_moieties_in_screening_pose_.

Referenced by initialize_from_command_line().

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::integration_test_mode ( ) const
inline

References integration_test_mode_.

Referenced by setup_modeler_options().

core::Real const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::just_min_after_mutation_frequency ( ) const
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::list_options_read ( utility::options::OptionKeyList &  opts)
static
bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::local_redock_only ( ) const
inline

References local_redock_only_.

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::make_movie ( ) const
inline

References make_movie_.

core::Real const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::max_missing_weight ( ) const
inline

References max_missing_weight_.

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::minimize_after_delete ( ) const
inline
core::Real const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::minimize_single_res_frequency ( ) const
inline
core::Size const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::n_sample ( ) const
inline

References n_sample_.

Referenced by setup_modeler_options().

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::new_move_selector ( ) const
inline

References new_move_selector_.

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::o2prime_legacy_mode ( ) const
inline

References o2prime_legacy_mode_.

Referenced by setup_modeler_options().

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::pack_protein_side_chains ( ) const
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::parse_my_tag ( utility::tag::TagCOP  )
inlineoverridevirtual

Initialize from the recursive "tag" structure.

Reimplemented from protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions.

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::preminimize ( ) const
inline

References preminimize_.

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::protein_prepack ( ) const
inline

References protein_prepack_.

Referenced by setup_modeler_options().

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::rebuild_bulge_mode ( ) const
inline

References rebuild_bulge_mode_.

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::recover_low ( ) const
inline

References recover_low_.

core::Real const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::sampler_max_centroid_distance ( ) const
inline
bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::sampler_perform_phosphate_pack ( ) const
inline
bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::save_times ( ) const
inline

References save_times_.

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_add_proposal_density_factor ( core::Real const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_allow_split_off ( bool const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_allow_virtual_o2prime_hydrogens ( bool const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_allow_virtual_side_chains ( bool const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_chainbreak_weight ( core::Real const &  setting)
inline

References chainbreak_weight_.

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_checkpoint ( bool const  setting)
inline

References checkpoint_.

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_checkpointing_frequency ( core::Size const  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_continue_until_none_missing ( bool const  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_cycles ( core::Size const &  setting)
inline

References cycles_.

Referenced by initialize_from_options_collection().

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_designing_with_noncanonicals ( bool const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_enumerate ( bool const &  setting)
inline

References enumerate_.

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_erraser ( bool const &  setting)
inline

References erraser_.

Referenced by initialize_from_options_collection().

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_eval_base_pairs ( bool const  setting)
inline

References eval_base_pairs_.

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_exclude_submotifs ( utility::vector1< std::string > const &  setting)
inline

References exclude_submotifs_.

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_filter_native_big_bins ( bool const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_force_centroid_interaction ( bool const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_force_moving_res_for_erraser ( bool const  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_force_phosphate_instantiation ( bool const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_integration_test_mode ( bool const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_just_min_after_mutation_frequency ( core::Real const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_local_redock_only ( bool const &  setting)
inline

References local_redock_only_.

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_make_movie ( bool const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_max_missing_weight ( core::Real const &  setting)
inline

References max_missing_weight_.

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_minimize_after_delete ( bool const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_minimize_single_res_frequency ( core::Real const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_n_sample ( core::Size const &  setting)
inline

References n_sample_.

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_new_move_selector ( bool const &  setting)
inline

References new_move_selector_.

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_o2prime_legacy_mode ( bool const &  setting)
inline

References o2prime_legacy_mode_.

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_pack_protein_side_chains ( bool const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_preminimize ( bool const &  setting)
inline

References preminimize_.

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_protein_prepack ( bool const &  setting)
inline

References protein_prepack_.

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_rebuild_bulge_mode ( bool const &  setting)
inline

References rebuild_bulge_mode_.

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_recover_low ( bool const &  setting)
inline

References recover_low_.

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_sampler_max_centroid_distance ( core::Real const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_sampler_perform_phosphate_pack ( bool const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_save_times ( bool const &  setting)
inline

References save_times_.

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_skip_coord_constraints ( bool const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_skip_deletions ( bool const &  setting)
inline

References skip_deletions_.

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_skip_preminimize ( bool const &  setting)
inline

References skip_preminimize_.

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_superimpose_over_all ( bool const  setting)
inline

References superimpose_over_all_.

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_temperature ( core::Real const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_test_all_moves ( bool const &  setting)
inline

References test_all_moves_.

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_tether_jump ( bool const &  setting)
inline

References tether_jump_.

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_use_first_jump_for_submotif ( bool const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_use_phenix_geo ( bool const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_use_precomputed_library ( bool const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_verbose_scores ( bool const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_virtual_sugar_do_minimize ( bool const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_virtual_sugar_keep_base_fixed ( bool const &  setting)
inline
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_virtualize_packable_moieties_in_screening_pose ( bool const &  setting)
inline
protocols::stepwise::modeler::options::StepWiseModelerOptionsOP protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::setup_modeler_options ( ) const
virtual void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::show ( std::ostream &  ) const
inlinevirtual

Describe this instance to a given output stream.

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::skip_coord_constraints ( ) const
inline
bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::skip_deletions ( ) const
inline

References skip_deletions_.

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::skip_preminimize ( ) const
inline

References skip_preminimize_.

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::superimpose_over_all ( ) const
inline

References superimpose_over_all_.

core::Real const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::temperature ( ) const
inline

References temperature_.

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::test_all_moves ( ) const
inline

References test_all_moves_.

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::tether_jump ( ) const
inline

References tether_jump_.

Referenced by setup_modeler_options().

std::string protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::type ( ) const
inlineoverridevirtual

The class name (its type) for a particular instance. This function allows for better error message delivery.

Reimplemented from protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions.

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::use_first_jump_for_submotif ( ) const
inline
bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::use_phenix_geo ( ) const
inline

References use_phenix_geo_.

Referenced by setup_modeler_options().

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::use_precomputed_library ( ) const
inline
bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::verbose_scores ( ) const
inline

References verbose_scores_.

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::virtual_sugar_do_minimize ( ) const
inline
bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::virtual_sugar_keep_base_fixed ( ) const
inline
bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::virtualize_packable_moieties_in_screening_pose ( ) const
inline

Member Data Documentation

core::Real protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::add_proposal_density_factor_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::allow_split_off_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::allow_virtual_o2prime_hydrogens_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::allow_virtual_side_chains_
private
core::Real protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::chainbreak_weight_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::checkpoint_
private
core::Size protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::checkpointing_frequency_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::continue_until_none_missing_
private
core::Size protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::cycles_
private

Referenced by cycles(), and set_cycles().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::designing_with_noncanonicals_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::enumerate_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::erraser_
private

Referenced by erraser(), and set_erraser().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::eval_base_pairs_
private
utility::vector1< std::string > protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::exclude_submotifs_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::filter_native_big_bins_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::force_centroid_interaction_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::force_moving_res_for_erraser_ = false
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::force_phosphate_instantiation_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::force_submotif_without_intervening_bulge_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::integration_test_mode_
private
core::Real protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::just_min_after_mutation_frequency_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::local_redock_only_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::make_movie_
private

Referenced by make_movie(), and set_make_movie().

core::Real protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::max_missing_weight_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::minimize_after_delete_
private
core::Real protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::minimize_single_res_frequency_
private
core::Size protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::n_sample_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::new_move_selector_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::o2prime_legacy_mode_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::pack_protein_side_chains_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::preminimize_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::protein_prepack_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::rebuild_bulge_mode_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::recover_low_
private
core::Real protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::sampler_max_centroid_distance_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::sampler_perform_phosphate_pack_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::save_times_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::skip_coord_constraints_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::skip_deletions_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::skip_preminimize_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::superimpose_over_all_
private
core::Real protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::temperature_
private

Referenced by set_temperature(), and temperature().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::test_all_moves_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::tether_jump_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::use_first_jump_for_submotif_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::use_phenix_geo_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::use_precomputed_library_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::verbose_scores_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::virtual_sugar_do_minimize_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::virtual_sugar_keep_base_fixed_
private
bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::virtualize_packable_moieties_in_screening_pose_
private

The documentation for this class was generated from the following files: