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

#include <StepWiseMonteCarloOptions.hh>

Inheritance diagram for protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions:

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

(

)

References protocols::stepwise::options::StepWiseBasicOptions::set_silent_file().

Member Function Documentation

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

inline

References add_proposal_density_factor_.

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

References allow_virtual_o2prime_hydrogens_.

Referenced by setup_modeler_options().

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::allow_virtual_side_chains ( ) const

inline

References allow_virtual_side_chains_.

Referenced by setup_modeler_options().

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

References checkpointing_frequency_.

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

References continue_until_none_missing_.

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

References designing_with_noncanonicals_.

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

References filter_native_big_bins_.

Referenced by setup_modeler_options().

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::force_centroid_interaction ( ) const

inline

References force_centroid_interaction_.

Referenced by setup_modeler_options().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::force_moving_res_for_erraser ( ) const

inline

References force_moving_res_for_erraser_.

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::force_phosphate_instantiation ( ) const

inline

References force_phosphate_instantiation_.

Referenced by setup_modeler_options().

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::initialize_from_command_line

(

)

References initialize_from_options_collection().

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

References just_min_after_mutation_frequency_.

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

References minimize_after_delete_.

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

inline

References minimize_single_res_frequency_.

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

References pack_protein_side_chains_.

Referenced by setup_modeler_options().

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

References sampler_max_centroid_distance_.

Referenced by setup_modeler_options().

bool const& protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::sampler_perform_phosphate_pack ( ) const

inline

References sampler_perform_phosphate_pack_.

Referenced by setup_modeler_options().

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

References add_proposal_density_factor_.

Referenced by initialize_from_options_collection().

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

inline

References allow_split_off_.

Referenced by initialize_from_options_collection().

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_allow_virtual_o2prime_hydrogens ( bool const &  setting )

inline

References allow_virtual_o2prime_hydrogens_.

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

inline

References allow_virtual_side_chains_.

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

References checkpointing_frequency_.

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

inline

References continue_until_none_missing_.

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

References designing_with_noncanonicals_.

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

References filter_native_big_bins_.

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

inline

References force_centroid_interaction_.

Referenced by initialize_from_options_collection().

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

inline

References force_moving_res_for_erraser_.

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

inline

References force_phosphate_instantiation_.

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

inline

References integration_test_mode_.

Referenced by initialize_from_options_collection().

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_just_min_after_mutation_frequency ( core::Real const &  setting )

inline

References just_min_after_mutation_frequency_.

Referenced by initialize_from_options_collection().

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

References make_movie_.

Referenced by initialize_from_options_collection().

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

References minimize_after_delete_.

Referenced by initialize_from_options_collection().

void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::set_minimize_single_res_frequency ( core::Real const &  setting )

inline

References minimize_single_res_frequency_.

Referenced by initialize_from_options_collection().

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

References pack_protein_side_chains_.

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

References sampler_max_centroid_distance_.

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

inline

References sampler_perform_phosphate_pack_.

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

References skip_coord_constraints_.

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

References temperature_.

Referenced by initialize_from_options_collection().

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

References use_first_jump_for_submotif_.

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

inline

References use_phenix_geo_.

Referenced by initialize_from_options_collection().

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

inline

References use_precomputed_library_.

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

inline

References verbose_scores_.

Referenced by initialize_from_options_collection().

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

inline

References virtual_sugar_do_minimize_.

Referenced by initialize_from_options_collection().

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

inline

References virtual_sugar_keep_base_fixed_.

Referenced by initialize_from_options_collection().

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

inline

References virtualize_packable_moieties_in_screening_pose_.

protocols::stepwise::modeler::options::StepWiseModelerOptionsOP protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::setup_modeler_options

(

)

const

References allow_virtual_o2prime_hydrogens(), allow_virtual_side_chains(), protocols::stepwise::options::StepWiseBasicOptions::atr_rep_screen(), enumerate_, erraser(), filter_native_big_bins(), force_centroid_interaction(), force_phosphate_instantiation(), integration_test_mode(), n_sample(), protocols::stepwise::options::StepWiseBasicOptions::num_pose_minimize(), protocols::stepwise::options::StepWiseBasicOptions::num_random_samples(), o2prime_legacy_mode(), pack_protein_side_chains(), preminimize_, protein_prepack(), rebuild_bulge_mode_, protocols::stepwise::options::StepWiseBasicOptions::rmsd_screen(), sampler_max_centroid_distance(), sampler_perform_phosphate_pack(), protocols::stepwise::options::StepWiseBasicOptions::set_num_pose_minimize(), skip_coord_constraints(), tether_jump(), use_phenix_geo(), protocols::stepwise::options::StepWiseBasicOptions::VDW_rep_screen_info(), virtual_sugar_do_minimize(), virtual_sugar_keep_base_fixed(), and virtualize_packable_moieties_in_screening_pose().

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

References skip_coord_constraints_.

Referenced by setup_modeler_options().

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

References use_first_jump_for_submotif_.

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

References use_precomputed_library_.

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

References virtual_sugar_do_minimize_.

Referenced by setup_modeler_options().

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

inline

References virtual_sugar_keep_base_fixed_.

Referenced by setup_modeler_options().

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

inline

References virtualize_packable_moieties_in_screening_pose_.

Referenced by setup_modeler_options().

Member Data Documentation

core::Real protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::add_proposal_density_factor_

private

Referenced by add_proposal_density_factor(), and set_add_proposal_density_factor().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::allow_split_off_

private

Referenced by allow_split_off(), and set_allow_split_off().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::allow_virtual_o2prime_hydrogens_

private

Referenced by allow_virtual_o2prime_hydrogens(), initialize_from_options_collection(), and set_allow_virtual_o2prime_hydrogens().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::allow_virtual_side_chains_

private

Referenced by allow_virtual_side_chains(), initialize_from_options_collection(), and set_allow_virtual_side_chains().

core::Real protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::chainbreak_weight_

private

Referenced by chainbreak_weight(), and set_chainbreak_weight().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::checkpoint_

private

Referenced by checkpoint(), initialize_from_options_collection(), and set_checkpoint().

core::Size protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::checkpointing_frequency_

private

Referenced by checkpointing_frequency(), initialize_from_options_collection(), and set_checkpointing_frequency().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::continue_until_none_missing_

private

Referenced by continue_until_none_missing(), initialize_from_options_collection(), and set_continue_until_none_missing().

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

Referenced by designing_with_noncanonicals(), initialize_from_options_collection(), and set_designing_with_noncanonicals().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::enumerate_

private

Referenced by enumerate(), initialize_from_options_collection(), set_enumerate(), and setup_modeler_options().

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

Referenced by eval_base_pairs(), initialize_from_options_collection(), and set_eval_base_pairs().

utility::vector1< std::string > protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::exclude_submotifs_

private

Referenced by exclude_submotifs(), initialize_from_options_collection(), and set_exclude_submotifs().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::filter_native_big_bins_

private

Referenced by filter_native_big_bins(), initialize_from_options_collection(), and set_filter_native_big_bins().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::force_centroid_interaction_

private

Referenced by force_centroid_interaction(), initialize_from_options_collection(), and set_force_centroid_interaction().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::force_moving_res_for_erraser_ = false

private

Referenced by force_moving_res_for_erraser(), initialize_from_options_collection(), and set_force_moving_res_for_erraser().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::force_phosphate_instantiation_

private

Referenced by force_phosphate_instantiation(), initialize_from_options_collection(), and set_force_phosphate_instantiation().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::force_submotif_without_intervening_bulge_

private

Referenced by initialize_from_options_collection().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::integration_test_mode_

private

Referenced by integration_test_mode(), and set_integration_test_mode().

core::Real protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::just_min_after_mutation_frequency_

private

Referenced by just_min_after_mutation_frequency(), and set_just_min_after_mutation_frequency().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::local_redock_only_

private

Referenced by initialize_from_options_collection(), local_redock_only(), and set_local_redock_only().

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

Referenced by max_missing_weight(), and set_max_missing_weight().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::minimize_after_delete_

private

Referenced by minimize_after_delete(), and set_minimize_after_delete().

core::Real protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::minimize_single_res_frequency_

private

Referenced by minimize_single_res_frequency(), and set_minimize_single_res_frequency().

core::Size protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::n_sample_

private

Referenced by initialize_from_options_collection(), n_sample(), and set_n_sample().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::new_move_selector_

private

Referenced by initialize_from_options_collection(), new_move_selector(), and set_new_move_selector().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::o2prime_legacy_mode_

private

Referenced by initialize_from_options_collection(), o2prime_legacy_mode(), and set_o2prime_legacy_mode().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::pack_protein_side_chains_

private

Referenced by initialize_from_options_collection(), pack_protein_side_chains(), and set_pack_protein_side_chains().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::preminimize_

private

Referenced by initialize_from_options_collection(), preminimize(), set_preminimize(), and setup_modeler_options().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::protein_prepack_

private

Referenced by initialize_from_options_collection(), protein_prepack(), and set_protein_prepack().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::rebuild_bulge_mode_

private

Referenced by initialize_from_options_collection(), rebuild_bulge_mode(), set_rebuild_bulge_mode(), and setup_modeler_options().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::recover_low_

private

Referenced by initialize_from_options_collection(), recover_low(), and set_recover_low().

core::Real protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::sampler_max_centroid_distance_

private

Referenced by initialize_from_options_collection(), sampler_max_centroid_distance(), and set_sampler_max_centroid_distance().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::sampler_perform_phosphate_pack_

private

Referenced by initialize_from_options_collection(), sampler_perform_phosphate_pack(), and set_sampler_perform_phosphate_pack().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::save_times_

private

Referenced by initialize_from_options_collection(), save_times(), and set_save_times().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::skip_coord_constraints_

private

Referenced by initialize_from_options_collection(), set_skip_coord_constraints(), and skip_coord_constraints().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::skip_deletions_

private

Referenced by set_skip_deletions(), and skip_deletions().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::skip_preminimize_

private

Referenced by initialize_from_options_collection(), set_skip_preminimize(), and skip_preminimize().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::superimpose_over_all_

private

Referenced by initialize_from_options_collection(), set_superimpose_over_all(), and superimpose_over_all().

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

Referenced by initialize_from_options_collection(), set_test_all_moves(), and test_all_moves().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::tether_jump_

private

Referenced by initialize_from_options_collection(), set_tether_jump(), and tether_jump().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::use_first_jump_for_submotif_

private

Referenced by initialize_from_options_collection(), set_use_first_jump_for_submotif(), and use_first_jump_for_submotif().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::use_phenix_geo_

private

Referenced by set_use_phenix_geo(), and use_phenix_geo().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::use_precomputed_library_

private

Referenced by initialize_from_options_collection(), set_use_precomputed_library(), and use_precomputed_library().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::verbose_scores_

private

Referenced by set_verbose_scores(), and verbose_scores().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::virtual_sugar_do_minimize_

private

Referenced by set_virtual_sugar_do_minimize(), and virtual_sugar_do_minimize().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::virtual_sugar_keep_base_fixed_

private

Referenced by set_virtual_sugar_keep_base_fixed(), and virtual_sugar_keep_base_fixed().

bool protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::virtualize_packable_moieties_in_screening_pose_

private

Referenced by initialize_from_options_collection(), set_virtualize_packable_moieties_in_screening_pose(), and virtualize_packable_moieties_in_screening_pose().

---

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

• src/protocols/stepwise/monte_carlo/options/StepWiseMonteCarloOptions.hh
• src/protocols/stepwise/monte_carlo/options/StepWiseMonteCarloOptions.cc