#include <StepWiseModelerOptions.hh>

Inheritance diagram for protocols::stepwise::modeler::options::StepWiseModelerOptions:

Public Member Functions
	StepWiseModelerOptions ()

StepWiseModelerOptionsOP	clone () const
	clone the options More...

void	show (std::ostream &) const override
	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...

void	initialize_from_command_line ()

void	setup_options_for_VDW_bin_checker (rna::checker::RNA_VDW_BinCheckerOP user_input_VDW_bin_checker) const

StepWiseModelerOptionsOP	get_sampler_options () const

Public Member Functions inherited from protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
	StepWiseBasicModelerOptions ()

StepWiseBasicModelerOptionsOP	clone () const
	clone the options More...

bool	use_green_packer () const

void	set_use_green_packer (bool const &setting)

bool	verbose () const

void	set_verbose (bool const &setting)

bool	choose_random () const

void	set_choose_random (bool const &setting)

void	set_dump (bool const &setting)

bool	dump () const

void	set_skip_minimize (bool const &setting)

bool	skip_minimize () const

bool	disallow_realign () const

void	set_disallow_realign (bool const setting)

bool	coordinate_constraints_during_minimize () const

void	set_coordinate_constraints_during_minimize (bool const setting)

bool	virtualize_packable_moieties_in_screening_pose () const

void	set_virtualize_packable_moieties_in_screening_pose (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::modeler::options::StepWiseProteinModelerOptions
	StepWiseProteinModelerOptions ()

StepWiseProteinModelerOptionsOP	clone () const
	clone the options More...

void	initialize_from_command_line ()

void	set_global_optimize (bool const &setting)

bool	global_optimize () const

void	set_sample_beta (bool const &setting)

bool	sample_beta () const

void	set_move_jumps_between_chains (bool const &setting)

bool	move_jumps_between_chains () const

void	set_disable_sampling_of_loop_takeoff (bool const &setting)

bool	disable_sampling_of_loop_takeoff () const

void	set_cart_min (bool const &setting)

bool	cart_min () const

void	set_n_sample (core::Size const &setting)

core::Size	n_sample () const

void	set_filter_native_big_bins (bool const &setting)

bool	filter_native_big_bins () const

void	set_allow_virtual_side_chains (bool const &setting)

bool	allow_virtual_side_chains () const

void	set_prepack (bool const &setting)

bool	prepack () const

void	set_pack_protein_side_chains (bool const &setting)

bool	pack_protein_side_chains () const

void	set_centroid_output (bool const &setting)

bool	centroid_output () const

void	set_centroid_screen (bool const &setting)

bool	centroid_screen () const

void	set_centroid_score_diff_cut (core::Real const &setting)

core::Real	centroid_score_diff_cut () const

void	set_centroid_weights (std::string const &setting)

std::string	centroid_weights () const

void	set_nstruct_centroid (core::Size const &setting)

core::Size	nstruct_centroid () const

void	set_ghost_loops (bool const &setting)

bool	ghost_loops () const

void	set_ccd_close (bool const &setting)

bool	ccd_close () const

void	set_cluster_by_all_atom_rmsd (bool const &setting)

bool	cluster_by_all_atom_rmsd () const

void	set_pack_weights (std::string const &setting)

std::string	pack_weights () const

bool const &	expand_loop_takeoff () const

void	set_expand_loop_takeoff (bool const &setting)

bool const &	skip_coord_constraints () const

void	set_skip_coord_constraints (bool const &setting)

void	set_frag_files (utility::vector1< std::string > const &setting)

utility::vector1< std::string >	frag_files () const

void	set_bridge_res (utility::vector1< core::Size > const &setting)

utility::vector1< core::Size >	bridge_res () const

Public Member Functions inherited from protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
	StepWiseRNA_ModelerOptions ()

StepWiseRNA_ModelerOptionsOP	clone () const
	clone the options More...

void	initialize_from_command_line ()

core::Real const &	native_edensity_score_cutoff () const

void	set_native_edensity_score_cutoff (core::Real const &setting)

bool const &	o2prime_legacy_mode () const

void	set_o2prime_legacy_mode (bool const &setting)

bool const &	allow_virtual_o2prime_hydrogens () const

void	set_allow_virtual_o2prime_hydrogens (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 &	distinguish_pucker () const

void	set_distinguish_pucker (bool const &setting)

bool const &	finer_sampling_at_chain_closure () const

void	set_finer_sampling_at_chain_closure (bool const &setting)

bool const &	PBP_clustering_at_chain_closure () const

void	set_PBP_clustering_at_chain_closure (bool const &setting)

bool const &	allow_syn_pyrimidine () const

void	set_allow_syn_pyrimidine (bool const &setting)

bool const &	extra_chi () const

void	set_extra_chi (bool const &setting)

void	set_sample_all_chi (bool const &setting)

bool	sample_all_chi () const

bool const &	use_phenix_geo () const

void	set_use_phenix_geo (bool const &setting)

bool const &	virtual_sugar_legacy_mode () const

void	set_virtual_sugar_legacy_mode (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 &	virtual_sugar_do_screens () const

void	set_virtual_sugar_do_screens (bool const &setting)

bool const &	kic_modeler_if_relevant () const

void	set_kic_modeler_if_relevant (bool const &setting)

bool const &	force_centroid_interaction () const

void	set_force_centroid_interaction (bool const &setting)

bool const &	minimize_and_score_sugar () const

void	set_minimize_and_score_sugar (bool const &setting)

bool const &	minimize_and_score_native_pose () const

void	set_minimize_and_score_native_pose (bool const &setting)

bool const &	rm_virt_phosphate () const

void	set_rm_virt_phosphate (bool const &setting)

core::Real const &	VDW_rep_alignment_RMSD_CUTOFF () const

void	set_VDW_rep_alignment_RMSD_CUTOFF (core::Real const &setting)

core::Real const &	sampler_max_centroid_distance () const

void	set_sampler_max_centroid_distance (core::Real const &setting)

utility::vector1< std::string > const &	VDW_rep_delete_matching_res () const

void	set_VDW_rep_delete_matching_res (utility::vector1< std::string > const &setting)

bool const &	VDW_rep_screen_physical_pose_clash_dist_cutoff () const

void	set_VDW_rep_screen_physical_pose_clash_dist_cutoff (bool const &setting)

bool const &	integration_test_mode () const

void	set_integration_test_mode (bool const &setting)

bool const &	allow_bulge_at_chainbreak () const

void	set_allow_bulge_at_chainbreak (bool const &setting)

bool const &	parin_favorite_output () const

void	set_parin_favorite_output (bool const &setting)

bool const &	reinitialize_CCD_torsions () const

void	set_reinitialize_CCD_torsions (bool const &setting)

bool const &	sampler_extra_epsilon_rotamer () const

void	set_sampler_extra_epsilon_rotamer (bool const &setting)

bool const &	sampler_extra_beta_rotamer () const

void	set_sampler_extra_beta_rotamer (bool const &setting)

bool const &	sampler_include_torsion_value_in_tag () const

void	set_sampler_include_torsion_value_in_tag (bool const &setting)

bool const &	combine_long_loop_mode () const

void	set_combine_long_loop_mode (bool const &setting)

bool const &	do_not_sample_multiple_virtual_sugar () const

void	set_do_not_sample_multiple_virtual_sugar (bool const &setting)

bool const &	sample_ONLY_multiple_virtual_sugar () const

void	set_sample_ONLY_multiple_virtual_sugar (bool const &setting)

bool const &	sampler_assert_no_virt_sugar_sampling () const

void	set_sampler_assert_no_virt_sugar_sampling (bool const &setting)

bool const &	sampler_try_sugar_instantiation () const

void	set_sampler_try_sugar_instantiation (bool const &setting)

bool const &	allow_base_pair_only_centroid_screen () const

void	set_allow_base_pair_only_centroid_screen (bool const &setting)

bool const &	minimizer_rename_tag () const

void	set_minimizer_rename_tag (bool const &setting)

bool const &	tether_jump () const

void	set_tether_jump (bool const &setting)

bool const &	turn_off_rna_chem_map_during_optimize () const

void	set_turn_off_rna_chem_map_during_optimize (bool const &setting)

bool const &	rna_legacy_output_mode () const

void	set_rna_legacy_output_mode (bool const &setting)

bool const &	allow_rebuild_bulge_mode () const

void	set_allow_rebuild_bulge_mode (bool const &setting)

Private Member Functions
void	initialize_variables ()

Additional Inherited Members
Static Public Member Functions inherited from protocols::stepwise::options::StepWiseBasicOptions
static void	list_options_read (utility::options::OptionKeyList &opt)

Protected Member Functions inherited from protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
void	initialize_from_command_line ()

void	initialize_variables ()

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 ()

Protected Member Functions inherited from protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
void	initialize_variables ()

Protected Member Functions inherited from protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
void	initialize_variables ()

Protected Attributes inherited from protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
bool	use_green_packer_

bool	verbose_

bool	choose_random_

bool	dump_

bool	skip_minimize_

bool	disallow_realign_

bool	coordinate_constraints_during_minimize_

bool	virtualize_packable_moieties_in_screening_pose_

Constructor & Destructor Documentation

protocols::stepwise::modeler::options::StepWiseModelerOptions::StepWiseModelerOptions ( )

Member Function Documentation

StepWiseModelerOptionsOP protocols::stepwise::modeler::options::StepWiseModelerOptions::clone ( ) const

clone the options

StepWiseModelerOptionsOP protocols::stepwise::modeler::options::StepWiseModelerOptions::get_sampler_options ( ) const

void protocols::stepwise::modeler::options::StepWiseModelerOptions::initialize_from_command_line ( )

void protocols::stepwise::modeler::options::StepWiseModelerOptions::initialize_variables ( )

private

void protocols::stepwise::modeler::options::StepWiseModelerOptions::parse_my_tag ( utility::tag::TagCOP )

inlineoverridevirtual

Initialize from the recursive "tag" structure.

Reimplemented from protocols::stepwise::modeler::options::StepWiseBasicModelerOptions.

void protocols::stepwise::modeler::options::StepWiseModelerOptions::setup_options_for_VDW_bin_checker ( rna::checker::RNA_VDW_BinCheckerOP user_input_VDW_bin_checker ) const

void protocols::stepwise::modeler::options::StepWiseModelerOptions::show ( std::ostream & ) const

inlineoverridevirtual

Describe this instance to a given output stream.

Reimplemented from protocols::stepwise::modeler::options::StepWiseProteinModelerOptions.

std::string protocols::stepwise::modeler::options::StepWiseModelerOptions::type ( ) const

inlineoverridevirtual

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

Reimplemented from protocols::stepwise::modeler::options::StepWiseBasicModelerOptions.

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

src/protocols/stepwise/modeler/options/StepWiseModelerOptions.hh
src/protocols/stepwise/modeler/options/StepWiseModelerOptions.cc

Public Member Functions

Private Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation