protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions Class Reference

#include <StepWiseRNA_ModelerOptions.hh>

Public Member Functions
	StepWiseRNA_ModelerOptions ()
	StepWiseRNA_ModelerOptions (StepWiseRNA_ModelerOptions const &src)
	copy constructor More...
	~StepWiseRNA_ModelerOptions ()
StepWiseRNA_ModelerOptionsOP	clone () const
	clone the options More...
StepWiseRNA_ModelerOptions &	operator= (StepWiseRNA_ModelerOptions const &src)
virtual void	show (std::ostream &) const
	Describe this instance to a given output stream. More...
virtual void	parse_my_tag (utility::tag::TagCOP)
	Initialize from the recursive "tag" structure. More...
virtual std::string	type () const
	The class name (its type) for a particular ResourceOptions instance. This function allows for better error message delivery. More...
void	initialize_from_command_line ()
void	setup_options_for_VDW_bin_checker (checker::RNA_VDW_BinCheckerOP user_input_VDW_bin_checker) const
std::string const &	silent_file () const
void	set_silent_file (std::string const &setting)
core::Size const &	sampler_num_pose_kept () const
void	set_sampler_num_pose_kept (core::Size const &setting)
core::Size const &	num_pose_minimize () const
void	set_num_pose_minimize (core::Size const &setting)
bool const &	sampler_native_rmsd_screen () const
void	set_sampler_native_rmsd_screen (bool const &setting)
core::Real const &	sampler_native_screen_rmsd_cutoff () const
void	set_sampler_native_screen_rmsd_cutoff (core::Real const &setting)
core::Real const &	cluster_rmsd () const
void	set_cluster_rmsd (core::Real const &setting)
core::Real const &	native_edensity_score_cutoff () const
void	set_native_edensity_score_cutoff (core::Real const &setting)
bool const &	sampler_perform_o2prime_pack () const
void	set_sampler_perform_o2prime_pack (bool const &setting)
bool const &	sampler_perform_phosphate_pack () const
void	set_sampler_perform_phosphate_pack (bool const &setting)
bool const &	use_green_packer () const
void	set_use_green_packer (bool const &setting)
bool const &	verbose () const
void	set_verbose (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)
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 &	kic_sampling_if_relevant () const
void	set_kic_sampling_if_relevant (bool const &setting)
bool const &	VDW_atr_rep_screen () const
void	set_VDW_atr_rep_screen (bool const &setting)
bool const &	force_centroid_interaction () const
void	set_force_centroid_interaction (bool const &setting)
bool const &	choose_random () const
void	set_choose_random (bool const &setting)
Size const &	num_random_samples () const
void	set_num_random_samples (Size const &setting)
bool const &	skip_sampling () const
void	set_skip_sampling (bool const &setting)
bool const &	perform_minimize () const
void	set_perform_minimize (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)
bool const &	output_pdb () const
void	set_output_pdb (bool const &setting)
bool const &	output_minimized_pose_list () const
void	set_output_minimized_pose_list (bool 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_perform_o2prime_pack () const
void	set_minimizer_perform_o2prime_pack (bool const &setting)
bool const &	minimizer_output_before_o2prime_pack () const
void	set_minimizer_output_before_o2prime_pack (bool const &setting)
bool const &	minimizer_rename_tag () const
void	set_minimizer_rename_tag (bool const &setting)
bool const &	minimizer_allow_variable_bond_geometry () const
void	set_minimizer_allow_variable_bond_geometry (bool const &setting)
core::Real const &	minimizer_vary_bond_geometry_frequency () const
void	set_minimizer_vary_bond_geometry_frequency (core::Real const &setting)
bool const &	unified_framework () const
void	set_unified_framework (bool const &setting)
bool const &	tether_jump () const
void	set_tether_jump (bool const &setting)

Private Member Functions
void	initialize_variables ()

Private Attributes
std::string	silent_file_
core::Size	sampler_num_pose_kept_
core::Size	num_pose_minimize_
bool	sampler_native_rmsd_screen_
core::Real	sampler_native_screen_rmsd_cutoff_
core::Real	cluster_rmsd_
core::Real	native_edensity_score_cutoff_
bool	sampler_perform_o2prime_pack_
bool	sampler_perform_phosphate_pack_
bool	use_green_packer_
bool	verbose_
bool	distinguish_pucker_
bool	finer_sampling_at_chain_closure_
bool	PBP_clustering_at_chain_closure_
bool	allow_syn_pyrimidine_
bool	extra_chi_
bool	use_phenix_geo_
bool	virtual_sugar_legacy_mode_
bool	virtual_sugar_keep_base_fixed_
bool	virtual_sugar_do_minimize_
bool	kic_sampling_if_relevant_
bool	VDW_atr_rep_screen_
bool	force_centroid_interaction_
bool	choose_random_
Size	num_random_samples_
bool	skip_sampling_
bool	perform_minimize_
bool	minimize_and_score_sugar_
bool	minimize_and_score_native_pose_
bool	rm_virt_phosphate_
bool	output_pdb_
bool	output_minimized_pose_list_
core::Real	VDW_rep_alignment_RMSD_CUTOFF_
core::Real	sampler_max_centroid_distance_
utility::vector1< std::string >	VDW_rep_delete_matching_res_
bool	VDW_rep_screen_physical_pose_clash_dist_cutoff_
bool	integration_test_mode_
bool	allow_bulge_at_chainbreak_
bool	parin_favorite_output_
bool	reinitialize_CCD_torsions_
bool	sampler_extra_epsilon_rotamer_
bool	sampler_extra_beta_rotamer_
bool	sampler_include_torsion_value_in_tag_
bool	combine_long_loop_mode_
bool	do_not_sample_multiple_virtual_sugar_
bool	sample_ONLY_multiple_virtual_sugar_
bool	sampler_assert_no_virt_sugar_sampling_
bool	sampler_try_sugar_instantiation_
bool	allow_base_pair_only_centroid_screen_
bool	minimizer_perform_o2prime_pack_
bool	minimizer_output_before_o2prime_pack_
bool	minimizer_rename_tag_
bool	minimizer_allow_variable_bond_geometry_
core::Real	minimizer_vary_bond_geometry_frequency_
bool	unified_framework_
bool	tether_jump_

Constructor & Destructor Documentation

protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::StepWiseRNA_ModelerOptions

(

)

Referenced by clone().

protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::StepWiseRNA_ModelerOptions

(

StepWiseRNA_ModelerOptions const &

src

)

copy constructor

protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::~StepWiseRNA_ModelerOptions

(

)

Member Function Documentation

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::allow_base_pair_only_centroid_screen ( ) const

inline

References allow_base_pair_only_centroid_screen_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::allow_bulge_at_chainbreak ( ) const

inline

References allow_bulge_at_chainbreak_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::allow_syn_pyrimidine ( ) const

inline

References allow_syn_pyrimidine_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::choose_random ( ) const

inline

References choose_random_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::set_options().

StepWiseRNA_ModelerOptionsOP protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::clone

(

)

const

clone the options

References StepWiseRNA_ModelerOptions().

core::Real const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::cluster_rmsd ( ) const

inline

References cluster_rmsd_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::combine_long_loop_mode ( ) const

inline

References combine_long_loop_mode_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::distinguish_pucker ( ) const

inline

References distinguish_pucker_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::do_not_sample_multiple_virtual_sugar ( ) const

inline

References do_not_sample_multiple_virtual_sugar_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::extra_chi ( ) const

inline

References extra_chi_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::finer_sampling_at_chain_closure ( ) const

inline

References finer_sampling_at_chain_closure_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::force_centroid_interaction ( ) const

inline

References force_centroid_interaction_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::initialize_from_command_line

(

)

References allow_base_pair_only_centroid_screen_, allow_bulge_at_chainbreak_, allow_syn_pyrimidine_, basic::options::OptionKeys::stepwise::choose_random, choose_random_, cluster_rmsd_, basic::options::OptionKeys::stepwise::rna::combine_long_loop_mode, combine_long_loop_mode_, basic::options::OptionKeys::rna::corrected_geo, distinguish_pucker_, do_not_sample_multiple_virtual_sugar_, extra_chi_, finer_sampling_at_chain_closure_, force_centroid_interaction_, integration_test_mode_, kic_sampling_if_relevant_, minimize_and_score_native_pose_, basic::options::OptionKeys::stepwise::rna::minimize_and_score_sugar, minimize_and_score_sugar_, minimizer_output_before_o2prime_pack_, minimizer_perform_o2prime_pack_, minimizer_rename_tag_, native_edensity_score_cutoff_, basic::options::OptionKeys::stepwise::num_pose_minimize, num_pose_minimize_, basic::options::OptionKeys::stepwise::num_random_samples, num_random_samples_, option, parin_favorite_output_, PBP_clustering_at_chain_closure_, perform_minimize_, reinitialize_CCD_torsions_, rm_virt_phosphate_, sample_ONLY_multiple_virtual_sugar_, sampler_assert_no_virt_sugar_sampling_, sampler_extra_beta_rotamer_, sampler_extra_epsilon_rotamer_, sampler_include_torsion_value_in_tag_, sampler_max_centroid_distance_, sampler_native_rmsd_screen_, sampler_native_screen_rmsd_cutoff_, basic::options::OptionKeys::stepwise::rna::sampler_num_pose_kept, sampler_num_pose_kept_, sampler_perform_o2prime_pack_, sampler_perform_phosphate_pack_, sampler_try_sugar_instantiation_, skip_sampling_, tether_jump_, unified_framework_, use_green_packer_, use_phenix_geo_, user, VDW_atr_rep_screen_, VDW_rep_alignment_RMSD_CUTOFF_, VDW_rep_delete_matching_res_, VDW_rep_screen_physical_pose_clash_dist_cutoff_, VERBOSE, verbose_, virtual_sugar_do_minimize_, virtual_sugar_keep_base_fixed_, and virtual_sugar_legacy_mode_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::initialize_variables ( )

private

References allow_base_pair_only_centroid_screen_, allow_bulge_at_chainbreak_, allow_syn_pyrimidine_, choose_random_, cluster_rmsd_, combine_long_loop_mode_, distinguish_pucker_, do_not_sample_multiple_virtual_sugar_, extra_chi_, finer_sampling_at_chain_closure_, force_centroid_interaction_, integration_test_mode_, kic_sampling_if_relevant_, minimize_and_score_native_pose_, minimize_and_score_sugar_, minimizer_allow_variable_bond_geometry_, minimizer_output_before_o2prime_pack_, minimizer_perform_o2prime_pack_, minimizer_rename_tag_, minimizer_vary_bond_geometry_frequency_, native_edensity_score_cutoff_, num_pose_minimize_, num_random_samples_, output_minimized_pose_list_, output_pdb_, parin_favorite_output_, PBP_clustering_at_chain_closure_, perform_minimize_, reinitialize_CCD_torsions_, rm_virt_phosphate_, sample_ONLY_multiple_virtual_sugar_, sampler_assert_no_virt_sugar_sampling_, sampler_extra_beta_rotamer_, sampler_extra_epsilon_rotamer_, sampler_include_torsion_value_in_tag_, sampler_max_centroid_distance_, sampler_native_rmsd_screen_, sampler_native_screen_rmsd_cutoff_, sampler_num_pose_kept_, sampler_perform_o2prime_pack_, sampler_perform_phosphate_pack_, sampler_try_sugar_instantiation_, silent_file_, skip_sampling_, tether_jump_, unified_framework_, use_green_packer_, use_phenix_geo_, VDW_atr_rep_screen_, VDW_rep_alignment_RMSD_CUTOFF_, VDW_rep_screen_physical_pose_clash_dist_cutoff_, verbose_, virtual_sugar_do_minimize_, virtual_sugar_keep_base_fixed_, and virtual_sugar_legacy_mode_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::integration_test_mode ( ) const

inline

References integration_test_mode_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::set_options().

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::kic_sampling_if_relevant ( ) const

inline

References kic_sampling_if_relevant_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::minimize_and_score_native_pose ( ) const

inline

References minimize_and_score_native_pose_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::minimize_and_score_sugar ( ) const

inline

References minimize_and_score_sugar_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::apply(), and protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::output_parameters().

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::minimizer_allow_variable_bond_geometry ( ) const

inline

References minimizer_allow_variable_bond_geometry_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::minimizer_output_before_o2prime_pack ( ) const

inline

References minimizer_output_before_o2prime_pack_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::apply(), and protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::output_parameters().

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::minimizer_perform_o2prime_pack ( ) const

inline

References minimizer_perform_o2prime_pack_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::apply(), and protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::output_parameters().

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::minimizer_rename_tag ( ) const

inline

References minimizer_rename_tag_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::output_minimized_pose_list(), and protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::output_parameters().

core::Real const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::minimizer_vary_bond_geometry_frequency ( ) const

inline

References minimizer_vary_bond_geometry_frequency_.

core::Real const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::native_edensity_score_cutoff ( ) const

inline

References native_edensity_score_cutoff_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::apply(), protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::native_edensity_score_checker(), and protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::output_parameters().

core::Size const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::num_pose_minimize ( ) const

inline

References num_pose_minimize_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::apply(), and protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::output_parameters().

Size const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::num_random_samples ( ) const

inline

References num_random_samples_.

StepWiseRNA_ModelerOptions & protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::operator=

(

StepWiseRNA_ModelerOptions const &

src

)

References allow_base_pair_only_centroid_screen_, allow_bulge_at_chainbreak_, allow_syn_pyrimidine_, choose_random_, cluster_rmsd_, combine_long_loop_mode_, distinguish_pucker_, do_not_sample_multiple_virtual_sugar_, extra_chi_, finer_sampling_at_chain_closure_, force_centroid_interaction_, integration_test_mode_, kic_sampling_if_relevant_, minimize_and_score_native_pose_, minimize_and_score_sugar_, minimizer_allow_variable_bond_geometry_, minimizer_output_before_o2prime_pack_, minimizer_perform_o2prime_pack_, minimizer_rename_tag_, minimizer_vary_bond_geometry_frequency_, native_edensity_score_cutoff_, num_pose_minimize_, num_random_samples_, output_minimized_pose_list_, output_pdb_, parin_favorite_output_, PBP_clustering_at_chain_closure_, perform_minimize_, reinitialize_CCD_torsions_, rm_virt_phosphate_, sample_ONLY_multiple_virtual_sugar_, sampler_assert_no_virt_sugar_sampling_, sampler_extra_beta_rotamer_, sampler_extra_epsilon_rotamer_, sampler_include_torsion_value_in_tag_, sampler_max_centroid_distance_, sampler_native_rmsd_screen_, sampler_native_screen_rmsd_cutoff_, sampler_num_pose_kept_, sampler_perform_o2prime_pack_, sampler_perform_phosphate_pack_, sampler_try_sugar_instantiation_, silent_file_, skip_sampling_, tether_jump_, unified_framework_, use_green_packer_, use_phenix_geo_, VDW_atr_rep_screen_, VDW_rep_alignment_RMSD_CUTOFF_, VDW_rep_screen_physical_pose_clash_dist_cutoff_, verbose_, virtual_sugar_do_minimize_, virtual_sugar_keep_base_fixed_, and virtual_sugar_legacy_mode_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::output_minimized_pose_list ( ) const

inline

References output_minimized_pose_list_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::apply().

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::output_pdb ( ) const

inline

References output_pdb_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::parin_favorite_output ( ) const

inline

References parin_favorite_output_.

virtual void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::parse_my_tag ( utility::tag::TagCOP  )

inlinevirtual

Initialize from the recursive "tag" structure.

Implements basic::resource_manager::ResourceOptions.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::PBP_clustering_at_chain_closure ( ) const

inline

References PBP_clustering_at_chain_closure_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::perform_minimize ( ) const

inline

References perform_minimize_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::apply(), and protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::output_parameters().

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::reinitialize_CCD_torsions ( ) const

inline

References reinitialize_CCD_torsions_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::rm_virt_phosphate ( ) const

inline

References rm_virt_phosphate_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::apply(), and protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::output_parameters().

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sample_ONLY_multiple_virtual_sugar ( ) const

inline

References sample_ONLY_multiple_virtual_sugar_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sampler_assert_no_virt_sugar_sampling ( ) const

inline

References sampler_assert_no_virt_sugar_sampling_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sampler_extra_beta_rotamer ( ) const

inline

References sampler_extra_beta_rotamer_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sampler_extra_epsilon_rotamer ( ) const

inline

References sampler_extra_epsilon_rotamer_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sampler_include_torsion_value_in_tag ( ) const

inline

References sampler_include_torsion_value_in_tag_.

core::Real const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sampler_max_centroid_distance ( ) const

inline

References sampler_max_centroid_distance_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sampler_native_rmsd_screen ( ) const

inline

References sampler_native_rmsd_screen_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::output_parameters(), and protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::pass_all_pose_screens().

core::Real const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sampler_native_screen_rmsd_cutoff ( ) const

inline

References sampler_native_screen_rmsd_cutoff_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::output_parameters(), and protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::pass_all_pose_screens().

core::Size const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sampler_num_pose_kept ( ) const

inline

References sampler_num_pose_kept_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sampler_perform_o2prime_pack ( ) const

inline

References sampler_perform_o2prime_pack_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sampler_perform_phosphate_pack ( ) const

inline

References sampler_perform_phosphate_pack_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sampler_try_sugar_instantiation ( ) const

inline

References sampler_try_sugar_instantiation_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_allow_base_pair_only_centroid_screen ( bool const &  setting )

inline

References allow_base_pair_only_centroid_screen_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_allow_bulge_at_chainbreak ( bool const &  setting )

inline

References allow_bulge_at_chainbreak_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_allow_syn_pyrimidine ( bool const &  setting )

inline

References allow_syn_pyrimidine_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_choose_random ( bool const &  setting )

inline

References choose_random_.

Referenced by protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::setup_rna_modeler_options().

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_cluster_rmsd ( core::Real const &  setting )

inline

References cluster_rmsd_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::set_options().

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_combine_long_loop_mode ( bool const &  setting )

inline

References combine_long_loop_mode_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_distinguish_pucker ( bool const &  setting )

inline

References distinguish_pucker_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_do_not_sample_multiple_virtual_sugar ( bool const &  setting )

inline

References do_not_sample_multiple_virtual_sugar_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_extra_chi ( bool const &  setting )

inline

References extra_chi_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_finer_sampling_at_chain_closure ( bool const &  setting )

inline

References finer_sampling_at_chain_closure_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_force_centroid_interaction ( bool const &  setting )

inline

References force_centroid_interaction_.

Referenced by protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::setup_rna_modeler_options().

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_integration_test_mode ( bool const &  setting )

inline

References integration_test_mode_.

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::bulge_chain_closure_complete(), and protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::setup_rna_modeler_options().

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_kic_sampling_if_relevant ( bool const &  setting )

inline

References kic_sampling_if_relevant_.

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::bulge_chain_closure_complete(), and protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::setup_rna_modeler_options().

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_minimize_and_score_native_pose ( bool const &  setting )

inline

References minimize_and_score_native_pose_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_minimize_and_score_sugar ( bool const &  setting )

inline

References minimize_and_score_sugar_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_minimizer_allow_variable_bond_geometry ( bool const &  setting )

inline

References minimizer_allow_variable_bond_geometry_.

Referenced by protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::setup_rna_modeler_options().

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_minimizer_output_before_o2prime_pack ( bool const &  setting )

inline

References minimizer_output_before_o2prime_pack_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_minimizer_perform_o2prime_pack ( bool const &  setting )

inline

References minimizer_perform_o2prime_pack_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_minimizer_rename_tag ( bool const &  setting )

inline

References minimizer_rename_tag_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_minimizer_vary_bond_geometry_frequency ( core::Real const &  setting )

inline

References minimizer_vary_bond_geometry_frequency_.

Referenced by protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::setup_rna_modeler_options().

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_native_edensity_score_cutoff ( core::Real const &  setting )

inline

References native_edensity_score_cutoff_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_num_pose_minimize ( core::Size const &  setting )

inline

References num_pose_minimize_.

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::bulge_chain_closure_complete(), and protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::setup_rna_modeler_options().

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_num_random_samples ( Size const &  setting )

inline

References num_random_samples_.

Referenced by protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::setup_rna_modeler_options().

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_output_minimized_pose_list ( bool const &  setting )

inline

References output_minimized_pose_list_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_output_pdb ( bool const &  setting )

inline

References output_pdb_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_parin_favorite_output ( bool const &  setting )

inline

References parin_favorite_output_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_PBP_clustering_at_chain_closure ( bool const &  setting )

inline

References PBP_clustering_at_chain_closure_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_perform_minimize ( bool const &  setting )

inline

References perform_minimize_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_reinitialize_CCD_torsions ( bool const &  setting )

inline

References reinitialize_CCD_torsions_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_rm_virt_phosphate ( bool const &  setting )

inline

References rm_virt_phosphate_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_sample_ONLY_multiple_virtual_sugar ( bool const &  setting )

inline

References sample_ONLY_multiple_virtual_sugar_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_sampler_assert_no_virt_sugar_sampling ( bool const &  setting )

inline

References sampler_assert_no_virt_sugar_sampling_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_sampler_extra_beta_rotamer ( bool const &  setting )

inline

References sampler_extra_beta_rotamer_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_sampler_extra_epsilon_rotamer ( bool const &  setting )

inline

References sampler_extra_epsilon_rotamer_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_sampler_include_torsion_value_in_tag ( bool const &  setting )

inline

References sampler_include_torsion_value_in_tag_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_sampler_max_centroid_distance ( core::Real const &  setting )

inline

References sampler_max_centroid_distance_.

Referenced by protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::setup_rna_modeler_options().

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_sampler_native_rmsd_screen ( bool const &  setting )

inline

References sampler_native_rmsd_screen_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::set_options().

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_sampler_native_screen_rmsd_cutoff ( core::Real const &  setting )

inline

References sampler_native_screen_rmsd_cutoff_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::do_minimizing(), and protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::set_options().

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_sampler_num_pose_kept ( core::Size const &  setting )

inline

References sampler_num_pose_kept_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::set_options().

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_sampler_perform_o2prime_pack ( bool const &  setting )

inline

References sampler_perform_o2prime_pack_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_sampler_perform_phosphate_pack ( bool const &  setting )

inline

References sampler_perform_phosphate_pack_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_sampler_try_sugar_instantiation ( bool const &  setting )

inline

References sampler_try_sugar_instantiation_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_silent_file ( std::string const &  setting )

inline

References silent_file_.

Referenced by protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::setup_rna_modeler_options().

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_skip_sampling ( bool const &  setting )

inline

References skip_sampling_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::set_skip_sampling().

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_tether_jump ( bool const &  setting )

inline

References tether_jump_.

Referenced by protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::setup_rna_modeler_options().

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_unified_framework ( bool const &  setting )

inline

References unified_framework_.

Referenced by protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::setup_rna_modeler_options().

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_use_green_packer ( bool const &  setting )

inline

References use_green_packer_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_use_phenix_geo ( bool const &  setting )

inline

References use_phenix_geo_.

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::bulge_chain_closure_complete(), and protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::setup_rna_modeler_options().

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_VDW_atr_rep_screen ( bool const &  setting )

inline

References VDW_atr_rep_screen_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_VDW_rep_alignment_RMSD_CUTOFF ( core::Real const &  setting )

inline

References VDW_rep_alignment_RMSD_CUTOFF_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_VDW_rep_screen_physical_pose_clash_dist_cutoff ( bool const &  setting )

inline

References VDW_rep_screen_physical_pose_clash_dist_cutoff_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_verbose ( bool const &  setting )

inline

References verbose_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_virtual_sugar_do_minimize ( bool const &  setting )

inline

References virtual_sugar_do_minimize_.

Referenced by protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::setup_rna_modeler_options().

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_virtual_sugar_keep_base_fixed ( bool const &  setting )

inline

References virtual_sugar_keep_base_fixed_.

Referenced by protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::setup_rna_modeler_options().

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_virtual_sugar_legacy_mode ( bool const &  setting )

inline

References virtual_sugar_legacy_mode_.

void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::setup_options_for_VDW_bin_checker

(

checker::RNA_VDW_BinCheckerOP

user_input_VDW_bin_checker

)

const

References output_pdb_, protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::set_output_pdb(), protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::set_physical_pose_clash_dist_cutoff(), protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::set_VDW_rep_alignment_RMSD_CUTOFF(), protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::set_VDW_rep_delete_matching_res(), VDW_rep_alignment_RMSD_CUTOFF_, VDW_rep_delete_matching_res_, and VDW_rep_screen_physical_pose_clash_dist_cutoff_.

virtual void protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::show ( std::ostream &  ) const

inlinevirtual

Describe this instance to a given output stream.

std::string const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::silent_file ( ) const

inline

References silent_file_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::skip_sampling ( ) const

inline

References skip_sampling_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::tether_jump ( ) const

inline

References tether_jump_.

virtual std::string protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::type ( ) const

inlinevirtual

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

Implements basic::resource_manager::ResourceOptions.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::unified_framework ( ) const

inline

References unified_framework_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::use_green_packer ( ) const

inline

References use_green_packer_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::use_phenix_geo ( ) const

inline

References use_phenix_geo_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::VDW_atr_rep_screen ( ) const

inline

References VDW_atr_rep_screen_.

core::Real const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::VDW_rep_alignment_RMSD_CUTOFF ( ) const

inline

References VDW_rep_alignment_RMSD_CUTOFF_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::VDW_rep_screen_physical_pose_clash_dist_cutoff ( ) const

inline

References VDW_rep_screen_physical_pose_clash_dist_cutoff_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::verbose ( ) const

inline

References verbose_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::apply(), protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::output_parameters(), and protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::pass_all_pose_screens().

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::virtual_sugar_do_minimize ( ) const

inline

References virtual_sugar_do_minimize_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::virtual_sugar_keep_base_fixed ( ) const

inline

References virtual_sugar_keep_base_fixed_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::virtual_sugar_legacy_mode ( ) const

inline

References virtual_sugar_legacy_mode_.

Member Data Documentation

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::allow_base_pair_only_centroid_screen_

private

Referenced by allow_base_pair_only_centroid_screen(), initialize_from_command_line(), initialize_variables(), operator=(), and set_allow_base_pair_only_centroid_screen().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::allow_bulge_at_chainbreak_

private

Referenced by allow_bulge_at_chainbreak(), initialize_from_command_line(), initialize_variables(), operator=(), and set_allow_bulge_at_chainbreak().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::allow_syn_pyrimidine_

private

Referenced by allow_syn_pyrimidine(), initialize_from_command_line(), initialize_variables(), operator=(), and set_allow_syn_pyrimidine().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::choose_random_

private

Referenced by choose_random(), initialize_from_command_line(), initialize_variables(), operator=(), and set_choose_random().

core::Real protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::cluster_rmsd_

private

Referenced by cluster_rmsd(), initialize_from_command_line(), initialize_variables(), operator=(), and set_cluster_rmsd().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::combine_long_loop_mode_

private

Referenced by combine_long_loop_mode(), initialize_from_command_line(), initialize_variables(), operator=(), and set_combine_long_loop_mode().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::distinguish_pucker_

private

Referenced by distinguish_pucker(), initialize_from_command_line(), initialize_variables(), operator=(), and set_distinguish_pucker().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::do_not_sample_multiple_virtual_sugar_

private

Referenced by do_not_sample_multiple_virtual_sugar(), initialize_from_command_line(), initialize_variables(), operator=(), and set_do_not_sample_multiple_virtual_sugar().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::extra_chi_

private

Referenced by extra_chi(), initialize_from_command_line(), initialize_variables(), operator=(), and set_extra_chi().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::finer_sampling_at_chain_closure_

private

Referenced by finer_sampling_at_chain_closure(), initialize_from_command_line(), initialize_variables(), operator=(), and set_finer_sampling_at_chain_closure().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::force_centroid_interaction_

private

Referenced by force_centroid_interaction(), initialize_from_command_line(), initialize_variables(), operator=(), and set_force_centroid_interaction().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::integration_test_mode_

private

Referenced by initialize_from_command_line(), initialize_variables(), integration_test_mode(), operator=(), and set_integration_test_mode().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::kic_sampling_if_relevant_

private

Referenced by initialize_from_command_line(), initialize_variables(), kic_sampling_if_relevant(), operator=(), and set_kic_sampling_if_relevant().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::minimize_and_score_native_pose_

private

Referenced by initialize_from_command_line(), initialize_variables(), minimize_and_score_native_pose(), operator=(), and set_minimize_and_score_native_pose().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::minimize_and_score_sugar_

private

Referenced by initialize_from_command_line(), initialize_variables(), minimize_and_score_sugar(), operator=(), and set_minimize_and_score_sugar().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::minimizer_allow_variable_bond_geometry_

private

Referenced by initialize_variables(), minimizer_allow_variable_bond_geometry(), operator=(), and set_minimizer_allow_variable_bond_geometry().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::minimizer_output_before_o2prime_pack_

private

Referenced by initialize_from_command_line(), initialize_variables(), minimizer_output_before_o2prime_pack(), operator=(), and set_minimizer_output_before_o2prime_pack().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::minimizer_perform_o2prime_pack_

private

Referenced by initialize_from_command_line(), initialize_variables(), minimizer_perform_o2prime_pack(), operator=(), and set_minimizer_perform_o2prime_pack().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::minimizer_rename_tag_

private

Referenced by initialize_from_command_line(), initialize_variables(), minimizer_rename_tag(), operator=(), and set_minimizer_rename_tag().

core::Real protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::minimizer_vary_bond_geometry_frequency_

private

Referenced by initialize_variables(), minimizer_vary_bond_geometry_frequency(), operator=(), and set_minimizer_vary_bond_geometry_frequency().

core::Real protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::native_edensity_score_cutoff_

private

Referenced by initialize_from_command_line(), initialize_variables(), native_edensity_score_cutoff(), operator=(), and set_native_edensity_score_cutoff().

core::Size protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::num_pose_minimize_

private

Referenced by initialize_from_command_line(), initialize_variables(), num_pose_minimize(), operator=(), and set_num_pose_minimize().

Size protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::num_random_samples_

private

Referenced by initialize_from_command_line(), initialize_variables(), num_random_samples(), operator=(), and set_num_random_samples().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::output_minimized_pose_list_

private

Referenced by initialize_variables(), operator=(), output_minimized_pose_list(), and set_output_minimized_pose_list().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::output_pdb_

private

Referenced by initialize_variables(), operator=(), output_pdb(), set_output_pdb(), and setup_options_for_VDW_bin_checker().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::parin_favorite_output_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), parin_favorite_output(), and set_parin_favorite_output().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::PBP_clustering_at_chain_closure_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), PBP_clustering_at_chain_closure(), and set_PBP_clustering_at_chain_closure().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::perform_minimize_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), perform_minimize(), and set_perform_minimize().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::reinitialize_CCD_torsions_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), reinitialize_CCD_torsions(), and set_reinitialize_CCD_torsions().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::rm_virt_phosphate_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), rm_virt_phosphate(), and set_rm_virt_phosphate().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sample_ONLY_multiple_virtual_sugar_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), sample_ONLY_multiple_virtual_sugar(), and set_sample_ONLY_multiple_virtual_sugar().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sampler_assert_no_virt_sugar_sampling_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), sampler_assert_no_virt_sugar_sampling(), and set_sampler_assert_no_virt_sugar_sampling().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sampler_extra_beta_rotamer_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), sampler_extra_beta_rotamer(), and set_sampler_extra_beta_rotamer().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sampler_extra_epsilon_rotamer_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), sampler_extra_epsilon_rotamer(), and set_sampler_extra_epsilon_rotamer().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sampler_include_torsion_value_in_tag_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), sampler_include_torsion_value_in_tag(), and set_sampler_include_torsion_value_in_tag().

core::Real protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sampler_max_centroid_distance_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), sampler_max_centroid_distance(), and set_sampler_max_centroid_distance().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sampler_native_rmsd_screen_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), sampler_native_rmsd_screen(), and set_sampler_native_rmsd_screen().

core::Real protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sampler_native_screen_rmsd_cutoff_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), sampler_native_screen_rmsd_cutoff(), and set_sampler_native_screen_rmsd_cutoff().

core::Size protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sampler_num_pose_kept_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), sampler_num_pose_kept(), and set_sampler_num_pose_kept().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sampler_perform_o2prime_pack_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), sampler_perform_o2prime_pack(), and set_sampler_perform_o2prime_pack().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sampler_perform_phosphate_pack_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), sampler_perform_phosphate_pack(), and set_sampler_perform_phosphate_pack().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::sampler_try_sugar_instantiation_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), sampler_try_sugar_instantiation(), and set_sampler_try_sugar_instantiation().

std::string protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::silent_file_

private

Referenced by initialize_variables(), operator=(), set_silent_file(), and silent_file().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::skip_sampling_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), set_skip_sampling(), and skip_sampling().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::tether_jump_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), set_tether_jump(), and tether_jump().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::unified_framework_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), set_unified_framework(), and unified_framework().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::use_green_packer_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), set_use_green_packer(), and use_green_packer().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::use_phenix_geo_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), set_use_phenix_geo(), and use_phenix_geo().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::VDW_atr_rep_screen_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), set_VDW_atr_rep_screen(), and VDW_atr_rep_screen().

core::Real protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::VDW_rep_alignment_RMSD_CUTOFF_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), set_VDW_rep_alignment_RMSD_CUTOFF(), setup_options_for_VDW_bin_checker(), and VDW_rep_alignment_RMSD_CUTOFF().

utility::vector1< std::string > protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::VDW_rep_delete_matching_res_

private

Referenced by initialize_from_command_line(), and setup_options_for_VDW_bin_checker().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::VDW_rep_screen_physical_pose_clash_dist_cutoff_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), set_VDW_rep_screen_physical_pose_clash_dist_cutoff(), setup_options_for_VDW_bin_checker(), and VDW_rep_screen_physical_pose_clash_dist_cutoff().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::verbose_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), set_verbose(), and verbose().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::virtual_sugar_do_minimize_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), set_virtual_sugar_do_minimize(), and virtual_sugar_do_minimize().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::virtual_sugar_keep_base_fixed_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), set_virtual_sugar_keep_base_fixed(), and virtual_sugar_keep_base_fixed().

bool protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::virtual_sugar_legacy_mode_

private

Referenced by initialize_from_command_line(), initialize_variables(), operator=(), set_virtual_sugar_legacy_mode(), and virtual_sugar_legacy_mode().

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

• symlinks/rosetta/src/protocols/stepwise/sampling/rna/StepWiseRNA_ModelerOptions.hh
• symlinks/rosetta/src/protocols/stepwise/sampling/rna/StepWiseRNA_ModelerOptions.cc