protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions Class Reference

#include <StepWiseRNA_ModelerOptions.hh>

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

Public Member Functions
	StepWiseRNA_ModelerOptions ()
StepWiseRNA_ModelerOptionsOP	clone () const
	clone the options More...
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 instance. This function allows for better error message delivery. 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)

Protected Member Functions
void	initialize_variables ()

Private Attributes
core::Real	native_edensity_score_cutoff_
bool	o2prime_legacy_mode_
bool	allow_virtual_o2prime_hydrogens_
bool	sampler_perform_phosphate_pack_
bool	force_phosphate_instantiation_
bool	distinguish_pucker_
bool	finer_sampling_at_chain_closure_
bool	PBP_clustering_at_chain_closure_
bool	allow_syn_pyrimidine_
bool	extra_chi_
bool	sample_all_chi_
bool	use_phenix_geo_
bool	virtual_sugar_legacy_mode_
bool	virtual_sugar_keep_base_fixed_
bool	virtual_sugar_do_minimize_
bool	virtual_sugar_do_screens_
bool	kic_modeler_if_relevant_
bool	force_centroid_interaction_
bool	minimize_and_score_sugar_
bool	minimize_and_score_native_pose_
bool	rm_virt_phosphate_
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_rename_tag_
bool	tether_jump_
bool	turn_off_rna_chem_map_during_optimize_
bool	rna_legacy_output_mode_
bool	allow_rebuild_bulge_mode_

Constructor & Destructor Documentation

protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::StepWiseRNA_ModelerOptions

(

)

Member Function Documentation

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::allow_base_pair_only_centroid_screen ( ) const

inline

References allow_base_pair_only_centroid_screen_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::allow_bulge_at_chainbreak ( ) const

inline

References allow_bulge_at_chainbreak_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::allow_rebuild_bulge_mode ( ) const

inline

References allow_rebuild_bulge_mode_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::allow_syn_pyrimidine ( ) const

inline

References allow_syn_pyrimidine_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::allow_virtual_o2prime_hydrogens ( ) const

inline

References allow_virtual_o2prime_hydrogens_.

StepWiseRNA_ModelerOptionsOP protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::clone

(

)

const

clone the options

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::combine_long_loop_mode ( ) const

inline

References combine_long_loop_mode_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::distinguish_pucker ( ) const

inline

References distinguish_pucker_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::do_not_sample_multiple_virtual_sugar ( ) const

inline

References do_not_sample_multiple_virtual_sugar_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::extra_chi ( ) const

inline

References extra_chi_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::finer_sampling_at_chain_closure ( ) const

inline

References finer_sampling_at_chain_closure_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::force_centroid_interaction ( ) const

inline

References force_centroid_interaction_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::force_phosphate_instantiation ( ) const

inline

References force_phosphate_instantiation_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::initialize_from_command_line

(

)

References TR().

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

protected

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::integration_test_mode ( ) const

inline

References integration_test_mode_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::kic_modeler_if_relevant ( ) const

inline

References kic_modeler_if_relevant_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::minimize_and_score_native_pose ( ) const

inline

References minimize_and_score_native_pose_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::minimize_and_score_sugar ( ) const

inline

References minimize_and_score_sugar_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::minimizer_rename_tag ( ) const

inline

References minimizer_rename_tag_.

core::Real const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::native_edensity_score_cutoff ( ) const

inline

References native_edensity_score_cutoff_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::o2prime_legacy_mode ( ) const

inline

References o2prime_legacy_mode_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::parin_favorite_output ( ) const

inline

References parin_favorite_output_.

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

inlinevirtual

Initialize from the recursive "tag" structure.

Reimplemented in protocols::stepwise::modeler::options::StepWiseModelerOptions.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::PBP_clustering_at_chain_closure ( ) const

inline

References PBP_clustering_at_chain_closure_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::reinitialize_CCD_torsions ( ) const

inline

References reinitialize_CCD_torsions_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::rm_virt_phosphate ( ) const

inline

References rm_virt_phosphate_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::rna_legacy_output_mode ( ) const

inline

References rna_legacy_output_mode_.

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sample_all_chi ( ) const

inline

References sample_all_chi_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sample_ONLY_multiple_virtual_sugar ( ) const

inline

References sample_ONLY_multiple_virtual_sugar_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_assert_no_virt_sugar_sampling ( ) const

inline

References sampler_assert_no_virt_sugar_sampling_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_extra_beta_rotamer ( ) const

inline

References sampler_extra_beta_rotamer_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_extra_epsilon_rotamer ( ) const

inline

References sampler_extra_epsilon_rotamer_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_include_torsion_value_in_tag ( ) const

inline

References sampler_include_torsion_value_in_tag_.

core::Real const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_max_centroid_distance ( ) const

inline

References sampler_max_centroid_distance_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_perform_phosphate_pack ( ) const

inline

References sampler_perform_phosphate_pack_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_try_sugar_instantiation ( ) const

inline

References sampler_try_sugar_instantiation_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_allow_base_pair_only_centroid_screen ( bool const &  setting )

inline

References allow_base_pair_only_centroid_screen_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_allow_bulge_at_chainbreak ( bool const &  setting )

inline

References allow_bulge_at_chainbreak_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_allow_rebuild_bulge_mode ( bool const &  setting )

inline

References allow_rebuild_bulge_mode_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_allow_syn_pyrimidine ( bool const &  setting )

inline

References allow_syn_pyrimidine_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_allow_virtual_o2prime_hydrogens ( bool const &  setting )

inline

References allow_virtual_o2prime_hydrogens_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_combine_long_loop_mode ( bool const &  setting )

inline

References combine_long_loop_mode_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_distinguish_pucker ( bool const &  setting )

inline

References distinguish_pucker_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_do_not_sample_multiple_virtual_sugar ( bool const &  setting )

inline

References do_not_sample_multiple_virtual_sugar_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_extra_chi ( bool const &  setting )

inline

References extra_chi_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_finer_sampling_at_chain_closure ( bool const &  setting )

inline

References finer_sampling_at_chain_closure_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_force_centroid_interaction ( bool const &  setting )

inline

References force_centroid_interaction_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_force_phosphate_instantiation ( bool const &  setting )

inline

References force_phosphate_instantiation_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_integration_test_mode ( bool const &  setting )

inline

References integration_test_mode_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_kic_modeler_if_relevant ( bool const &  setting )

inline

References kic_modeler_if_relevant_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_minimize_and_score_native_pose ( bool const &  setting )

inline

References minimize_and_score_native_pose_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_minimize_and_score_sugar ( bool const &  setting )

inline

References minimize_and_score_sugar_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_minimizer_rename_tag ( bool const &  setting )

inline

References minimizer_rename_tag_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_native_edensity_score_cutoff ( core::Real const &  setting )

inline

References native_edensity_score_cutoff_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_o2prime_legacy_mode ( bool const &  setting )

inline

References o2prime_legacy_mode_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_parin_favorite_output ( bool const &  setting )

inline

References parin_favorite_output_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_PBP_clustering_at_chain_closure ( bool const &  setting )

inline

References PBP_clustering_at_chain_closure_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_reinitialize_CCD_torsions ( bool const &  setting )

inline

References reinitialize_CCD_torsions_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_rm_virt_phosphate ( bool const &  setting )

inline

References rm_virt_phosphate_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_rna_legacy_output_mode ( bool const &  setting )

inline

References rna_legacy_output_mode_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_sample_all_chi ( bool const &  setting )

inline

References sample_all_chi_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_sample_ONLY_multiple_virtual_sugar ( bool const &  setting )

inline

References sample_ONLY_multiple_virtual_sugar_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_sampler_assert_no_virt_sugar_sampling ( bool const &  setting )

inline

References sampler_assert_no_virt_sugar_sampling_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_sampler_extra_beta_rotamer ( bool const &  setting )

inline

References sampler_extra_beta_rotamer_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_sampler_extra_epsilon_rotamer ( bool const &  setting )

inline

References sampler_extra_epsilon_rotamer_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_sampler_include_torsion_value_in_tag ( bool const &  setting )

inline

References sampler_include_torsion_value_in_tag_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_sampler_max_centroid_distance ( core::Real const &  setting )

inline

References sampler_max_centroid_distance_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_sampler_perform_phosphate_pack ( bool const &  setting )

inline

References sampler_perform_phosphate_pack_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_sampler_try_sugar_instantiation ( bool const &  setting )

inline

References sampler_try_sugar_instantiation_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_tether_jump ( bool const &  setting )

inline

References tether_jump_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_turn_off_rna_chem_map_during_optimize ( bool const &  setting )

inline

References turn_off_rna_chem_map_during_optimize_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_use_phenix_geo ( bool const &  setting )

inline

References use_phenix_geo_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_VDW_rep_alignment_RMSD_CUTOFF ( core::Real const &  setting )

inline

References VDW_rep_alignment_RMSD_CUTOFF_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_VDW_rep_delete_matching_res ( utility::vector1< std::string > const &  setting )

inline

References VDW_rep_delete_matching_res_.

void protocols::stepwise::modeler::options::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::modeler::options::StepWiseRNA_ModelerOptions::set_virtual_sugar_do_minimize ( bool const &  setting )

inline

References virtual_sugar_do_minimize_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_virtual_sugar_do_screens ( bool const &  setting )

inline

References virtual_sugar_do_screens_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_virtual_sugar_keep_base_fixed ( bool const &  setting )

inline

References virtual_sugar_keep_base_fixed_.

void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_virtual_sugar_legacy_mode ( bool const &  setting )

inline

References virtual_sugar_legacy_mode_.

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

inlinevirtual

Describe this instance to a given output stream.

Reimplemented in protocols::stepwise::modeler::options::StepWiseModelerOptions.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::tether_jump ( ) const

inline

References tether_jump_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::turn_off_rna_chem_map_during_optimize ( ) const

inline

References turn_off_rna_chem_map_during_optimize_.

virtual std::string protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::type ( ) const

inlinevirtual

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

Reimplemented in protocols::stepwise::modeler::options::StepWiseModelerOptions.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::use_phenix_geo ( ) const

inline

References use_phenix_geo_.

core::Real const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::VDW_rep_alignment_RMSD_CUTOFF ( ) const

inline

References VDW_rep_alignment_RMSD_CUTOFF_.

utility::vector1< std::string > const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::VDW_rep_delete_matching_res ( ) const

inline

References VDW_rep_delete_matching_res_.

bool const& protocols::stepwise::modeler::options::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::modeler::options::StepWiseRNA_ModelerOptions::virtual_sugar_do_minimize ( ) const

inline

References virtual_sugar_do_minimize_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::virtual_sugar_do_screens ( ) const

inline

References virtual_sugar_do_screens_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::virtual_sugar_keep_base_fixed ( ) const

inline

References virtual_sugar_keep_base_fixed_.

bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::virtual_sugar_legacy_mode ( ) const

inline

References virtual_sugar_legacy_mode_.

Member Data Documentation

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::allow_base_pair_only_centroid_screen_

private

Referenced by allow_base_pair_only_centroid_screen(), and set_allow_base_pair_only_centroid_screen().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::allow_bulge_at_chainbreak_

private

Referenced by allow_bulge_at_chainbreak(), and set_allow_bulge_at_chainbreak().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::allow_rebuild_bulge_mode_

private

Referenced by allow_rebuild_bulge_mode(), and set_allow_rebuild_bulge_mode().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::allow_syn_pyrimidine_

private

Referenced by allow_syn_pyrimidine(), and set_allow_syn_pyrimidine().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::allow_virtual_o2prime_hydrogens_

private

Referenced by allow_virtual_o2prime_hydrogens(), and set_allow_virtual_o2prime_hydrogens().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::combine_long_loop_mode_

private

Referenced by combine_long_loop_mode(), and set_combine_long_loop_mode().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::distinguish_pucker_

private

Referenced by distinguish_pucker(), and set_distinguish_pucker().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::do_not_sample_multiple_virtual_sugar_

private

Referenced by do_not_sample_multiple_virtual_sugar(), and set_do_not_sample_multiple_virtual_sugar().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::extra_chi_

private

Referenced by extra_chi(), and set_extra_chi().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::finer_sampling_at_chain_closure_

private

Referenced by finer_sampling_at_chain_closure(), and set_finer_sampling_at_chain_closure().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::force_centroid_interaction_

private

Referenced by force_centroid_interaction(), and set_force_centroid_interaction().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::force_phosphate_instantiation_

private

Referenced by force_phosphate_instantiation(), and set_force_phosphate_instantiation().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::integration_test_mode_

private

Referenced by integration_test_mode(), and set_integration_test_mode().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::kic_modeler_if_relevant_

private

Referenced by kic_modeler_if_relevant(), and set_kic_modeler_if_relevant().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::minimize_and_score_native_pose_

private

Referenced by minimize_and_score_native_pose(), and set_minimize_and_score_native_pose().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::minimize_and_score_sugar_

private

Referenced by minimize_and_score_sugar(), and set_minimize_and_score_sugar().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::minimizer_rename_tag_

private

Referenced by minimizer_rename_tag(), and set_minimizer_rename_tag().

core::Real protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::native_edensity_score_cutoff_

private

Referenced by native_edensity_score_cutoff(), and set_native_edensity_score_cutoff().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::o2prime_legacy_mode_

private

Referenced by o2prime_legacy_mode(), and set_o2prime_legacy_mode().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::parin_favorite_output_

private

Referenced by parin_favorite_output(), and set_parin_favorite_output().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::PBP_clustering_at_chain_closure_

private

Referenced by PBP_clustering_at_chain_closure(), and set_PBP_clustering_at_chain_closure().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::reinitialize_CCD_torsions_

private

Referenced by reinitialize_CCD_torsions(), and set_reinitialize_CCD_torsions().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::rm_virt_phosphate_

private

Referenced by rm_virt_phosphate(), and set_rm_virt_phosphate().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::rna_legacy_output_mode_

private

Referenced by rna_legacy_output_mode(), and set_rna_legacy_output_mode().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sample_all_chi_

private

Referenced by sample_all_chi(), and set_sample_all_chi().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sample_ONLY_multiple_virtual_sugar_

private

Referenced by sample_ONLY_multiple_virtual_sugar(), and set_sample_ONLY_multiple_virtual_sugar().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_assert_no_virt_sugar_sampling_

private

Referenced by sampler_assert_no_virt_sugar_sampling(), and set_sampler_assert_no_virt_sugar_sampling().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_extra_beta_rotamer_

private

Referenced by sampler_extra_beta_rotamer(), and set_sampler_extra_beta_rotamer().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_extra_epsilon_rotamer_

private

Referenced by sampler_extra_epsilon_rotamer(), and set_sampler_extra_epsilon_rotamer().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_include_torsion_value_in_tag_

private

Referenced by sampler_include_torsion_value_in_tag(), and set_sampler_include_torsion_value_in_tag().

core::Real protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_max_centroid_distance_

private

Referenced by sampler_max_centroid_distance(), and set_sampler_max_centroid_distance().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_perform_phosphate_pack_

private

Referenced by sampler_perform_phosphate_pack(), and set_sampler_perform_phosphate_pack().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_try_sugar_instantiation_

private

Referenced by sampler_try_sugar_instantiation(), and set_sampler_try_sugar_instantiation().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::tether_jump_

private

Referenced by set_tether_jump(), and tether_jump().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::turn_off_rna_chem_map_during_optimize_

private

Referenced by set_turn_off_rna_chem_map_during_optimize(), and turn_off_rna_chem_map_during_optimize().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::use_phenix_geo_

private

Referenced by set_use_phenix_geo(), and use_phenix_geo().

core::Real protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::VDW_rep_alignment_RMSD_CUTOFF_

private

Referenced by set_VDW_rep_alignment_RMSD_CUTOFF(), and VDW_rep_alignment_RMSD_CUTOFF().

utility::vector1< std::string > protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::VDW_rep_delete_matching_res_

private

Referenced by set_VDW_rep_delete_matching_res(), and VDW_rep_delete_matching_res().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::VDW_rep_screen_physical_pose_clash_dist_cutoff_

private

Referenced by set_VDW_rep_screen_physical_pose_clash_dist_cutoff(), and VDW_rep_screen_physical_pose_clash_dist_cutoff().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::virtual_sugar_do_minimize_

private

Referenced by set_virtual_sugar_do_minimize(), and virtual_sugar_do_minimize().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::virtual_sugar_do_screens_

private

Referenced by set_virtual_sugar_do_screens(), and virtual_sugar_do_screens().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::virtual_sugar_keep_base_fixed_

private

Referenced by set_virtual_sugar_keep_base_fixed(), and virtual_sugar_keep_base_fixed().

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::virtual_sugar_legacy_mode_

private

Referenced by 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:

• src/protocols/stepwise/modeler/options/StepWiseRNA_ModelerOptions.hh
• src/protocols/stepwise/modeler/options/StepWiseRNA_ModelerOptions.cc