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

#include <StepWiseRNA_ModelerOptions.hh>

Inheritance diagram for protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions:
Inheritance graph
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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
bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::allow_bulge_at_chainbreak ( ) const
inline
bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::allow_rebuild_bulge_mode ( ) const
inline
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
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
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
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
bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::force_centroid_interaction ( ) const
inline
bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::force_phosphate_instantiation ( ) const
inline
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
bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::kic_modeler_if_relevant ( ) const
inline
bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::minimize_and_score_native_pose ( ) const
inline
bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::minimize_and_score_sugar ( ) const
inline
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
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
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
bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::reinitialize_CCD_torsions ( ) const
inline
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
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
bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_assert_no_virt_sugar_sampling ( ) const
inline
bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_extra_beta_rotamer ( ) const
inline
bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_extra_epsilon_rotamer ( ) const
inline
bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_include_torsion_value_in_tag ( ) const
inline
core::Real const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_max_centroid_distance ( ) const
inline
bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_perform_phosphate_pack ( ) const
inline
bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_try_sugar_instantiation ( ) const
inline
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_allow_base_pair_only_centroid_screen ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_allow_bulge_at_chainbreak ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_allow_rebuild_bulge_mode ( bool const &  setting)
inline
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
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_combine_long_loop_mode ( bool const &  setting)
inline
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
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
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_force_centroid_interaction ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_force_phosphate_instantiation ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_integration_test_mode ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_kic_modeler_if_relevant ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_minimize_and_score_native_pose ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_minimize_and_score_sugar ( bool const &  setting)
inline
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
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
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_PBP_clustering_at_chain_closure ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_reinitialize_CCD_torsions ( bool const &  setting)
inline
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
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
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_sampler_assert_no_virt_sugar_sampling ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_sampler_extra_beta_rotamer ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_sampler_extra_epsilon_rotamer ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_sampler_include_torsion_value_in_tag ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_sampler_max_centroid_distance ( core::Real const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_sampler_perform_phosphate_pack ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_sampler_try_sugar_instantiation ( bool const &  setting)
inline
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
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
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_VDW_rep_delete_matching_res ( utility::vector1< std::string > const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_VDW_rep_screen_physical_pose_clash_dist_cutoff ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_virtual_sugar_do_minimize ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_virtual_sugar_do_screens ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_virtual_sugar_keep_base_fixed ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::set_virtual_sugar_legacy_mode ( bool const &  setting)
inline
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
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
utility::vector1< std::string > const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::VDW_rep_delete_matching_res ( ) const
inline
bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::VDW_rep_screen_physical_pose_clash_dist_cutoff ( ) const
inline
bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::virtual_sugar_do_minimize ( ) const
inline
bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::virtual_sugar_do_screens ( ) const
inline
bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::virtual_sugar_keep_base_fixed ( ) const
inline
bool const& protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::virtual_sugar_legacy_mode ( ) const
inline

Member Data Documentation

bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::allow_base_pair_only_centroid_screen_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::allow_bulge_at_chainbreak_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::allow_rebuild_bulge_mode_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::allow_syn_pyrimidine_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::allow_virtual_o2prime_hydrogens_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::combine_long_loop_mode_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::distinguish_pucker_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::do_not_sample_multiple_virtual_sugar_
private
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
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::force_centroid_interaction_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::force_phosphate_instantiation_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::integration_test_mode_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::kic_modeler_if_relevant_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::minimize_and_score_native_pose_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::minimize_and_score_sugar_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::minimizer_rename_tag_
private
core::Real protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::native_edensity_score_cutoff_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::o2prime_legacy_mode_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::parin_favorite_output_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::PBP_clustering_at_chain_closure_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::reinitialize_CCD_torsions_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::rm_virt_phosphate_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::rna_legacy_output_mode_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sample_all_chi_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sample_ONLY_multiple_virtual_sugar_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_assert_no_virt_sugar_sampling_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_extra_beta_rotamer_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_extra_epsilon_rotamer_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_include_torsion_value_in_tag_
private
core::Real protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_max_centroid_distance_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_perform_phosphate_pack_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::sampler_try_sugar_instantiation_
private
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
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::use_phenix_geo_
private
core::Real protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::VDW_rep_alignment_RMSD_CUTOFF_
private
utility::vector1< std::string > protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::VDW_rep_delete_matching_res_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::VDW_rep_screen_physical_pose_clash_dist_cutoff_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::virtual_sugar_do_minimize_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::virtual_sugar_do_screens_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::virtual_sugar_keep_base_fixed_
private
bool protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions::virtual_sugar_legacy_mode_
private

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