protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions Member List

This is the complete list of members for protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions, including all inherited members.

allow_base_pair_only_centroid_screen() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
allow_base_pair_only_centroid_screen_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
allow_bulge_at_chainbreak() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
allow_bulge_at_chainbreak_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
allow_rebuild_bulge_mode() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
allow_rebuild_bulge_mode_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
allow_syn_pyrimidine() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
allow_syn_pyrimidine_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
allow_virtual_o2prime_hydrogens() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
allow_virtual_o2prime_hydrogens_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
clone() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
combine_long_loop_mode() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
combine_long_loop_mode_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
distinguish_pucker() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
distinguish_pucker_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
do_not_sample_multiple_virtual_sugar() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
do_not_sample_multiple_virtual_sugar_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
extra_chi() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
extra_chi_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
finer_sampling_at_chain_closure() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
finer_sampling_at_chain_closure_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
force_centroid_interaction() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
force_centroid_interaction_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
force_phosphate_instantiation() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
force_phosphate_instantiation_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
initialize_from_command_line()	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
initialize_variables()	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	protected
integration_test_mode() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
integration_test_mode_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
kic_modeler_if_relevant() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
kic_modeler_if_relevant_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
minimize_and_score_native_pose() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
minimize_and_score_native_pose_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
minimize_and_score_sugar() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
minimize_and_score_sugar_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
minimizer_rename_tag() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
minimizer_rename_tag_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
native_edensity_score_cutoff() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
native_edensity_score_cutoff_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
o2prime_legacy_mode() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
o2prime_legacy_mode_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
parin_favorite_output() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
parin_favorite_output_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
parse_my_tag(utility::tag::TagCOP)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inlinevirtual
PBP_clustering_at_chain_closure() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
PBP_clustering_at_chain_closure_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
reinitialize_CCD_torsions() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
reinitialize_CCD_torsions_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
rm_virt_phosphate() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
rm_virt_phosphate_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
rna_legacy_output_mode() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
rna_legacy_output_mode_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
sample_all_chi() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
sample_all_chi_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
sample_ONLY_multiple_virtual_sugar() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
sample_ONLY_multiple_virtual_sugar_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
sampler_assert_no_virt_sugar_sampling() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
sampler_assert_no_virt_sugar_sampling_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
sampler_extra_beta_rotamer() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
sampler_extra_beta_rotamer_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
sampler_extra_epsilon_rotamer() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
sampler_extra_epsilon_rotamer_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
sampler_include_torsion_value_in_tag() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
sampler_include_torsion_value_in_tag_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
sampler_max_centroid_distance() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
sampler_max_centroid_distance_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
sampler_perform_phosphate_pack() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
sampler_perform_phosphate_pack_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
sampler_try_sugar_instantiation() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
sampler_try_sugar_instantiation_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
set_allow_base_pair_only_centroid_screen(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_allow_bulge_at_chainbreak(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_allow_rebuild_bulge_mode(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_allow_syn_pyrimidine(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_allow_virtual_o2prime_hydrogens(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_combine_long_loop_mode(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_distinguish_pucker(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_do_not_sample_multiple_virtual_sugar(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_extra_chi(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_finer_sampling_at_chain_closure(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_force_centroid_interaction(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_force_phosphate_instantiation(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_integration_test_mode(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_kic_modeler_if_relevant(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_minimize_and_score_native_pose(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_minimize_and_score_sugar(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_minimizer_rename_tag(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_native_edensity_score_cutoff(core::Real const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_o2prime_legacy_mode(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_parin_favorite_output(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_PBP_clustering_at_chain_closure(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_reinitialize_CCD_torsions(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_rm_virt_phosphate(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_rna_legacy_output_mode(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_sample_all_chi(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_sample_ONLY_multiple_virtual_sugar(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_sampler_assert_no_virt_sugar_sampling(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_sampler_extra_beta_rotamer(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_sampler_extra_epsilon_rotamer(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_sampler_include_torsion_value_in_tag(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_sampler_max_centroid_distance(core::Real const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_sampler_perform_phosphate_pack(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_sampler_try_sugar_instantiation(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_tether_jump(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_turn_off_rna_chem_map_during_optimize(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_use_phenix_geo(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_VDW_rep_alignment_RMSD_CUTOFF(core::Real const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_VDW_rep_delete_matching_res(utility::vector1< std::string > const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_VDW_rep_screen_physical_pose_clash_dist_cutoff(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_virtual_sugar_do_minimize(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_virtual_sugar_do_screens(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_virtual_sugar_keep_base_fixed(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
set_virtual_sugar_legacy_mode(bool const &setting)	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
show(std::ostream &) const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inlinevirtual
StepWiseRNA_ModelerOptions()	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
tether_jump() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
tether_jump_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
turn_off_rna_chem_map_during_optimize() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
turn_off_rna_chem_map_during_optimize_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
type() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inlinevirtual
use_phenix_geo() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
use_phenix_geo_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
VDW_rep_alignment_RMSD_CUTOFF() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
VDW_rep_alignment_RMSD_CUTOFF_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
VDW_rep_delete_matching_res() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
VDW_rep_delete_matching_res_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
VDW_rep_screen_physical_pose_clash_dist_cutoff() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
VDW_rep_screen_physical_pose_clash_dist_cutoff_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
virtual_sugar_do_minimize() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
virtual_sugar_do_minimize_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
virtual_sugar_do_screens() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
virtual_sugar_do_screens_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
virtual_sugar_keep_base_fixed() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
virtual_sugar_keep_base_fixed_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private
virtual_sugar_legacy_mode() const	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	inline
virtual_sugar_legacy_mode_	protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions	private