Rosetta Protocols  2014.16.56682
protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions Member List

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

allow_base_pair_only_centroid_screen() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
allow_base_pair_only_centroid_screen_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
allow_bulge_at_chainbreak() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
allow_bulge_at_chainbreak_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
allow_syn_pyrimidine() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
allow_syn_pyrimidine_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
choose_random() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
choose_random_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
clone() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions
cluster_rmsd() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
cluster_rmsd_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
combine_long_loop_mode() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
combine_long_loop_mode_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
distinguish_pucker() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
distinguish_pucker_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
do_not_sample_multiple_virtual_sugar() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
do_not_sample_multiple_virtual_sugar_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
extra_chi() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
extra_chi_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
finer_sampling_at_chain_closure() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
finer_sampling_at_chain_closure_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
force_centroid_interaction() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
force_centroid_interaction_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
initialize_from_command_line()protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions
initialize_variables()protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
integration_test_mode() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
integration_test_mode_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
kic_sampling_if_relevant() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
kic_sampling_if_relevant_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
minimize_and_score_native_pose() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
minimize_and_score_native_pose_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
minimize_and_score_sugar() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
minimize_and_score_sugar_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
minimizer_allow_variable_bond_geometry() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
minimizer_allow_variable_bond_geometry_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
minimizer_output_before_o2prime_pack() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
minimizer_output_before_o2prime_pack_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
minimizer_perform_o2prime_pack() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
minimizer_perform_o2prime_pack_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
minimizer_rename_tag() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
minimizer_rename_tag_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
minimizer_vary_bond_geometry_frequency() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
minimizer_vary_bond_geometry_frequency_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
native_edensity_score_cutoff() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
native_edensity_score_cutoff_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
num_pose_minimize() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
num_pose_minimize_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
num_random_samples() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
num_random_samples_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
operator=(StepWiseRNA_ModelerOptions const &src)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions
output_minimized_pose_list() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
output_minimized_pose_list_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
output_pdb() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
output_pdb_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
parin_favorite_output() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
parin_favorite_output_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
parse_my_tag(utility::tag::TagCOP)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinlinevirtual
PBP_clustering_at_chain_closure() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
PBP_clustering_at_chain_closure_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
perform_minimize() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
perform_minimize_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
reinitialize_CCD_torsions() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
reinitialize_CCD_torsions_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
rm_virt_phosphate() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
rm_virt_phosphate_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
sample_ONLY_multiple_virtual_sugar() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
sample_ONLY_multiple_virtual_sugar_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
sampler_assert_no_virt_sugar_sampling() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
sampler_assert_no_virt_sugar_sampling_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
sampler_extra_beta_rotamer() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
sampler_extra_beta_rotamer_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
sampler_extra_epsilon_rotamer() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
sampler_extra_epsilon_rotamer_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
sampler_include_torsion_value_in_tag() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
sampler_include_torsion_value_in_tag_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
sampler_max_centroid_distance() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
sampler_max_centroid_distance_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
sampler_native_rmsd_screen() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
sampler_native_rmsd_screen_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
sampler_native_screen_rmsd_cutoff() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
sampler_native_screen_rmsd_cutoff_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
sampler_num_pose_kept() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
sampler_num_pose_kept_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
sampler_perform_o2prime_pack() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
sampler_perform_o2prime_pack_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
sampler_perform_phosphate_pack() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
sampler_perform_phosphate_pack_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
sampler_try_sugar_instantiation() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
sampler_try_sugar_instantiation_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
set_allow_base_pair_only_centroid_screen(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_allow_bulge_at_chainbreak(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_allow_syn_pyrimidine(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_choose_random(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_cluster_rmsd(core::Real const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_combine_long_loop_mode(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_distinguish_pucker(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_do_not_sample_multiple_virtual_sugar(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_extra_chi(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_finer_sampling_at_chain_closure(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_force_centroid_interaction(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_integration_test_mode(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_kic_sampling_if_relevant(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_minimize_and_score_native_pose(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_minimize_and_score_sugar(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_minimizer_allow_variable_bond_geometry(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_minimizer_output_before_o2prime_pack(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_minimizer_perform_o2prime_pack(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_minimizer_rename_tag(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_minimizer_vary_bond_geometry_frequency(core::Real const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_native_edensity_score_cutoff(core::Real const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_num_pose_minimize(core::Size const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_num_random_samples(Size const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_output_minimized_pose_list(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_output_pdb(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_parin_favorite_output(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_PBP_clustering_at_chain_closure(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_perform_minimize(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_reinitialize_CCD_torsions(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_rm_virt_phosphate(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_sample_ONLY_multiple_virtual_sugar(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_sampler_assert_no_virt_sugar_sampling(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_sampler_extra_beta_rotamer(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_sampler_extra_epsilon_rotamer(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_sampler_include_torsion_value_in_tag(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_sampler_max_centroid_distance(core::Real const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_sampler_native_rmsd_screen(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_sampler_native_screen_rmsd_cutoff(core::Real const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_sampler_num_pose_kept(core::Size const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_sampler_perform_o2prime_pack(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_sampler_perform_phosphate_pack(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_sampler_try_sugar_instantiation(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_silent_file(std::string const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_skip_sampling(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_tether_jump(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_unified_framework(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_use_green_packer(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_use_phenix_geo(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_VDW_atr_rep_screen(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_VDW_rep_alignment_RMSD_CUTOFF(core::Real const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_VDW_rep_screen_physical_pose_clash_dist_cutoff(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_verbose(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_virtual_sugar_do_minimize(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_virtual_sugar_keep_base_fixed(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
set_virtual_sugar_legacy_mode(bool const &setting)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
setup_options_for_VDW_bin_checker(checker::RNA_VDW_BinCheckerOP user_input_VDW_bin_checker) const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions
show(std::ostream &) const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinlinevirtual
silent_file() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
silent_file_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
skip_sampling() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
skip_sampling_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
StepWiseRNA_ModelerOptions()protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions
StepWiseRNA_ModelerOptions(StepWiseRNA_ModelerOptions const &src)protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions
tether_jump() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
tether_jump_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
type() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinlinevirtual
unified_framework() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
unified_framework_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
use_green_packer() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
use_green_packer_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
use_phenix_geo() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
use_phenix_geo_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
VDW_atr_rep_screen() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
VDW_atr_rep_screen_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
VDW_rep_alignment_RMSD_CUTOFF() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
VDW_rep_alignment_RMSD_CUTOFF_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
VDW_rep_delete_matching_res_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
VDW_rep_screen_physical_pose_clash_dist_cutoff() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
VDW_rep_screen_physical_pose_clash_dist_cutoff_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
verbose() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
verbose_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
virtual_sugar_do_minimize() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
virtual_sugar_do_minimize_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
virtual_sugar_keep_base_fixed() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
virtual_sugar_keep_base_fixed_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
virtual_sugar_legacy_mode() const protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsinline
virtual_sugar_legacy_mode_protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsprivate
~StepWiseRNA_ModelerOptions()protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions
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