Rosetta  2020.37
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Functions
stepwise::rna Namespace Reference

Functions

BooleanOptionKey const rna ("stepwise:rna")
 
IntegerOptionKey const sampler_num_pose_kept ("stepwise:rna:sampler_num_pose_kept")
 
RealOptionKey const native_edensity_score_cutoff ("stepwise:rna:native_edensity_score_cutoff")
 
BooleanOptionKey const o2prime_legacy_mode ("stepwise:rna:o2prime_legacy_mode")
 
BooleanOptionKey const allow_virtual_o2prime_hydrogens ("stepwise:rna:allow_virtual_o2prime_hydrogens")
 
BooleanOptionKey const sampler_perform_phosphate_pack ("stepwise:rna:sampler_perform_phosphate_pack")
 
BooleanOptionKey const force_phosphate_instantiation ("stepwise:rna:force_phosphate_instantiation")
 
BooleanOptionKey const distinguish_pucker ("stepwise:rna:distinguish_pucker")
 
BooleanOptionKey const finer_sampling_at_chain_closure ("stepwise:rna:finer_sampling_at_chain_closure")
 
BooleanOptionKey const PBP_clustering_at_chain_closure ("stepwise:rna:PBP_clustering_at_chain_closure")
 
BooleanOptionKey const sample_all_chi ("stepwise:rna:sample_all_chi")
 
BooleanOptionKey const sampler_allow_syn_pyrimidine ("stepwise:rna:sampler_allow_syn_pyrimidine")
 
BooleanOptionKey const sampler_extra_chi_rotamer ("stepwise:rna:sampler_extra_chi_rotamer")
 
BooleanOptionKey const sampler_extra_beta_rotamer ("stepwise:rna:sampler_extra_beta_rotamer")
 
BooleanOptionKey const sampler_extra_epsilon_rotamer ("stepwise:rna:sampler_extra_epsilon_rotamer")
 
BooleanOptionKey const force_centroid_interaction ("stepwise:rna:force_centroid_interaction")
 
BooleanOptionKey const virtual_sugar_legacy_mode ("stepwise:rna:virtual_sugar_legacy_mode")
 
BooleanOptionKey const VDW_rep_optimize_memory_usage ("stepwise:rna:VDW_rep_optimize_memory_usage")
 
BooleanOptionKey const erraser ("stepwise:rna:erraser")
 
BooleanOptionKey const centroid_screen ("stepwise:rna:centroid_screen")
 
BooleanOptionKey const VDW_atr_rep_screen ("stepwise:rna:VDW_atr_rep_screen")
 
BooleanOptionKey const minimize_and_score_native_pose ("stepwise:rna:minimize_and_score_native_pose")
 
BooleanOptionKey const rm_virt_phosphate ("stepwise:rna:rm_virt_phosphate")
 
StringVectorOptionKey const VDW_rep_screen_info ("stepwise:rna:VDW_rep_screen_info")
 
RealOptionKey const VDW_rep_alignment_RMSD_CUTOFF ("stepwise:rna:VDW_rep_alignment_RMSD_CUTOFF")
 
StringVectorOptionKey const VDW_rep_delete_matching_res ("stepwise:rna:VDW_rep_delete_matching_res")
 
RealOptionKey const VDW_rep_screen_physical_pose_clash_dist_cutoff ("stepwise:rna:VDW_rep_screen_physical_pose_clash_dist_cutoff")
 
BooleanOptionKey const integration_test ("stepwise:rna:integration_test")
 
BooleanOptionKey const allow_bulge_at_chainbreak ("stepwise:rna:allow_bulge_at_chainbreak")
 
BooleanOptionKey const parin_favorite_output ("stepwise:rna:parin_favorite_output")
 
BooleanOptionKey const reinitialize_CCD_torsions ("stepwise:rna:reinitialize_CCD_torsions")
 
BooleanOptionKey const sample_both_sugar_base_rotamer ("stepwise:rna:sample_both_sugar_base_rotamer")
 
BooleanOptionKey const sampler_include_torsion_value_in_tag ("stepwise:rna:sampler_include_torsion_value_in_tag")
 
BooleanOptionKey const sampler_assert_no_virt_sugar_sampling ("stepwise:rna:sampler_assert_no_virt_sugar_sampling")
 
BooleanOptionKey const sampler_try_sugar_instantiation ("stepwise:rna:sampler_try_sugar_instantiation")
 
BooleanOptionKey const do_not_sample_multiple_virtual_sugar ("stepwise:rna:do_not_sample_multiple_virtual_sugar")
 
BooleanOptionKey const sample_ONLY_multiple_virtual_sugar ("stepwise:rna:sample_ONLY_multiple_virtual_sugar")
 
BooleanOptionKey const allow_base_pair_only_centroid_screen ("stepwise:rna:allow_base_pair_only_centroid_screen")
 
BooleanOptionKey const minimizer_rename_tag ("stepwise:rna:minimizer_rename_tag")
 
IntegerVectorOptionKey const minimize_res ("stepwise:rna:minimize_res")
 
StringVectorOptionKey const alignment_res ("stepwise:rna:alignment_res")
 
IntegerVectorOptionKey const native_alignment_res ("stepwise:rna:native_alignment_res")
 
IntegerVectorOptionKey const rmsd_res ("stepwise:rna:rmsd_res")
 
IntegerVectorOptionKey const missing_res ("stepwise:rna:missing_res")
 
IntegerVectorOptionKey const missing_res2 ("stepwise:rna:missing_res2")
 
IntegerOptionKey const job_queue_ID ("stepwise:rna:job_queue_ID")
 
BooleanOptionKey const minimize_and_score_sugar ("stepwise:rna:minimize_and_score_sugar")
 
IntegerVectorOptionKey const global_sample_res_list ("stepwise:rna:global_sample_res_list")
 
FileOptionKey const filter_output_filename ("stepwise:rna:filter_output_filename")
 
BooleanOptionKey const combine_long_loop_mode ("stepwise:rna:combine_long_loop_mode")
 
BooleanOptionKey const combine_helical_silent_file ("stepwise:rna:combine_helical_silent_file")
 
BooleanOptionKey const output_extra_RMSDs ("stepwise:rna:output_extra_RMSDs")
 
IntegerVectorOptionKey const protonated_H1_adenosine_list ("stepwise:rna:protonated_H1_adenosine_list")
 
IntegerVectorOptionKey const native_virtual_res ("stepwise:rna:native_virtual_res")
 
BooleanOptionKey const simple_append_map ("stepwise:rna:simple_append_map")
 
BooleanOptionKey const allow_fixed_res_at_moving_res ("stepwise:rna:allow_fixed_res_at_moving_res")
 
BooleanOptionKey const force_user_defined_jumps ("stepwise:rna:force_user_defined_jumps")
 
StringVectorOptionKey const jump_point_pairs ("stepwise:rna:jump_point_pairs")
 
BooleanOptionKey const add_virt_root ("stepwise:rna:add_virt_root")
 
BooleanOptionKey const floating_base ("stepwise:rna:floating_base")
 
IntegerOptionKey const floating_base_anchor_res ("stepwise:rna:floating_base_anchor_res")
 
BooleanOptionKey const allow_chain_boundary_jump_partner_right_at_fixed_BP ("stepwise:rna:allow_chain_boundary_jump_partner_right_at_fixed_BP")
 
BooleanOptionKey const rebuild_bulge_mode ("stepwise:rna:rebuild_bulge_mode")
 
BooleanOptionKey const virtual_sugar_keep_base_fixed ("stepwise:rna:virtual_sugar_keep_base_fixed")
 
BooleanOptionKey const virtual_sugar_do_minimize ("stepwise:rna:virtual_sugar_do_minimize")
 
RealOptionKey const sampler_max_centroid_distance ("stepwise:rna:sampler_max_centroid_distance")
 
BooleanOptionKey const filter_user_alignment_res ("stepwise:rna:filter_user_alignment_res")
 
BooleanOptionKey const tether_jump ("stepwise:rna:tether_jump")
 
BooleanOptionKey const turn_off_rna_chem_map_during_optimize ("stepwise:rna:turn_off_rna_chem_map_during_optimize")
 

Function Documentation

BooleanOptionKey const stepwise::rna::add_virt_root ( "stepwise:rna:add_virt_root"  )
StringVectorOptionKey const stepwise::rna::alignment_res ( "stepwise:rna:alignment_res"  )
BooleanOptionKey const stepwise::rna::allow_base_pair_only_centroid_screen ( "stepwise:rna:allow_base_pair_only_centroid_screen"  )
BooleanOptionKey const stepwise::rna::allow_bulge_at_chainbreak ( "stepwise:rna:allow_bulge_at_chainbreak"  )
BooleanOptionKey const stepwise::rna::allow_chain_boundary_jump_partner_right_at_fixed_BP ( "stepwise:rna:allow_chain_boundary_jump_partner_right_at_fixed_BP"  )
BooleanOptionKey const stepwise::rna::allow_fixed_res_at_moving_res ( "stepwise:rna:allow_fixed_res_at_moving_res"  )
BooleanOptionKey const stepwise::rna::allow_virtual_o2prime_hydrogens ( "stepwise:rna:allow_virtual_o2prime_hydrogens"  )
BooleanOptionKey const stepwise::rna::centroid_screen ( "stepwise:rna:centroid_screen"  )
BooleanOptionKey const stepwise::rna::combine_helical_silent_file ( "stepwise:rna:combine_helical_silent_file"  )
BooleanOptionKey const stepwise::rna::combine_long_loop_mode ( "stepwise:rna:combine_long_loop_mode"  )
BooleanOptionKey const stepwise::rna::distinguish_pucker ( "stepwise:rna:distinguish_pucker"  )
BooleanOptionKey const stepwise::rna::do_not_sample_multiple_virtual_sugar ( "stepwise:rna:do_not_sample_multiple_virtual_sugar"  )
BooleanOptionKey const stepwise::rna::erraser ( "stepwise:rna:erraser"  )
FileOptionKey const stepwise::rna::filter_output_filename ( "stepwise:rna:filter_output_filename"  )
BooleanOptionKey const stepwise::rna::filter_user_alignment_res ( "stepwise:rna:filter_user_alignment_res"  )
BooleanOptionKey const stepwise::rna::finer_sampling_at_chain_closure ( "stepwise:rna:finer_sampling_at_chain_closure"  )
BooleanOptionKey const stepwise::rna::floating_base ( "stepwise:rna:floating_base"  )
IntegerOptionKey const stepwise::rna::floating_base_anchor_res ( "stepwise:rna:floating_base_anchor_res"  )
BooleanOptionKey const stepwise::rna::force_centroid_interaction ( "stepwise:rna:force_centroid_interaction"  )
BooleanOptionKey const stepwise::rna::force_phosphate_instantiation ( "stepwise:rna:force_phosphate_instantiation"  )
BooleanOptionKey const stepwise::rna::force_user_defined_jumps ( "stepwise:rna:force_user_defined_jumps"  )
IntegerVectorOptionKey const stepwise::rna::global_sample_res_list ( "stepwise:rna:global_sample_res_list"  )
BooleanOptionKey const stepwise::rna::integration_test ( "stepwise:rna:integration_test"  )
IntegerOptionKey const stepwise::rna::job_queue_ID ( "stepwise:rna:job_queue_ID"  )
StringVectorOptionKey const stepwise::rna::jump_point_pairs ( "stepwise:rna:jump_point_pairs"  )
BooleanOptionKey const stepwise::rna::minimize_and_score_native_pose ( "stepwise:rna:minimize_and_score_native_pose"  )
BooleanOptionKey const stepwise::rna::minimize_and_score_sugar ( "stepwise:rna:minimize_and_score_sugar"  )
IntegerVectorOptionKey const stepwise::rna::minimize_res ( "stepwise:rna:minimize_res"  )
BooleanOptionKey const stepwise::rna::minimizer_rename_tag ( "stepwise:rna:minimizer_rename_tag"  )
IntegerVectorOptionKey const stepwise::rna::missing_res ( "stepwise:rna:missing_res"  )
IntegerVectorOptionKey const stepwise::rna::missing_res2 ( "stepwise:rna:missing_res2"  )
IntegerVectorOptionKey const stepwise::rna::native_alignment_res ( "stepwise:rna:native_alignment_res"  )
RealOptionKey const stepwise::rna::native_edensity_score_cutoff ( "stepwise:rna:native_edensity_score_cutoff"  )
IntegerVectorOptionKey const stepwise::rna::native_virtual_res ( "stepwise:rna:native_virtual_res"  )
BooleanOptionKey const stepwise::rna::o2prime_legacy_mode ( "stepwise:rna:o2prime_legacy_mode"  )
BooleanOptionKey const stepwise::rna::output_extra_RMSDs ( "stepwise:rna:output_extra_RMSDs"  )
BooleanOptionKey const stepwise::rna::parin_favorite_output ( "stepwise:rna:parin_favorite_output"  )
BooleanOptionKey const stepwise::rna::PBP_clustering_at_chain_closure ( "stepwise:rna:PBP_clustering_at_chain_closure"  )
IntegerVectorOptionKey const stepwise::rna::protonated_H1_adenosine_list ( "stepwise:rna:protonated_H1_adenosine_list"  )
BooleanOptionKey const stepwise::rna::rebuild_bulge_mode ( "stepwise:rna:rebuild_bulge_mode"  )
BooleanOptionKey const stepwise::rna::reinitialize_CCD_torsions ( "stepwise:rna:reinitialize_CCD_torsions"  )
BooleanOptionKey const stepwise::rna::rm_virt_phosphate ( "stepwise:rna:rm_virt_phosphate"  )
IntegerVectorOptionKey const stepwise::rna::rmsd_res ( "stepwise:rna:rmsd_res"  )
BooleanOptionKey const stepwise::rna::rna ( "stepwise:rna"  )
BooleanOptionKey const stepwise::rna::sample_all_chi ( "stepwise:rna:sample_all_chi"  )
BooleanOptionKey const stepwise::rna::sample_both_sugar_base_rotamer ( "stepwise:rna:sample_both_sugar_base_rotamer"  )
BooleanOptionKey const stepwise::rna::sample_ONLY_multiple_virtual_sugar ( "stepwise:rna:sample_ONLY_multiple_virtual_sugar"  )
BooleanOptionKey const stepwise::rna::sampler_allow_syn_pyrimidine ( "stepwise:rna:sampler_allow_syn_pyrimidine"  )
BooleanOptionKey const stepwise::rna::sampler_assert_no_virt_sugar_sampling ( "stepwise:rna:sampler_assert_no_virt_sugar_sampling"  )
BooleanOptionKey const stepwise::rna::sampler_extra_beta_rotamer ( "stepwise:rna:sampler_extra_beta_rotamer"  )
BooleanOptionKey const stepwise::rna::sampler_extra_chi_rotamer ( "stepwise:rna:sampler_extra_chi_rotamer"  )
BooleanOptionKey const stepwise::rna::sampler_extra_epsilon_rotamer ( "stepwise:rna:sampler_extra_epsilon_rotamer"  )
BooleanOptionKey const stepwise::rna::sampler_include_torsion_value_in_tag ( "stepwise:rna:sampler_include_torsion_value_in_tag"  )
RealOptionKey const stepwise::rna::sampler_max_centroid_distance ( "stepwise:rna:sampler_max_centroid_distance"  )
IntegerOptionKey const stepwise::rna::sampler_num_pose_kept ( "stepwise:rna:sampler_num_pose_kept"  )
BooleanOptionKey const stepwise::rna::sampler_perform_phosphate_pack ( "stepwise:rna:sampler_perform_phosphate_pack"  )
BooleanOptionKey const stepwise::rna::sampler_try_sugar_instantiation ( "stepwise:rna:sampler_try_sugar_instantiation"  )
BooleanOptionKey const stepwise::rna::simple_append_map ( "stepwise:rna:simple_append_map"  )
BooleanOptionKey const stepwise::rna::tether_jump ( "stepwise:rna:tether_jump"  )
BooleanOptionKey const stepwise::rna::turn_off_rna_chem_map_during_optimize ( "stepwise:rna:turn_off_rna_chem_map_during_optimize"  )
BooleanOptionKey const stepwise::rna::VDW_atr_rep_screen ( "stepwise:rna:VDW_atr_rep_screen"  )
RealOptionKey const stepwise::rna::VDW_rep_alignment_RMSD_CUTOFF ( "stepwise:rna:VDW_rep_alignment_RMSD_CUTOFF"  )
StringVectorOptionKey const stepwise::rna::VDW_rep_delete_matching_res ( "stepwise:rna:VDW_rep_delete_matching_res"  )
BooleanOptionKey const stepwise::rna::VDW_rep_optimize_memory_usage ( "stepwise:rna:VDW_rep_optimize_memory_usage"  )
StringVectorOptionKey const stepwise::rna::VDW_rep_screen_info ( "stepwise:rna:VDW_rep_screen_info"  )
RealOptionKey const stepwise::rna::VDW_rep_screen_physical_pose_clash_dist_cutoff ( "stepwise:rna:VDW_rep_screen_physical_pose_clash_dist_cutoff"  )
BooleanOptionKey const stepwise::rna::virtual_sugar_do_minimize ( "stepwise:rna:virtual_sugar_do_minimize"  )
BooleanOptionKey const stepwise::rna::virtual_sugar_keep_base_fixed ( "stepwise:rna:virtual_sugar_keep_base_fixed"  )
BooleanOptionKey const stepwise::rna::virtual_sugar_legacy_mode ( "stepwise:rna:virtual_sugar_legacy_mode"  )