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Variables
basic::options::OptionKeys::stepwise::rna Namespace Reference

Variables

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

Variable Documentation

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::add_virt_root

Referenced by add_rosetta_options_14().

StringVectorOptionKey const basic::options::OptionKeys::stepwise::rna::alignment_res

Referenced by add_rosetta_options_14().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::allow_base_pair_only_centroid_screen

Referenced by add_rosetta_options_14(), and main().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::allow_bulge_at_chainbreak

Referenced by add_rosetta_options_14(), and main().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::allow_chain_boundary_jump_partner_right_at_fixed_BP

Referenced by add_rosetta_options_14().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::allow_fixed_res_at_moving_res

Referenced by add_rosetta_options_14().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::allow_virtual_o2prime_hydrogens

Referenced by add_rosetta_options_14().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::centroid_screen

Referenced by add_rosetta_options_14(), and main().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::combine_helical_silent_file
BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::combine_long_loop_mode

Referenced by add_rosetta_options_14(), and main().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::distinguish_pucker
BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::do_not_sample_multiple_virtual_sugar

Referenced by add_rosetta_options_14(), and main().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::erraser

Referenced by add_rosetta_options_14().

FileOptionKey const basic::options::OptionKeys::stepwise::rna::filter_output_filename
BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::filter_user_alignment_res

Referenced by add_rosetta_options_14().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::finer_sampling_at_chain_closure

Referenced by add_rosetta_options_14().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::floating_base

Referenced by add_rosetta_options_14().

IntegerOptionKey const basic::options::OptionKeys::stepwise::rna::floating_base_anchor_res

Referenced by add_rosetta_options_14().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::force_centroid_interaction

Referenced by add_rosetta_options_14(), and main().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::force_phosphate_instantiation

Referenced by add_rosetta_options_14().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::force_user_defined_jumps

Referenced by add_rosetta_options_14().

IntegerVectorOptionKey const basic::options::OptionKeys::stepwise::rna::global_sample_res_list

Referenced by add_rosetta_options_14().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::integration_test
IntegerOptionKey const basic::options::OptionKeys::stepwise::rna::job_queue_ID

Referenced by add_rosetta_options_14().

StringVectorOptionKey const basic::options::OptionKeys::stepwise::rna::jump_point_pairs

Referenced by add_rosetta_options_14().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::minimize_and_score_native_pose

Referenced by add_rosetta_options_14(), and main().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::minimize_and_score_sugar

Referenced by add_rosetta_options_14(), and main().

IntegerVectorOptionKey const basic::options::OptionKeys::stepwise::rna::minimize_res

Referenced by add_rosetta_options_14().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::minimizer_rename_tag

Referenced by add_rosetta_options_14(), and main().

IntegerVectorOptionKey const basic::options::OptionKeys::stepwise::rna::missing_res

Referenced by add_rosetta_options_14().

IntegerVectorOptionKey const basic::options::OptionKeys::stepwise::rna::missing_res2

Referenced by add_rosetta_options_14().

IntegerVectorOptionKey const basic::options::OptionKeys::stepwise::rna::native_alignment_res

Referenced by add_rosetta_options_14().

RealOptionKey const basic::options::OptionKeys::stepwise::rna::native_edensity_score_cutoff

Referenced by add_rosetta_options_14(), and main().

IntegerVectorOptionKey const basic::options::OptionKeys::stepwise::rna::native_virtual_res
BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::o2prime_legacy_mode

Referenced by add_rosetta_options_14(), and main().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::output_extra_RMSDs

Referenced by add_rosetta_options_14().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::parin_favorite_output
BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::PBP_clustering_at_chain_closure
IntegerVectorOptionKey const basic::options::OptionKeys::stepwise::rna::protonated_H1_adenosine_list
BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::rebuild_bulge_mode

Referenced by add_rosetta_options_14(), and main().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::reinitialize_CCD_torsions

Referenced by add_rosetta_options_14(), and main().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::rm_virt_phosphate

Referenced by add_rosetta_options_14(), and main().

IntegerVectorOptionKey const basic::options::OptionKeys::stepwise::rna::rmsd_res
BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::rna

Referenced by add_rosetta_options_14().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::sample_all_chi

Referenced by add_rosetta_options_14().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::sample_both_sugar_base_rotamer

Referenced by add_rosetta_options_14(), and main().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::sample_ONLY_multiple_virtual_sugar

Referenced by add_rosetta_options_14(), and main().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::sampler_allow_syn_pyrimidine

Referenced by add_rosetta_options_14(), and main().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::sampler_assert_no_virt_sugar_sampling

Referenced by add_rosetta_options_14(), and main().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::sampler_extra_beta_rotamer

Referenced by add_rosetta_options_14(), and main().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::sampler_extra_chi_rotamer

Referenced by add_rosetta_options_14(), and main().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::sampler_extra_epsilon_rotamer

Referenced by add_rosetta_options_14(), and main().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::sampler_include_torsion_value_in_tag

Referenced by add_rosetta_options_14(), and main().

RealOptionKey const basic::options::OptionKeys::stepwise::rna::sampler_max_centroid_distance

Referenced by add_rosetta_options_14().

IntegerOptionKey const basic::options::OptionKeys::stepwise::rna::sampler_num_pose_kept

Referenced by add_rosetta_options_14(), and main().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::sampler_perform_phosphate_pack

Referenced by add_rosetta_options_14().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::sampler_try_sugar_instantiation

Referenced by add_rosetta_options_14(), and main().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::simple_append_map

Referenced by add_rosetta_options_14().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::tether_jump

Referenced by add_rosetta_options_14().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::turn_off_rna_chem_map_during_optimize

Referenced by add_rosetta_options_14().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::VDW_atr_rep_screen

Referenced by add_rosetta_options_14(), and main().

RealOptionKey const basic::options::OptionKeys::stepwise::rna::VDW_rep_alignment_RMSD_CUTOFF
StringVectorOptionKey const basic::options::OptionKeys::stepwise::rna::VDW_rep_delete_matching_res
BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::VDW_rep_optimize_memory_usage

Referenced by add_rosetta_options_14().

StringVectorOptionKey const basic::options::OptionKeys::stepwise::rna::VDW_rep_screen_info
RealOptionKey const basic::options::OptionKeys::stepwise::rna::VDW_rep_screen_physical_pose_clash_dist_cutoff
BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::virtual_sugar_do_minimize

Referenced by add_rosetta_options_14().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::virtual_sugar_keep_base_fixed

Referenced by add_rosetta_options_14(), and main().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::virtual_sugar_legacy_mode