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

Referenced by add_rosetta_options_14(), and filter_combine_long_loop().

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

Referenced by add_rosetta_options_14(), main(), and swa_rna_cluster().

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

Referenced by add_rosetta_options_14(), and filter_combine_long_loop().

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

Referenced by add_rosetta_options_14(), and rna_sample_virtual_sugar().

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

Referenced by add_rosetta_options_14(), align_pdbs(), and main().

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

Referenced by add_rosetta_options_14(), filter_combine_long_loop(), and main().

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

Referenced by add_rosetta_options_14(), main(), and swa_rna_cluster().

IntegerVectorOptionKey const basic::options::OptionKeys::stepwise::rna::protonated_H1_adenosine_list

Referenced by add_rosetta_options_14(), and post_rebuild_bulge_assembly().

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

Referenced by add_rosetta_options_14(), drrafter_error_estimation(), main(), and swa_rna_cluster().

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

Referenced by add_rosetta_options_14(), main(), and swa_rna_cluster().

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

Referenced by add_rosetta_options_14(), main(), and swa_rna_cluster().

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

Referenced by add_rosetta_options_14(), main(), and swa_rna_cluster().

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

Referenced by add_rosetta_options_14(), main(), and swa_rna_cluster().

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

Referenced by add_rosetta_options_14(), main(), and rna_sample_virtual_sugar().