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

Variables
BooleanOptionKey const	rna ("stepwise:rna")
IntegerOptionKey const	sampler_num_pose_kept ("stepwise:rna:sampler_num_pose_kept")
BooleanOptionKey const	sampler_native_rmsd_screen ("stepwise:rna:sampler_native_rmsd_screen")
RealOptionKey const	sampler_native_screen_rmsd_cutoff ("stepwise:rna:sampler_native_screen_rmsd_cutoff")
RealOptionKey const	sampler_cluster_rmsd ("stepwise:rna:sampler_cluster_rmsd")
RealOptionKey const	native_edensity_score_cutoff ("stepwise:rna:native_edensity_score_cutoff")
BooleanOptionKey const	sampler_perform_o2prime_pack ("stepwise:rna:sampler_perform_o2prime_pack")
BooleanOptionKey const	sampler_perform_phosphate_pack ("stepwise:rna:sampler_perform_phosphate_pack")
BooleanOptionKey const	VERBOSE ("stepwise:rna:VERBOSE")
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	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	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	skip_sampling ("stepwise:rna:skip_sampling")
BooleanOptionKey const	minimizer_perform_minimize ("stepwise:rna:minimizer_perform_minimize")
BooleanOptionKey const	minimize_and_score_native_pose ("stepwise:rna:minimize_and_score_native_pose")
BooleanOptionKey const	rm_virt_phosphate ("stepwise:rna:rm_virt_phosphate")
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_output_before_o2prime_pack ("stepwise:rna:minimizer_output_before_o2prime_pack")
BooleanOptionKey const	minimizer_perform_o2prime_pack ("stepwise:rna:minimizer_perform_o2prime_pack")
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	force_syn_chi_res_list ("stepwise:rna:force_syn_chi_res_list")
IntegerVectorOptionKey const	force_north_sugar_list ("stepwise:rna:force_north_sugar_list")
IntegerVectorOptionKey const	force_south_sugar_list ("stepwise:rna:force_south_sugar_list")
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")
IntegerVectorOptionKey const	terminal_res ("stepwise:rna:terminal_res")
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")
IntegerVectorOptionKey const	bulge_res ("stepwise:rna:bulge_res")
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	output_pdb ("stepwise:rna:output_pdb")
BooleanOptionKey const	tether_jump ("stepwise:rna:tether_jump")
BooleanOptionKey const	unified_framework ("stepwise:rna:unified_framework")

Variable Documentation

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_0(), and add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::minimizer_output_before_o2prime_pack

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::minimizer_perform_o2prime_pack

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_2(), and add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::stepwise::rna::sampler_perform_o2prime_pack

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().

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

Referenced by add_rosetta_options_3().