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

add_virt_root

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

extern

Referenced by main(), and setup_rna_working_parameters().

alignment_res

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

extern

Referenced by main(), and setup_rna_working_parameters().

allow_base_pair_only_centroid_screen

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

extern

Referenced by main().

allow_bulge_at_chainbreak

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

extern

Referenced by main().

allow_chain_boundary_jump_partner_right_at_fixed_BP

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

extern

Referenced by main(), and setup_rna_working_parameters().

allow_fixed_res_at_moving_res

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

extern

Referenced by main(), and setup_rna_working_parameters().

allow_virtual_o2prime_hydrogens

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

extern

centroid_screen

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

extern

Referenced by main(), and rna_resample_test().

combine_helical_silent_file

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

extern

Referenced by filter_combine_long_loop(), and main().

combine_long_loop_mode

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

extern

Referenced by main().

distinguish_pucker

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

extern

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

do_not_sample_multiple_virtual_sugar

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

extern

Referenced by main().

erraser

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

extern

filter_output_filename

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

extern

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

filter_user_alignment_res

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

extern

Referenced by main().

finer_sampling_at_chain_closure

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

extern

Referenced by main(), and rna_resample_test().

floating_base

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

extern

Referenced by main().

floating_base_anchor_res

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

extern

force_centroid_interaction

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

extern

Referenced by main().

force_phosphate_instantiation

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

extern

force_user_defined_jumps

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

extern

global_sample_res_list

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

extern

Referenced by main().

integration_test

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

extern

Referenced by rna_sample_virtual_sugar().

job_queue_ID

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

extern

Referenced by get_silent_file_tags(), and main().

jump_point_pairs

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

extern

Referenced by main(), and setup_rna_working_parameters().

minimize_and_score_native_pose

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

extern

Referenced by main(), and rna_resample_test().

minimize_and_score_sugar

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

extern

Referenced by create_scorefxn(), main(), and rna_resample_test().

minimize_res

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

extern

minimizer_rename_tag

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

extern

Referenced by main().

missing_res

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

extern

Referenced by get_input_res(), and main().

missing_res2

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

extern

Referenced by get_input_res(), and main().

native_alignment_res

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

extern

Referenced by hermann_phase_two_minimize(), main(), and setup_rna_working_parameters().

native_edensity_score_cutoff

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

extern

Referenced by main(), and rna_resample_test().

native_virtual_res

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

extern

Referenced by align_pdbs(), hermann_phase_two_minimize(), main(), and setup_pose_setup_class().

o2prime_legacy_mode

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

extern

Referenced by main().

output_extra_RMSDs

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

extern

Referenced by main().

parin_favorite_output

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

extern

Referenced by filter_combine_long_loop(), and main().

PBP_clustering_at_chain_closure

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

extern

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

protonated_H1_adenosine_list

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

extern

Referenced by main(), and post_rebuild_bulge_assembly().

rebuild_bulge_mode

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

extern

Referenced by main().

reinitialize_CCD_torsions

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

extern

Referenced by main().

rm_virt_phosphate

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

extern

Referenced by main().

rmsd_res

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

extern

Referenced by drrafter_error_estimation(), get_rmsd(), hermann_phase_two_minimize(), main(), setup_rna_working_parameters(), and swa_rna_cluster().

rna

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

extern

sample_all_chi

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

extern

sample_both_sugar_base_rotamer

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

extern

Referenced by main().

sample_ONLY_multiple_virtual_sugar

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

extern

Referenced by main().

sampler_allow_syn_pyrimidine

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

extern

Referenced by main().

sampler_assert_no_virt_sugar_sampling

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

extern

Referenced by main().

sampler_extra_beta_rotamer

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

extern

Referenced by main().

sampler_extra_chi_rotamer

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

extern

Referenced by main().

sampler_extra_epsilon_rotamer

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

extern

Referenced by main().

sampler_include_torsion_value_in_tag

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

extern

Referenced by main().

sampler_max_centroid_distance

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

extern

sampler_num_pose_kept

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

extern

Referenced by main(), and rna_resample_test().

sampler_perform_phosphate_pack

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

extern

sampler_try_sugar_instantiation

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

extern

Referenced by main().

simple_append_map

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

extern

Referenced by main().

tether_jump

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

extern

turn_off_rna_chem_map_during_optimize

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

extern

VDW_atr_rep_screen

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

extern

Referenced by main(), and rna_resample_test().

VDW_rep_alignment_RMSD_CUTOFF

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

extern

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

VDW_rep_delete_matching_res

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

extern

Referenced by main(), and swa_rna_cluster().

VDW_rep_optimize_memory_usage

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

extern

VDW_rep_screen_info

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

extern

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

VDW_rep_screen_physical_pose_clash_dist_cutoff

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

extern

Referenced by main(), and swa_rna_cluster().

virtual_sugar_do_minimize

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

extern

virtual_sugar_keep_base_fixed

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

extern

Referenced by main().

virtual_sugar_legacy_mode

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

extern

Referenced by main(), and rna_sample_virtual_sugar().