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	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_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"

)