Namespaces
	design

	domainFusion

	RemodelLoopMover

	staged_sampling

Variables
BooleanOptionKey const	remodel ("remodel")

FileOptionKey const	blueprint ("remodel:blueprint")

IntegerOptionKey const	cstfilter ("remodel:cstfilter")

StringOptionKey const	cen_sfxn ("remodel:cen_sfxn")

BooleanOptionKey const	check_scored_centroid ("remodel:check_scored_centroid")

IntegerOptionKey const	num_trajectory ("remodel:num_trajectory")

IntegerOptionKey const	save_top ("remodel:save_top")

BooleanOptionKey const	swap_refine_confirm_protocols ("remodel:swap_refine_confirm_protocols")

BooleanOptionKey const	bypass_fragments ("remodel:bypass_fragments")

BooleanOptionKey const	use_same_length_fragments ("remodel:use_same_length_fragments")

BooleanOptionKey const	no_jumps ("remodel:no_jumps")

BooleanOptionKey const	use_blueprint_sequence ("remodel:use_blueprint_sequence ")

BooleanOptionKey const	quick_and_dirty ("remodel:quick_and_dirty ")

BooleanOptionKey const	checkpoint ("remodel:checkpoint ")

BooleanOptionKey const	use_pose_relax ("remodel:use_pose_relax ")

BooleanOptionKey const	use_cart_relax ("remodel:use_cart_relax ")

BooleanOptionKey const	free_relax ("remodel:free_relax ")

StringOptionKey const	generic_aa ("remodel:generic_aa")

RealOptionKey const	cluster_radius ("remodel:cluster_radius")

BooleanOptionKey const	use_clusters ("remodel:use_clusters")

BooleanOptionKey const	run_confirmation ("remodel:run_confirmation")

BooleanOptionKey const	cluster_on_entire_pose ("remodel:cluster_on_entire_pose")

IntegerOptionKey const	dr_cycles ("remodel:dr_cycles")

IntegerOptionKey const	two_chain_tree ("remodel:two_chain_tree")

IntegerOptionKey const	repeat_structure ("remodel:repeat_structure")

IntegerOptionKey const	lh_ex_limit ("remodel:lh_ex_limit")

StringVectorOptionKey const	lh_filter_string ("remodel:lh_filter_string")

IntegerOptionKey const	lh_cbreak_selection ("remodel:lh_cbreak_selection")

BooleanOptionKey const	lh_closure_filter ("remodel:lh_closure_filter")

BooleanOptionKey const	cen_minimize ("remodel:cen_minimize")

IntegerOptionKey const	core_cutoff ("remodel:core_cutoff")

IntegerOptionKey const	boundary_cutoff ("remodel:boundary_cutoff")

BooleanOptionKey const	resclass_by_sasa ("remodel:resclass_by_sasa")

RealOptionKey const	helical_rise ("remodel:helical_rise")

RealOptionKey const	helical_radius ("remodel:helical_radius")

RealOptionKey const	helical_omega ("remodel:helical_omega")

RealOptionKey const	COM_sd ("remodel:COM_sd")

RealOptionKey const	COM_tolerance ("remodel:COM_tolerance")

RealOptionKey const	vdw ("remodel:vdw")

RealOptionKey const	rama ("remodel:rama")

RealOptionKey const	cbeta ("remodel:cbeta")

RealOptionKey const	cenpack ("remodel:cenpack")

RealOptionKey const	rg_local ("remodel:rg_local")

RealOptionKey const	hb_lrbb ("remodel:hb_lrbb")

RealOptionKey const	hb_srbb ("remodel:hb_srbb")

RealOptionKey const	rg ("remodel:rg")

RealOptionKey const	rsigma ("remodel:rsigma")

RealOptionKey const	ss_pair ("remodel:ss_pair")

BooleanOptionKey const	build_disulf ("remodel:build_disulf")

RealOptionKey const	match_rt_limit ("remodel:match_rt_limit")

IntegerVectorOptionKey const	disulf_landing_range ("remodel:disulf_landing_range")