basic::options::OptionKeys::loops Namespace Reference

Namespaces
	ccd

Variables
BooleanOptionKey const	loops
StringOptionKey const	cen_weights
StringOptionKey const	cen_patch
FileOptionKey const	input_pdb
	Input options#####################################. More...
StringVectorOptionKey const	loop_file
FileOptionKey const	extended_loop_file
FileOptionKey const	mm_loop_file
BooleanOptionKey const	fix_natsc
BooleanOptionKey const	refine_only
BooleanOptionKey const	fast
FileOptionKey const	vall_file
IntegerVectorOptionKey const	frag_sizes
FileVectorOptionKey const	frag_files
FileOptionKey const	output_pdb
BooleanOptionKey const	debug
BooleanOptionKey const	build_initial
BooleanOptionKey const	extended
BooleanOptionKey const	remove_extended_loops
BooleanOptionKey const	idealize_after_loop_close
BooleanOptionKey const	idealize_before_loop_close
IntegerOptionKey const	select_best_loop_from
IntegerOptionKey const	build_attempts
IntegerOptionKey const	grow_attempts
RealOptionKey const	random_grow_loops_by
BooleanOptionKey const	accept_aborted_loops
BooleanOptionKey const	strict_loops
BooleanOptionKey const	superimpose_native
IntegerVectorOptionKey const	build_specific_loops
BooleanOptionKey const	random_order
BooleanOptionKey const	build_all_loops
BooleanOptionKey const	fa_closure_protocol
RealOptionKey const	combine_rate
BooleanOptionKey const	skip_initial_loop_build
StringOptionKey const	remodel
StringOptionKey const	intermedrelax
StringOptionKey const	refine
StringOptionKey const	relax
BooleanOptionKey const	final_clean_fastrelax
BooleanOptionKey const	relax_with_foldtree
RealOptionKey const	constrain_rigid_segments
StringOptionKey const	loopscores
BooleanOptionKey const	timer
BooleanOptionKey const	vicinity_sampling
RealOptionKey const	vicinity_degree
RealOptionKey const	neighbor_dist
IntegerOptionKey const	kic_max_seglen
BooleanOptionKey const	kic_recover_last
BooleanOptionKey const	kic_min_after_repack
BooleanOptionKey const	optimize_only_kic_region_sidechains_after_move
IntegerOptionKey const	max_kic_build_attempts
IntegerOptionKey const	remodel_kic_attempts
IntegerOptionKey const	max_kic_perturber_samples
BooleanOptionKey const	nonpivot_torsion_sampling
BooleanOptionKey const	fix_ca_bond_angles
BooleanOptionKey const	kic_use_linear_chainbreak
BooleanOptionKey const	sample_omega_at_pre_prolines
BooleanOptionKey const	allow_omega_move
BooleanOptionKey const	kic_with_cartmin
BooleanOptionKey const	allow_takeoff_torsion_move
IntegerOptionKey const	extend_length
IntegerOptionKey const	perturb_outer_cycles
IntegerOptionKey const	refine_outer_cycles
IntegerOptionKey const	max_inner_cycles
IntegerOptionKey const	repack_period
RealOptionKey const	remodel_init_temp
RealOptionKey const	remodel_final_temp
RealOptionKey const	refine_init_temp
RealOptionKey const	refine_final_temp
IntegerOptionKey const	gapspan
IntegerOptionKey const	spread
IntegerOptionKey const	kinematic_wrapper_cycles
IntegerOptionKey const	kic_num_rotamer_trials
BooleanOptionKey const	kic_omega_sampling
RealOptionKey const	kic_bump_overlap_factor
IntegerOptionKey const	minimize_max_iter
StringOptionKey const	restrict_kic_sampling_to_torsion_string
BooleanOptionKey const	derive_torsion_string_from_native_pose
BooleanOptionKey const	always_remodel_full_loop
BooleanOptionKey const	taboo_sampling
BooleanOptionKey const	taboo_in_fa
BooleanOptionKey const	ramp_fa_rep
BooleanOptionKey const	ramp_rama
BooleanOptionKey const	kic_rama2b
BooleanOptionKey const	kic_leave_centroid_after_initial_closure
BooleanOptionKey const	legacy_kic
BooleanOptionKey const	alternative_closure_protocol
RealOptionKey const	chainbreak_max_accept
BooleanOptionKey const	debug_loop_closure
BooleanOptionKey const	non_ideal_loop_closing
RealOptionKey const	scored_frag_cycles
RealOptionKey const	short_frag_cycles
RealOptionKey const	rmsd_tol
RealOptionKey const	chain_break_tol
BooleanOptionKey const	random_loop
FileVectorOptionKey const	stealfrags
IntegerOptionKey const	stealfrags_times
RealOptionKey const	coord_cst
RealOptionKey const	skip_1mers
RealOptionKey const	skip_3mers
RealOptionKey const	skip_9mers
BooleanOptionKey const	loop_model
RealOptionKey const	score_filter_cutoff
BooleanOptionKey const	ccd_closure
BooleanOptionKey const	skip_ccd_moves
BooleanOptionKey const	no_randomize_loop
BooleanOptionKey const	loops_subset
IntegerOptionKey const	num_desired_loops
RealOptionKey const	loop_combine_rate
RealOptionKey const	final_score_filter
BooleanOptionKey const	no_combine_if_fail
BooleanOptionKey const	shorten_long_terminal_loop
IntegerOptionKey const	backrub_trials
RealOptionKey const	looprlx_cycle_ratio
RealOptionKey const	extended_beta
BooleanOptionKey const	no_looprebuild
BooleanOptionKey const	allow_lig_move
FileOptionKey const	keep_natro
IntegerOptionKey const	refine_design_iterations

Variable Documentation

BooleanOptionKey const basic::options::OptionKeys::loops::accept_aborted_loops

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::allow_lig_move

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::allow_omega_move

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::allow_takeoff_torsion_move

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::alternative_closure_protocol

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::always_remodel_full_loop

Referenced by add_rosetta_options_4().

IntegerOptionKey const basic::options::OptionKeys::loops::backrub_trials

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::build_all_loops

Referenced by add_rosetta_options_3().

IntegerOptionKey const basic::options::OptionKeys::loops::build_attempts

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::build_initial

Referenced by add_rosetta_options_3().

IntegerVectorOptionKey const basic::options::OptionKeys::loops::build_specific_loops

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::ccd_closure

Referenced by add_rosetta_options_4().

StringOptionKey const basic::options::OptionKeys::loops::cen_patch

Referenced by add_rosetta_options_3().

StringOptionKey const basic::options::OptionKeys::loops::cen_weights

Referenced by add_rosetta_options_3().

RealOptionKey const basic::options::OptionKeys::loops::chain_break_tol

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::chainbreak_max_accept

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::combine_rate

Referenced by add_rosetta_options_3().

RealOptionKey const basic::options::OptionKeys::loops::constrain_rigid_segments

Referenced by add_rosetta_options_3().

RealOptionKey const basic::options::OptionKeys::loops::coord_cst

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::debug

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::debug_loop_closure

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::derive_torsion_string_from_native_pose

Referenced by add_rosetta_options_4().

IntegerOptionKey const basic::options::OptionKeys::loops::extend_length

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::extended

Referenced by add_rosetta_options_3().

RealOptionKey const basic::options::OptionKeys::loops::extended_beta

Referenced by add_rosetta_options_4().

FileOptionKey const basic::options::OptionKeys::loops::extended_loop_file

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::fa_closure_protocol

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::fast

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::final_clean_fastrelax

Referenced by add_rosetta_options_3().

RealOptionKey const basic::options::OptionKeys::loops::final_score_filter

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::fix_ca_bond_angles

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::fix_natsc

Referenced by add_rosetta_options_3().

FileVectorOptionKey const basic::options::OptionKeys::loops::frag_files

Referenced by add_rosetta_options_3(), CaToAllAtom::apply(), and my_main().

IntegerVectorOptionKey const basic::options::OptionKeys::loops::frag_sizes

Referenced by add_rosetta_options_3(), and my_main().

IntegerOptionKey const basic::options::OptionKeys::loops::gapspan

Referenced by add_rosetta_options_4().

IntegerOptionKey const basic::options::OptionKeys::loops::grow_attempts

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::idealize_after_loop_close

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::idealize_before_loop_close

Referenced by add_rosetta_options_3().

FileOptionKey const basic::options::OptionKeys::loops::input_pdb

Input options#####################################.

Referenced by add_rosetta_options_3(), and main().

StringOptionKey const basic::options::OptionKeys::loops::intermedrelax

Referenced by add_rosetta_options_3().

FileOptionKey const basic::options::OptionKeys::loops::keep_natro

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::kic_bump_overlap_factor

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::kic_leave_centroid_after_initial_closure

Referenced by add_rosetta_options_4().

IntegerOptionKey const basic::options::OptionKeys::loops::kic_max_seglen

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::kic_min_after_repack

Referenced by add_rosetta_options_3().

IntegerOptionKey const basic::options::OptionKeys::loops::kic_num_rotamer_trials

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::kic_omega_sampling

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::kic_rama2b

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::kic_recover_last

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::kic_use_linear_chainbreak

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::kic_with_cartmin

Referenced by add_rosetta_options_3().

IntegerOptionKey const basic::options::OptionKeys::loops::kinematic_wrapper_cycles

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::legacy_kic

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::loop_combine_rate

Referenced by add_rosetta_options_4().

StringVectorOptionKey const basic::options::OptionKeys::loops::loop_file

Referenced by add_rosetta_options_3(), UBQ_GTPase_disulfide_Mover::init_on_new_input(), and UBQ_E2Mover::init_on_new_input().

BooleanOptionKey const basic::options::OptionKeys::loops::loop_model

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::looprlx_cycle_ratio

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::loops

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::loops_subset

Referenced by add_rosetta_options_4().

StringOptionKey const basic::options::OptionKeys::loops::loopscores

Referenced by add_rosetta_options_3().

IntegerOptionKey const basic::options::OptionKeys::loops::max_inner_cycles

Referenced by add_rosetta_options_4(), and main().

IntegerOptionKey const basic::options::OptionKeys::loops::max_kic_build_attempts

Referenced by add_rosetta_options_3().

IntegerOptionKey const basic::options::OptionKeys::loops::max_kic_perturber_samples

Referenced by add_rosetta_options_3().

IntegerOptionKey const basic::options::OptionKeys::loops::minimize_max_iter

Referenced by add_rosetta_options_4().

FileOptionKey const basic::options::OptionKeys::loops::mm_loop_file

Referenced by add_rosetta_options_3().

RealOptionKey const basic::options::OptionKeys::loops::neighbor_dist

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::no_combine_if_fail

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::no_looprebuild

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::no_randomize_loop

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::non_ideal_loop_closing

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::nonpivot_torsion_sampling

Referenced by add_rosetta_options_3().

IntegerOptionKey const basic::options::OptionKeys::loops::num_desired_loops

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::optimize_only_kic_region_sidechains_after_move

Referenced by add_rosetta_options_3().

FileOptionKey const basic::options::OptionKeys::loops::output_pdb

Referenced by add_rosetta_options_3(), and main().

IntegerOptionKey const basic::options::OptionKeys::loops::perturb_outer_cycles

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::ramp_fa_rep

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::ramp_rama

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::random_grow_loops_by

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::random_loop

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::random_order

Referenced by add_rosetta_options_3().

StringOptionKey const basic::options::OptionKeys::loops::refine

Referenced by add_rosetta_options_3().

IntegerOptionKey const basic::options::OptionKeys::loops::refine_design_iterations

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::refine_final_temp

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::refine_init_temp

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::refine_only

Referenced by add_rosetta_options_3().

IntegerOptionKey const basic::options::OptionKeys::loops::refine_outer_cycles

Referenced by add_rosetta_options_4(), and main().

StringOptionKey const basic::options::OptionKeys::loops::relax

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::relax_with_foldtree

Referenced by add_rosetta_options_3().

StringOptionKey const basic::options::OptionKeys::loops::remodel

Referenced by add_rosetta_options_3().

RealOptionKey const basic::options::OptionKeys::loops::remodel_final_temp

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::remodel_init_temp

Referenced by add_rosetta_options_4().

IntegerOptionKey const basic::options::OptionKeys::loops::remodel_kic_attempts

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::remove_extended_loops

Referenced by add_rosetta_options_3().

IntegerOptionKey const basic::options::OptionKeys::loops::repack_period

Referenced by add_rosetta_options_4().

StringOptionKey const basic::options::OptionKeys::loops::restrict_kic_sampling_to_torsion_string

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::rmsd_tol

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::sample_omega_at_pre_prolines

Referenced by add_rosetta_options_3().

RealOptionKey const basic::options::OptionKeys::loops::score_filter_cutoff

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::scored_frag_cycles

Referenced by add_rosetta_options_4().

IntegerOptionKey const basic::options::OptionKeys::loops::select_best_loop_from

Referenced by add_rosetta_options_3().

RealOptionKey const basic::options::OptionKeys::loops::short_frag_cycles

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::shorten_long_terminal_loop

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::skip_1mers

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::skip_3mers

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::skip_9mers

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::skip_ccd_moves

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::skip_initial_loop_build

Referenced by add_rosetta_options_3().

IntegerOptionKey const basic::options::OptionKeys::loops::spread

Referenced by add_rosetta_options_4().

FileVectorOptionKey const basic::options::OptionKeys::loops::stealfrags

Referenced by add_rosetta_options_4().

IntegerOptionKey const basic::options::OptionKeys::loops::stealfrags_times

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::strict_loops

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::superimpose_native

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::taboo_in_fa

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::taboo_sampling

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::timer

Referenced by add_rosetta_options_3().

FileOptionKey const basic::options::OptionKeys::loops::vall_file

Referenced by add_rosetta_options_3().

RealOptionKey const basic::options::OptionKeys::loops::vicinity_degree

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::vicinity_sampling

Referenced by add_rosetta_options_3().