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

Namespaces
	ccd

Variables
BooleanOptionKey const	loops
StringOptionKey const	cen_weights
StringOptionKey const	cen_patch
FileOptionKey const	input_pdb
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

accept_aborted_loops

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

extern

allow_lig_move

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

extern

allow_omega_move

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

extern

allow_takeoff_torsion_move

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

extern

alternative_closure_protocol

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

extern

always_remodel_full_loop

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

extern

backrub_trials

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

extern

build_all_loops

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

extern

build_attempts

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

extern

build_initial

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

extern

Referenced by LoopBuild_main().

build_specific_loops

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

extern

ccd_closure

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

extern

Referenced by main().

cen_patch

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

extern

cen_weights

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

extern

chain_break_tol

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

extern

chainbreak_max_accept

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

extern

combine_rate

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

extern

constrain_rigid_segments

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

extern

coord_cst

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

extern

Referenced by main().

debug

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

extern

debug_loop_closure

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

extern

Referenced by protocols::abinitio::JumpSpecificAbrelax::close_loops(), and protocols::abinitio::JumpSpecificAbrelax::register_options().

derive_torsion_string_from_native_pose

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

extern

extend_length

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

extern

Referenced by main().

extended

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

extern

extended_beta

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

extern

extended_loop_file

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

extern

fa_closure_protocol

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

extern

fast

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

extern

Referenced by main().

final_clean_fastrelax

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

extern

final_score_filter

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

extern

fix_ca_bond_angles

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

extern

fix_natsc

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

extern

Referenced by my_main().

frag_files

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

extern

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

frag_sizes

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

extern

Referenced by my_main().

gapspan

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

extern

grow_attempts

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

extern

idealize_after_loop_close

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

extern

idealize_before_loop_close

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

extern

input_pdb

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

extern

Referenced by LoopBuild_main(), and main().

intermedrelax

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

extern

Referenced by LoopBuild_main(), and main().

keep_natro

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

extern

Referenced by main().

kic_bump_overlap_factor

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

extern

kic_leave_centroid_after_initial_closure

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

extern

kic_max_seglen

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

extern

kic_min_after_repack

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

extern

kic_num_rotamer_trials

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

extern

kic_omega_sampling

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

extern

Referenced by UniformPerturber::perturb_chain().

kic_rama2b

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

extern

kic_recover_last

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

extern

kic_use_linear_chainbreak

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

extern

kic_with_cartmin

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

extern

kinematic_wrapper_cycles

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

extern

legacy_kic

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

extern

loop_combine_rate

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

extern

loop_file

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

extern

Referenced by UBQ_E2Mover::init_on_new_input(), UBQ_GTPase_disulfide_Mover::init_on_new_input(), FloppyTailMover::init_on_new_input(), main(), and UBQ_E2Mover::UBQ_E2Mover().

loop_model

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

extern

looprlx_cycle_ratio

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

extern

loops

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

extern

loops_subset

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

extern

loopscores

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

extern

max_inner_cycles

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

extern

Referenced by main().

max_kic_build_attempts

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

extern

max_kic_perturber_samples

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

extern

minimize_max_iter

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

extern

Referenced by main().

mm_loop_file

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

extern

neighbor_dist

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

extern

no_combine_if_fail

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

extern

no_looprebuild

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

extern

no_randomize_loop

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

extern

non_ideal_loop_closing

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

extern

nonpivot_torsion_sampling

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

extern

num_desired_loops

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

extern

optimize_only_kic_region_sidechains_after_move

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

extern

output_pdb

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

extern

perturb_outer_cycles

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

extern

ramp_fa_rep

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

extern

Referenced by main().

ramp_rama

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

extern

Referenced by main().

random_grow_loops_by

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

extern

Referenced by protocols::abinitio::JumpSpecificAbrelax::do_distributed_rerun(), and protocols::abinitio::JumpSpecificAbrelax::setup_fold().

random_loop

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

extern

random_order

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

extern

refine

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

extern

Referenced by LoopBuild_main().

refine_design_iterations

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

extern

Referenced by main().

refine_final_temp

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

extern

refine_init_temp

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

extern

refine_only

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

extern

refine_outer_cycles

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

extern

Referenced by main().

relax

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

extern

Referenced by LoopBuild_main().

relax_with_foldtree

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

extern

remodel

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

extern

Referenced by LoopBuild_main().

remodel_final_temp

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

extern

remodel_init_temp

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

extern

remodel_kic_attempts

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

extern

remove_extended_loops

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

extern

repack_period

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

extern

Referenced by main().

restrict_kic_sampling_to_torsion_string

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

extern

rmsd_tol

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

extern

sample_omega_at_pre_prolines

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

extern

score_filter_cutoff

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

extern

scored_frag_cycles

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

extern

Referenced by protocols::abinitio::JumpSpecificAbrelax::close_loops(), protocols::abinitio::JumpSpecificAbrelax::register_options(), and protocols::abinitio::JumpSpecificAbrelax::setup_fold().

select_best_loop_from

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

extern

short_frag_cycles

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

extern

Referenced by protocols::abinitio::JumpSpecificAbrelax::close_loops(), protocols::abinitio::JumpSpecificAbrelax::register_options(), and protocols::abinitio::JumpSpecificAbrelax::setup_fold().

shorten_long_terminal_loop

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

extern

skip_1mers

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

extern

skip_3mers

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

extern

skip_9mers

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

extern

skip_ccd_moves

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

extern

skip_initial_loop_build

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

extern

spread

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

extern

stealfrags

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

extern

stealfrags_times

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

extern

strict_loops

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

extern

superimpose_native

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

extern

taboo_in_fa

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

extern

taboo_sampling

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

extern

timer

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

extern

Referenced by LoopBuild_main(), and run_parallel_docking().

vall_file

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

extern

Referenced by create_rna_benchmark_test(), setup_loops_fragment_libraries_with_ss(), simple_frag_test(), and simple_loop_modeling_test().

vicinity_degree

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

extern

vicinity_sampling

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

extern