basic::options::OptionKeys::cluster Namespace Reference

Namespaces
	energy_based_clustering

Variables
BooleanOptionKey const	cluster
BooleanOptionKey const	lite
RealOptionKey const	input_score_filter
RealOptionKey const	output_score_filter
IntegerVectorOptionKey const	exclude_res
RealOptionKey const	thinout_factor
RealOptionKey const	radius
IntegerOptionKey const	limit_cluster_size
RealOptionKey const	limit_cluster_size_percent
RealOptionKey const	random_limit_cluster_size_percent
IntegerOptionKey const	limit_clusters
IntegerOptionKey const	limit_total_structures
IntegerOptionKey const	max_total_cluster
BooleanOptionKey const	gdtmm
BooleanOptionKey const	skip_align
IntegerOptionKey const	max_rms_matrix
BooleanOptionKey const	rna_P
BooleanOptionKey const	sort_groups_by_energy
BooleanOptionKey const	sort_groups_by_size
BooleanOptionKey const	remove_singletons
BooleanOptionKey const	export_only_low
BooleanOptionKey const	remove_highest_energy_member
BooleanOptionKey const	idealize_final_structures
IntegerOptionKey const	limit_dist_matrix
BooleanOptionKey const	make_ensemble_cst
BooleanOptionKey const	hotspot_hash
BooleanOptionKey const	loops
RealOptionKey const	population_weight
StringOptionKey const	template_scores
IntegerOptionKey const	K_level
RealVectorOptionKey const	K_radius
IntegerVectorOptionKey const	K_n_cluster
StringVectorOptionKey const	K_style
IntegerOptionKey const	K_n_sub
IntegerOptionKey const	K_deque_size
IntegerOptionKey const	K_deque_level
BooleanOptionKey const	K_redundant
BooleanOptionKey const	K_not_fit_xyz
BooleanOptionKey const	K_save_headers
RealOptionKey const	score_diff_cut
BooleanOptionKey const	auto_tune
BooleanOptionKey const	write_centers

Variable Documentation

auto_tune

BooleanOptionKey const basic::options::OptionKeys::cluster::auto_tune

extern

Referenced by cluster_outfile_test(), cluster_test(), and main().

cluster

BooleanOptionKey const basic::options::OptionKeys::cluster::cluster

extern

Referenced by cluster_outfile_test_OLD(), compute_intrinsic_deviation(), main(), recover_clustered_frags(), register_options(), run(), score12_plot_test(), and write_cluster_frags().

exclude_res

IntegerVectorOptionKey const basic::options::OptionKeys::cluster::exclude_res

extern

Referenced by ConstraintToolMover::apply(), create_base_pair_step_database_test(), create_bp_jump_database_test(), create_rna_vall_torsions_test(), and main().

export_only_low

BooleanOptionKey const basic::options::OptionKeys::cluster::export_only_low

extern

Referenced by main().

gdtmm

BooleanOptionKey const basic::options::OptionKeys::cluster::gdtmm

extern

Referenced by ConstraintMinimizer::apply(), myspace::CArmsd_and_superimpose_pose(), dump_pose(), myspace::evaluate_and_write(), and main().

hotspot_hash

BooleanOptionKey const basic::options::OptionKeys::cluster::hotspot_hash

extern

idealize_final_structures

BooleanOptionKey const basic::options::OptionKeys::cluster::idealize_final_structures

extern

input_score_filter

RealOptionKey const basic::options::OptionKeys::cluster::input_score_filter

extern

Referenced by main().

K_deque_level

IntegerOptionKey const basic::options::OptionKeys::cluster::K_deque_level

extern

K_deque_size

IntegerOptionKey const basic::options::OptionKeys::cluster::K_deque_size

extern

K_level

IntegerOptionKey const basic::options::OptionKeys::cluster::K_level

extern

Referenced by main().

K_n_cluster

IntegerVectorOptionKey const basic::options::OptionKeys::cluster::K_n_cluster

extern

K_n_sub

IntegerOptionKey const basic::options::OptionKeys::cluster::K_n_sub

extern

K_not_fit_xyz

BooleanOptionKey const basic::options::OptionKeys::cluster::K_not_fit_xyz

extern

K_radius

RealVectorOptionKey const basic::options::OptionKeys::cluster::K_radius

extern

K_redundant

BooleanOptionKey const basic::options::OptionKeys::cluster::K_redundant

extern

K_save_headers

BooleanOptionKey const basic::options::OptionKeys::cluster::K_save_headers

extern

K_style

StringVectorOptionKey const basic::options::OptionKeys::cluster::K_style

extern

limit_cluster_size

IntegerOptionKey const basic::options::OptionKeys::cluster::limit_cluster_size

extern

Referenced by main().

limit_cluster_size_percent

RealOptionKey const basic::options::OptionKeys::cluster::limit_cluster_size_percent

extern

Referenced by main().

limit_clusters

IntegerOptionKey const basic::options::OptionKeys::cluster::limit_clusters

extern

Referenced by main().

limit_dist_matrix

IntegerOptionKey const basic::options::OptionKeys::cluster::limit_dist_matrix

extern

Referenced by main().

limit_total_structures

IntegerOptionKey const basic::options::OptionKeys::cluster::limit_total_structures

extern

Referenced by main().

lite

BooleanOptionKey const basic::options::OptionKeys::cluster::lite

extern

loops

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

extern

Referenced by LoopHashRelax_Sampler::apply(), APDBCMover::apply(), CaToAllAtom::apply(), MPFoldingMover::apply(), capri_t033_loop_test(), diversify_sam_loop_test(), dna_dr_loop_test(), fold_tree_from_loops(), get_unaligned(), if(), loop_modeling_test(), loop_rebuilding_test(), main(), my_main(), not1_loop_test(), prepare_full_length_start_model(), read_loops_from_text_file(), rebuild_trimmed_loops(), relax_test(), sample_rna_dofs_new(), and UBQ_E2Mover::UBQ_E2Mover().

make_ensemble_cst

BooleanOptionKey const basic::options::OptionKeys::cluster::make_ensemble_cst

extern

Referenced by main().

max_rms_matrix

IntegerOptionKey const basic::options::OptionKeys::cluster::max_rms_matrix

extern

Referenced by main().

max_total_cluster

IntegerOptionKey const basic::options::OptionKeys::cluster::max_total_cluster

extern

Referenced by main().

output_score_filter

RealOptionKey const basic::options::OptionKeys::cluster::output_score_filter

extern

Referenced by main().

population_weight

RealOptionKey const basic::options::OptionKeys::cluster::population_weight

extern

Referenced by main().

radius

RealOptionKey const basic::options::OptionKeys::cluster::radius

extern

Referenced by aidr_as_float(), MPFoldingMover::apply(), base_pair_to_base_pair_test(), PairDistance::calc_rsd_sasa(), calculate_helical_parameters(), ClosabilityScore::closability_score(), cluster_outfile_test(), cluster_outfile_test_OLD(), cluster_silent_file_data(), cluster_test(), define_states_test(), detect_neighbors(), find_close_parents(), gather_info_all_repeats(), gather_info_canonical_repeats(), CrystFFTDock::get_interfaces_allatom(), get_radius_in_frag_set(), CrystFFTDock::get_radius_of_pose(), CrystFFTDock::get_transform_distance(), numeric::geometry::hashing::xyzStripeHash::init(), numeric::geometry::hashing::SixDOffsetTree::insert(), numeric::geometry::hashing::SixDOffsetTree::lookup(), ClosabilityScore::loophash_query(), main(), modeler_closure_test(), near_chain(), output_packstat_pdb(), numeric::geometry::hashing::SixDCoordinateBinner::radial_bin_index(), rebuild_centroid_test(), basic::sampling::orientations::QuaternionGridManager::request_by_radius(), numeric::geometry::hashing::SixDOffsetTree::sum_radius(), numeric::random::uniform_vector_sphere(), and update_vesicle_radius().

random_limit_cluster_size_percent

RealOptionKey const basic::options::OptionKeys::cluster::random_limit_cluster_size_percent

extern

Referenced by main().

remove_highest_energy_member

BooleanOptionKey const basic::options::OptionKeys::cluster::remove_highest_energy_member

extern

Referenced by main().

remove_singletons

BooleanOptionKey const basic::options::OptionKeys::cluster::remove_singletons

extern

Referenced by cluster_outfile_test_OLD(), and main().

rna_P

BooleanOptionKey const basic::options::OptionKeys::cluster::rna_P

extern

score_diff_cut

RealOptionKey const basic::options::OptionKeys::cluster::score_diff_cut

extern

Referenced by cluster_outfile_test(), cluster_silent_file_data(), cluster_test(), main(), rebuild_centroid_test(), and swa_rna_cluster().

skip_align

BooleanOptionKey const basic::options::OptionKeys::cluster::skip_align

extern

sort_groups_by_energy

BooleanOptionKey const basic::options::OptionKeys::cluster::sort_groups_by_energy

extern

Referenced by main().

sort_groups_by_size

BooleanOptionKey const basic::options::OptionKeys::cluster::sort_groups_by_size

extern

Referenced by main().

template_scores

StringOptionKey const basic::options::OptionKeys::cluster::template_scores

extern

thinout_factor

RealOptionKey const basic::options::OptionKeys::cluster::thinout_factor

extern

Referenced by main().

write_centers

BooleanOptionKey const basic::options::OptionKeys::cluster::write_centers

extern