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Namespaces | Functions
cluster Namespace Reference

Namespaces

 energy_based_clustering
 

Functions

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

Function Documentation

BooleanOptionKey const cluster::auto_tune ( "cluster:auto_tune"  )

Referenced by main().

BooleanOptionKey const cluster::cluster ( "cluster"  )
IntegerVectorOptionKey const cluster::exclude_res ( "cluster:exclude_res"  )
BooleanOptionKey const cluster::export_only_low ( "cluster:export_only_low"  )
BooleanOptionKey const cluster::gdtmm ( "cluster:gdtmm"  )
BooleanOptionKey const cluster::hotspot_hash ( "cluster:hotspot_hash"  )
BooleanOptionKey const cluster::idealize_final_structures ( "cluster:idealize_final_structures"  )
RealOptionKey const cluster::input_score_filter ( "cluster:input_score_filter"  )
IntegerOptionKey const cluster::K_deque_level ( "cluster:K_deque_level"  )
IntegerOptionKey const cluster::K_deque_size ( "cluster:K_deque_size"  )
IntegerOptionKey const cluster::K_level ( "cluster:K_level"  )
IntegerVectorOptionKey const cluster::K_n_cluster ( "cluster:K_n_cluster"  )
IntegerOptionKey const cluster::K_n_sub ( "cluster:K_n_sub"  )
BooleanOptionKey const cluster::K_not_fit_xyz ( "cluster:K_not_fit_xyz"  )
RealVectorOptionKey const cluster::K_radius ( "cluster:K_radius"  )
BooleanOptionKey const cluster::K_redundant ( "cluster:K_redundant"  )
BooleanOptionKey const cluster::K_save_headers ( "cluster:K_save_headers"  )
StringVectorOptionKey const cluster::K_style ( "cluster:K_style"  )
IntegerOptionKey const cluster::limit_cluster_size ( "cluster:limit_cluster_size"  )

Referenced by register_options().

RealOptionKey const cluster::limit_cluster_size_percent ( "cluster:limit_cluster_size_percent"  )
IntegerOptionKey const cluster::limit_clusters ( "cluster:limit_clusters"  )
IntegerOptionKey const cluster::limit_dist_matrix ( "cluster:limit_dist_matrix"  )
IntegerOptionKey const cluster::limit_total_structures ( "cluster:limit_total_structures"  )
BooleanOptionKey const cluster::lite ( "cluster:lite"  )
BooleanOptionKey const cluster::loops ( "cluster:loops"  )
BooleanOptionKey const cluster::make_ensemble_cst ( "cluster:make_ensemble_cst"  )
IntegerOptionKey const cluster::max_rms_matrix ( "cluster:max_rms_matrix"  )
IntegerOptionKey const cluster::max_total_cluster ( "cluster:max_total_cluster"  )
RealOptionKey const cluster::output_score_filter ( "cluster:output_score_filter"  )
RealOptionKey const cluster::population_weight ( "cluster:population_weight"  )
RealOptionKey const cluster::radius ( "cluster:radius"  )

Referenced by main().

RealOptionKey const cluster::random_limit_cluster_size_percent ( "cluster:random_limit_cluster_size_percent"  )
BooleanOptionKey const cluster::remove_highest_energy_member ( "cluster:remove_highest_energy_member"  )
BooleanOptionKey const cluster::remove_singletons ( "cluster:remove_singletons"  )
BooleanOptionKey const cluster::rna_P ( "cluster:rna_P"  )
RealOptionKey const cluster::score_diff_cut ( "cluster:score_diff_cut"  )

Referenced by main().

BooleanOptionKey const cluster::skip_align ( "cluster:skip_align"  )
BooleanOptionKey const cluster::sort_groups_by_energy ( "cluster:sort_groups_by_energy"  )
BooleanOptionKey const cluster::sort_groups_by_size ( "cluster:sort_groups_by_size"  )
StringOptionKey const cluster::template_scores ( "cluster:template_scores"  )
RealOptionKey const cluster::thinout_factor ( "cluster:thinout_factor"  )
BooleanOptionKey const cluster::write_centers ( "cluster:write_centers"  )