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Functions
legacy_sewing Namespace Reference

Functions

BooleanOptionKey const legacy_sewing ("legacy_sewing")
 
FileOptionKey const model_file_name ("legacy_sewing:model_file_name")
 
FileOptionKey const score_file_name ("legacy_sewing:score_file_name")
 
FileOptionKey const new_model_file_name ("legacy_sewing:new_model_file_name")
 
StringOptionKey const remove_any_dssp ("legacy_sewing:remove_any_dssp")
 
StringOptionKey const remove_all_dssp ("legacy_sewing:remove_all_dssp")
 
IntegerOptionKey const min_helix_length ("legacy_sewing:min_helix_length")
 
IntegerOptionKey const max_helix_length ("legacy_sewing:max_helix_length")
 
IntegerOptionKey const min_loop_length ("legacy_sewing:min_loop_length")
 
IntegerOptionKey const max_loop_length ("legacy_sewing:max_loop_length")
 
IntegerOptionKey const min_strand_length ("legacy_sewing:min_strand_length")
 
IntegerOptionKey const max_strand_length ("legacy_sewing:max_strand_length")
 
BooleanOptionKey const leave_models_by_ss_num ("legacy_sewing:leave_models_by_ss_num")
 
IntegerOptionKey const model_should_have_this_num_of_ss ("legacy_sewing:model_should_have_this_num_of_ss")
 
BooleanOptionKey const model_should_have_at_least_1_E_at_terminal_segment ("legacy_sewing:model_should_have_at_least_1_E_at_terminal_segment")
 
BooleanOptionKey const model_should_have_at_least_1_E ("legacy_sewing:model_should_have_at_least_1_E")
 
BooleanOptionKey const model_should_have_at_least_1_H ("legacy_sewing:model_should_have_at_least_1_H")
 
BooleanOptionKey const leave_models_with_E_terminal_ss ("legacy_sewing:leave_models_with_E_terminal_ss")
 
BooleanOptionKey const leave_models_with_H_terminal_ss ("legacy_sewing:leave_models_with_H_terminal_ss")
 
BooleanOptionKey const leave_antiparallel_way_H_bonded_models_by_terminal_strands ("legacy_sewing:leave_antiparallel_way_H_bonded_models_by_terminal_strands")
 
BooleanOptionKey const leave_parallel_way_H_bonded_models_by_terminal_strands ("legacy_sewing:leave_parallel_way_H_bonded_models_by_terminal_strands")
 
BooleanOptionKey const leave_certain_model_ids ("legacy_sewing:leave_certain_model_ids")
 
StringOptionKey const leave_these_model_ids ("legacy_sewing:leave_these_model_ids")
 
IntegerOptionKey const box_length ("legacy_sewing:box_length")
 
StringOptionKey const mode ("legacy_sewing:mode")
 
BooleanOptionKey const disregard_num_segment_matches ("legacy_sewing:disregard_num_segment_matches")
 
BooleanOptionKey const do_not_remove_connection_inconsistencies ("legacy_sewing:do_not_remove_connection_inconsistencies")
 
BooleanOptionKey const score_between_opposite_terminal_segments ("legacy_sewing:score_between_opposite_terminal_segments")
 
IntegerOptionKey const num_models_to_dump ("legacy_sewing:num_models_to_dump")
 
IntegerVectorOptionKey const models_to_dump ("legacy_sewing:models_to_dump")
 
IntegerOptionKey const min_hash_score ("legacy_sewing:min_hash_score")
 
IntegerOptionKey const max_clash_score ("legacy_sewing:max_clash_score")
 
IntegerOptionKey const num_segments_to_match ("legacy_sewing:num_segments_to_match")
 
IntegerVectorOptionKey const match_segments ("legacy_sewing:match_segments")
 
IntegerOptionKey const max_models ("legacy_sewing:max_models")
 
IntegerOptionKey const starting_model ("legacy_sewing:starting_model")
 
IntegerOptionKey const num_procs ("legacy_sewing:num_procs")
 
IntegerOptionKey const rank ("legacy_sewing:rank")
 
BooleanOptionKey const hash_tag_only_terminal_Es ("legacy_sewing:hash_tag_only_terminal_Es")
 
StringOptionKey const assembly_type ("legacy_sewing:assembly_type")
 
IntegerOptionKey const num_edges_to_follow ("legacy_sewing:num_edges_to_follow")
 
RealOptionKey const base_native_bonus ("legacy_sewing:base_native_bonus")
 
IntegerOptionKey const neighbor_cutoff ("legacy_sewing:neighbor_cutoff")
 
BooleanOptionKey const dump_pdbs ("legacy_sewing:dump_pdbs")
 
BooleanOptionKey const skip_refinement ("legacy_sewing:skip_refinement")
 
BooleanOptionKey const skip_filters ("legacy_sewing:skip_filters")
 
RealOptionKey const min_motif_score ("legacy_sewing:min_motif_score")
 
BooleanOptionKey const may_add_already_added_model ("legacy_sewing:may_add_already_added_model")
 
RealOptionKey const offset_bump_dsq ("legacy_sewing:offset_bump_dsq")
 
IntegerOptionKey const num_repeats ("legacy_sewing:num_repeats")
 
BooleanOptionKey const repeat ("legacy_sewing:repeat")
 
IntegerVectorOptionKey const pose_segment_starts ("legacy_sewing:pose_segment_starts")
 
IntegerVectorOptionKey const pose_segment_ends ("legacy_sewing:pose_segment_ends")
 
BooleanOptionKey const keep_source_segments ("legacy_sewing:keep_source_segments")
 
FileOptionKey const partner_pdb ("legacy_sewing:partner_pdb")
 
IntegerVectorOptionKey const keep_model_residues ("legacy_sewing:keep_model_residues")
 
BooleanOptionKey const output_alignments_to_file ("legacy_sewing:output_alignments_to_file")
 
IntegerOptionKey const min_lh_fragments ("legacy_sewing:min_lh_fragments")
 
BooleanOptionKey const skip_loop_generation ("legacy_sewing:skip_loop_generation")
 
RealOptionKey const calcium_motif_score_weight ("legacy_sewing:calcium_motif_score_weight")
 
IntegerOptionKey const max_ss_num ("legacy_sewing:max_ss_num")
 
BooleanOptionKey const dump_every_model ("legacy_sewing:dump_every_model")
 

Function Documentation

StringOptionKey const legacy_sewing::assembly_type ( "legacy_sewing:assembly_type"  )
RealOptionKey const legacy_sewing::base_native_bonus ( "legacy_sewing:base_native_bonus"  )
IntegerOptionKey const legacy_sewing::box_length ( "legacy_sewing:box_length"  )
RealOptionKey const legacy_sewing::calcium_motif_score_weight ( "legacy_sewing:calcium_motif_score_weight"  )
BooleanOptionKey const legacy_sewing::disregard_num_segment_matches ( "legacy_sewing:disregard_num_segment_matches"  )
BooleanOptionKey const legacy_sewing::do_not_remove_connection_inconsistencies ( "legacy_sewing:do_not_remove_connection_inconsistencies"  )
BooleanOptionKey const legacy_sewing::dump_every_model ( "legacy_sewing:dump_every_model"  )
BooleanOptionKey const legacy_sewing::dump_pdbs ( "legacy_sewing:dump_pdbs"  )
BooleanOptionKey const legacy_sewing::hash_tag_only_terminal_Es ( "legacy_sewing:hash_tag_only_terminal_Es"  )
IntegerVectorOptionKey const legacy_sewing::keep_model_residues ( "legacy_sewing:keep_model_residues"  )
BooleanOptionKey const legacy_sewing::keep_source_segments ( "legacy_sewing:keep_source_segments"  )
BooleanOptionKey const legacy_sewing::leave_antiparallel_way_H_bonded_models_by_terminal_strands ( "legacy_sewing:leave_antiparallel_way_H_bonded_models_by_terminal_strands"  )
BooleanOptionKey const legacy_sewing::leave_certain_model_ids ( "legacy_sewing:leave_certain_model_ids"  )
BooleanOptionKey const legacy_sewing::leave_models_by_ss_num ( "legacy_sewing:leave_models_by_ss_num"  )
BooleanOptionKey const legacy_sewing::leave_models_with_E_terminal_ss ( "legacy_sewing:leave_models_with_E_terminal_ss"  )
BooleanOptionKey const legacy_sewing::leave_models_with_H_terminal_ss ( "legacy_sewing:leave_models_with_H_terminal_ss"  )
BooleanOptionKey const legacy_sewing::leave_parallel_way_H_bonded_models_by_terminal_strands ( "legacy_sewing:leave_parallel_way_H_bonded_models_by_terminal_strands"  )
StringOptionKey const legacy_sewing::leave_these_model_ids ( "legacy_sewing:leave_these_model_ids"  )
BooleanOptionKey const legacy_sewing::legacy_sewing ( "legacy_sewing"  )
IntegerVectorOptionKey const legacy_sewing::match_segments ( "legacy_sewing:match_segments"  )
IntegerOptionKey const legacy_sewing::max_clash_score ( "legacy_sewing:max_clash_score"  )
IntegerOptionKey const legacy_sewing::max_helix_length ( "legacy_sewing:max_helix_length"  )
IntegerOptionKey const legacy_sewing::max_loop_length ( "legacy_sewing:max_loop_length"  )
IntegerOptionKey const legacy_sewing::max_models ( "legacy_sewing:max_models"  )
IntegerOptionKey const legacy_sewing::max_ss_num ( "legacy_sewing:max_ss_num"  )
IntegerOptionKey const legacy_sewing::max_strand_length ( "legacy_sewing:max_strand_length"  )
BooleanOptionKey const legacy_sewing::may_add_already_added_model ( "legacy_sewing:may_add_already_added_model"  )
IntegerOptionKey const legacy_sewing::min_hash_score ( "legacy_sewing:min_hash_score"  )
IntegerOptionKey const legacy_sewing::min_helix_length ( "legacy_sewing:min_helix_length"  )
IntegerOptionKey const legacy_sewing::min_lh_fragments ( "legacy_sewing:min_lh_fragments"  )
IntegerOptionKey const legacy_sewing::min_loop_length ( "legacy_sewing:min_loop_length"  )
RealOptionKey const legacy_sewing::min_motif_score ( "legacy_sewing:min_motif_score"  )
IntegerOptionKey const legacy_sewing::min_strand_length ( "legacy_sewing:min_strand_length"  )
StringOptionKey const legacy_sewing::mode ( "legacy_sewing:mode"  )
FileOptionKey const legacy_sewing::model_file_name ( "legacy_sewing:model_file_name"  )
BooleanOptionKey const legacy_sewing::model_should_have_at_least_1_E ( "legacy_sewing:model_should_have_at_least_1_E"  )
BooleanOptionKey const legacy_sewing::model_should_have_at_least_1_E_at_terminal_segment ( "legacy_sewing:model_should_have_at_least_1_E_at_terminal_segment"  )
BooleanOptionKey const legacy_sewing::model_should_have_at_least_1_H ( "legacy_sewing:model_should_have_at_least_1_H"  )
IntegerOptionKey const legacy_sewing::model_should_have_this_num_of_ss ( "legacy_sewing:model_should_have_this_num_of_ss"  )
IntegerVectorOptionKey const legacy_sewing::models_to_dump ( "legacy_sewing:models_to_dump"  )
IntegerOptionKey const legacy_sewing::neighbor_cutoff ( "legacy_sewing:neighbor_cutoff"  )
FileOptionKey const legacy_sewing::new_model_file_name ( "legacy_sewing:new_model_file_name"  )
IntegerOptionKey const legacy_sewing::num_edges_to_follow ( "legacy_sewing:num_edges_to_follow"  )
IntegerOptionKey const legacy_sewing::num_models_to_dump ( "legacy_sewing:num_models_to_dump"  )
IntegerOptionKey const legacy_sewing::num_procs ( "legacy_sewing:num_procs"  )
IntegerOptionKey const legacy_sewing::num_repeats ( "legacy_sewing:num_repeats"  )
IntegerOptionKey const legacy_sewing::num_segments_to_match ( "legacy_sewing:num_segments_to_match"  )
RealOptionKey const legacy_sewing::offset_bump_dsq ( "legacy_sewing:offset_bump_dsq"  )
BooleanOptionKey const legacy_sewing::output_alignments_to_file ( "legacy_sewing:output_alignments_to_file"  )
FileOptionKey const legacy_sewing::partner_pdb ( "legacy_sewing:partner_pdb"  )
IntegerVectorOptionKey const legacy_sewing::pose_segment_ends ( "legacy_sewing:pose_segment_ends"  )
IntegerVectorOptionKey const legacy_sewing::pose_segment_starts ( "legacy_sewing:pose_segment_starts"  )
IntegerOptionKey const legacy_sewing::rank ( "legacy_sewing:rank"  )
StringOptionKey const legacy_sewing::remove_all_dssp ( "legacy_sewing:remove_all_dssp"  )
StringOptionKey const legacy_sewing::remove_any_dssp ( "legacy_sewing:remove_any_dssp"  )
BooleanOptionKey const legacy_sewing::repeat ( "legacy_sewing:repeat"  )
BooleanOptionKey const legacy_sewing::score_between_opposite_terminal_segments ( "legacy_sewing:score_between_opposite_terminal_segments"  )
FileOptionKey const legacy_sewing::score_file_name ( "legacy_sewing:score_file_name"  )
BooleanOptionKey const legacy_sewing::skip_filters ( "legacy_sewing:skip_filters"  )
BooleanOptionKey const legacy_sewing::skip_loop_generation ( "legacy_sewing:skip_loop_generation"  )
BooleanOptionKey const legacy_sewing::skip_refinement ( "legacy_sewing:skip_refinement"  )
IntegerOptionKey const legacy_sewing::starting_model ( "legacy_sewing:starting_model"  )