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Variables
basic::options::OptionKeys::legacy_sewing Namespace Reference

Variables

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

Variable Documentation

StringOptionKey const basic::options::OptionKeys::legacy_sewing::assembly_type

Referenced by add_rosetta_options_13(), and main().

RealOptionKey const basic::options::OptionKeys::legacy_sewing::base_native_bonus

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::legacy_sewing::box_length

Referenced by add_rosetta_options_13(), and main().

RealOptionKey const basic::options::OptionKeys::legacy_sewing::calcium_motif_score_weight

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::legacy_sewing::disregard_num_segment_matches

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::legacy_sewing::do_not_remove_connection_inconsistencies

Referenced by add_rosetta_options_13(), and main().

BooleanOptionKey const basic::options::OptionKeys::legacy_sewing::dump_every_model

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::legacy_sewing::dump_pdbs

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::legacy_sewing::hash_tag_only_terminal_Es

Referenced by add_rosetta_options_13(), and main().

IntegerVectorOptionKey const basic::options::OptionKeys::legacy_sewing::keep_model_residues

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::legacy_sewing::keep_source_segments

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::legacy_sewing::leave_antiparallel_way_H_bonded_models_by_terminal_strands

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::legacy_sewing::leave_certain_model_ids

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::legacy_sewing::leave_models_by_ss_num

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::legacy_sewing::leave_models_with_E_terminal_ss

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::legacy_sewing::leave_models_with_H_terminal_ss

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::legacy_sewing::leave_parallel_way_H_bonded_models_by_terminal_strands

Referenced by add_rosetta_options_13().

StringOptionKey const basic::options::OptionKeys::legacy_sewing::leave_these_model_ids

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::legacy_sewing::legacy_sewing

Referenced by add_rosetta_options_13(), and main().

IntegerVectorOptionKey const basic::options::OptionKeys::legacy_sewing::match_segments

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::legacy_sewing::max_clash_score

Referenced by add_rosetta_options_13(), and main().

IntegerOptionKey const basic::options::OptionKeys::legacy_sewing::max_helix_length

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::legacy_sewing::max_loop_length
IntegerOptionKey const basic::options::OptionKeys::legacy_sewing::max_models

Referenced by add_rosetta_options_13(), and main().

IntegerOptionKey const basic::options::OptionKeys::legacy_sewing::max_ss_num

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::legacy_sewing::max_strand_length

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::legacy_sewing::may_add_already_added_model

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::legacy_sewing::min_hash_score

Referenced by add_rosetta_options_13(), and main().

IntegerOptionKey const basic::options::OptionKeys::legacy_sewing::min_helix_length

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::legacy_sewing::min_lh_fragments

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::legacy_sewing::min_loop_length

Referenced by add_rosetta_options_13().

RealOptionKey const basic::options::OptionKeys::legacy_sewing::min_motif_score

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::legacy_sewing::min_strand_length

Referenced by add_rosetta_options_13().

StringOptionKey const basic::options::OptionKeys::legacy_sewing::mode

Referenced by add_rosetta_options_13(), and main().

FileOptionKey const basic::options::OptionKeys::legacy_sewing::model_file_name

Referenced by add_rosetta_options_13(), and main().

BooleanOptionKey const basic::options::OptionKeys::legacy_sewing::model_should_have_at_least_1_E

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::legacy_sewing::model_should_have_at_least_1_E_at_terminal_segment

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::legacy_sewing::model_should_have_at_least_1_H

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::legacy_sewing::model_should_have_this_num_of_ss

Referenced by add_rosetta_options_13().

IntegerVectorOptionKey const basic::options::OptionKeys::legacy_sewing::models_to_dump

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::legacy_sewing::neighbor_cutoff
FileOptionKey const basic::options::OptionKeys::legacy_sewing::new_model_file_name

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::legacy_sewing::num_edges_to_follow

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::legacy_sewing::num_models_to_dump

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::legacy_sewing::num_procs

Referenced by add_rosetta_options_13(), and main().

IntegerOptionKey const basic::options::OptionKeys::legacy_sewing::num_repeats

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::legacy_sewing::num_segments_to_match

Referenced by add_rosetta_options_13(), and main().

RealOptionKey const basic::options::OptionKeys::legacy_sewing::offset_bump_dsq

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::legacy_sewing::output_alignments_to_file

Referenced by add_rosetta_options_13().

FileOptionKey const basic::options::OptionKeys::legacy_sewing::partner_pdb

Referenced by add_rosetta_options_13().

IntegerVectorOptionKey const basic::options::OptionKeys::legacy_sewing::pose_segment_ends

Referenced by add_rosetta_options_13().

IntegerVectorOptionKey const basic::options::OptionKeys::legacy_sewing::pose_segment_starts

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::legacy_sewing::rank
StringOptionKey const basic::options::OptionKeys::legacy_sewing::remove_all_dssp

Referenced by add_rosetta_options_13().

StringOptionKey const basic::options::OptionKeys::legacy_sewing::remove_any_dssp

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::legacy_sewing::repeat
BooleanOptionKey const basic::options::OptionKeys::legacy_sewing::score_between_opposite_terminal_segments

Referenced by add_rosetta_options_13().

FileOptionKey const basic::options::OptionKeys::legacy_sewing::score_file_name

Referenced by add_rosetta_options_13(), and main().

BooleanOptionKey const basic::options::OptionKeys::legacy_sewing::skip_filters

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::legacy_sewing::skip_loop_generation

Referenced by add_rosetta_options_13().

BooleanOptionKey const basic::options::OptionKeys::legacy_sewing::skip_refinement

Referenced by add_rosetta_options_13().

IntegerOptionKey const basic::options::OptionKeys::legacy_sewing::starting_model

Referenced by add_rosetta_options_13(), and main().