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

assembly_type

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

extern

Referenced by main().

base_native_bonus

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

extern

box_length

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

extern

Referenced by main().

calcium_motif_score_weight

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

extern

disregard_num_segment_matches

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

extern

do_not_remove_connection_inconsistencies

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

extern

Referenced by main().

dump_every_model

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

extern

dump_pdbs

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

extern

hash_tag_only_terminal_Es

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

extern

Referenced by main().

keep_model_residues

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

extern

keep_source_segments

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

extern

leave_antiparallel_way_H_bonded_models_by_terminal_strands

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

extern

Referenced by main().

leave_certain_model_ids

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

extern

Referenced by main().

leave_models_by_ss_num

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

extern

Referenced by main().

leave_models_with_E_terminal_ss

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

extern

Referenced by main().

leave_models_with_H_terminal_ss

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

extern

Referenced by main().

leave_parallel_way_H_bonded_models_by_terminal_strands

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

extern

Referenced by main().

leave_these_model_ids

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

extern

Referenced by main().

legacy_sewing

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

extern

Referenced by main().

match_segments

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

extern

max_clash_score

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

extern

Referenced by main().

max_helix_length

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

extern

Referenced by main().

max_loop_length

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

extern

Referenced by main(), and slice_ellipsoid_envelope().

max_models

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

extern

Referenced by main().

max_ss_num

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

extern

max_strand_length

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

extern

Referenced by main().

may_add_already_added_model

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

extern

min_hash_score

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

extern

Referenced by main().

min_helix_length

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

extern

Referenced by main().

min_lh_fragments

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

extern

min_loop_length

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

extern

Referenced by main().

min_motif_score

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

extern

min_strand_length

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

extern

Referenced by main().

mode

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

extern

Referenced by main().

model_file_name

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

extern

Referenced by main(), svm_load_model(), and svm_save_model().

model_should_have_at_least_1_E

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

extern

Referenced by main().

model_should_have_at_least_1_E_at_terminal_segment

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

extern

Referenced by main().

model_should_have_at_least_1_H

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

extern

Referenced by main().

model_should_have_this_num_of_ss

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

extern

Referenced by main().

models_to_dump

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

extern

Referenced by main().

neighbor_cutoff

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

extern

Referenced by HemeBindingMover::apply(), xtal_water_bunsat::apply(), bunsats(), MatchSet::init_clash_check(), ClashCheck::init_clash_check(), ExposedStrandMover::is_exposed(), sasa_bunsats(), and vsasa_bunsats().

new_model_file_name

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

extern

Referenced by main().

num_edges_to_follow

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

extern

num_models_to_dump

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

extern

Referenced by main().

num_procs

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

extern

Referenced by main().

num_repeats

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

extern

num_segments_to_match

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

extern

Referenced by main().

offset_bump_dsq

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

extern

output_alignments_to_file

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

extern

partner_pdb

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

extern

pose_segment_ends

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

extern

pose_segment_starts

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

extern

rank

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

extern

Referenced by do_erraser2(), utility::graph::DisjointSets::ds_union(), erraser2_test(), get_tag(), protocols::jd2::RECONMPIJobDistributor::go(), protocols::jd2::RECONMPIJobDistributor::go_hardcoded(), main(), my_main(), and NativeEnsemble::ok_to_use_db().

remove_all_dssp

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

extern

Referenced by main().

remove_any_dssp

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

extern

Referenced by main().

repeat

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

extern

score_between_opposite_terminal_segments

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

extern

score_file_name

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

extern

Referenced by main().

skip_filters

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

extern

skip_loop_generation

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

extern

skip_refinement

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

extern

starting_model

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

extern

Referenced by main().