#include <apps/public/sewing/segment_file_generator.hh>
#include <basic/Tracer.hh>
#include <algorithm>
#include <regex>
#include <utility/string_util.hh>
#include <utility/exit.hh>
#include <boost/algorithm/string.hpp>
#include <devel/init.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/import_pose/import_pose.hh>
#include <core/select/residue_selector/ResidueSelector.fwd.hh>
#include <iostream>
#include <string>
#include <numeric/random/random.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <protocols/sewing/hashing/AlignmentFileGeneratorMover.hh>
#include <protocols/sewing/hashing/hasher_data.hh>
#include <protocols/sewing/data_storage/LigandResidue.hh>
#include <protocols/sewing/data_storage/SmartSegment.hh>
#include <core/conformation/Atom.hh>
#include <basic/options/option.hh>
#include <utility/stream_util.hh>
#include <basic/options/keys/OptionKeys.hh>

Namespaces
	apps

	apps::pilot

	apps::pilot::frankdt

Functions
utility::vector1< Motif >	apps::pilot::frankdt::import_motifs (std::string motif_filename)

void	apps::pilot::frankdt::invalid_motif (std::string bad_motif, std::string error_msg)

Motif	apps::pilot::frankdt::reverse_motif (Motif const motif)

bool	apps::pilot::frankdt::lt (Motif i, Motif j)

std::set< Motif, bool(*)(Motif, Motif) >	apps::pilot::frankdt::check_motifs (utility::vector1< Motif > motifs)

void	apps::pilot::frankdt::check_for_chain_breaks (std::map< core::Size, protocols::sewing::data_storage::SmartSegmentOP > &pdb_segments)

utility::vector1< Motif >	apps::pilot::frankdt::copy_set_to_vector (std::set< Motif, bool(*)(Motif, Motif) > const copy_set)

bool	apps::pilot::frankdt::dssp_code_matches (std::string motif_dssp, std::string segment_dssp)

utility::vector1< Motif >	apps::pilot::frankdt::compare_segment_to_motif (utility::vector1< Motif > &motifs_to_match, core::Size position, protocols::sewing::data_storage::SmartSegmentOP current_segment)

protocols::sewing::hashing::SegmentVectorOP	apps::pilot::frankdt::store_segment_motif_match (protocols::sewing::data_storage::SmartSegmentOP segment, core::Size last_segment_position)

void	apps::pilot::frankdt::write_segments_to_file (protocols::sewing::hashing::SegmentVectorOP seg_vec, utility::pointer::shared_ptr< utility::io::ozstream > file)

int	apps::pilot::frankdt::main (int argc, char *argv[])

int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.pilot.frankdt.segment_file_generator")

FileOptionKey const	motif_file ("motif_file")

FileOptionKey const	pdb_list_file ("pdb_list_file")

BooleanOptionKey const	strict_dssp_changes ("strict_dssp_changes")