MakeSegmentFile.cc File Reference

an app to make segment files More...

#include <devel/init.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/simple_metrics/SimpleMetric.hh>
#include <algorithm>
#include <regex>
#include <basic/options/option.hh>
#include <basic/options/keys/sewing.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/inout.OptionKeys.gen.hh>
#include <basic/options/keys/parser.OptionKeys.gen.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/file/FileName.hh>
#include <utility/pointer/memory.hh>
#include <utility/pointer/owning_ptr.hh>
#include <utility/vector1.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/variant_util.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/conformation/Residue.hh>
#include <core/import_pose/import_pose.hh>
#include <iostream>
#include <string>
#include <stdlib.h>
#include <core/conformation/Atom.hh>
#include <numeric/random/random.hh>
#include <numeric/HomogeneousTransform.hh>
#include <protocols/pose_sewing/data_storage/TerminalDSSPSortedPoseVector.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/rosetta_scripts/XmlObjects.hh>
#include <protocols/filters/Filter.hh>
#include <utility/options/OptionCollection.fwd.hh>
#include <utility/options/keys/OptionKeyList.fwd.hh>
#include <basic/options/keys/jd2.OptionKeys.gen.hh>
#include <apps/public/pose_sewing/MakeSegmentFile.hh>
#include <basic/Tracer.hh>

Classes
class	MakeSegmentFileMPI

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

Variables
static basic::Tracer	TR ("apps.public.pose_sewing.MakeSegmentFile")
FileOptionKey const	motifs ("motif_file")
FileOptionKey const	pdbs ("pdb_file")
FileOptionKey const	segment_path ("segment_path")
FileOptionKey const	seg_script_opt ("seg_xml")
StringOptionKey const	seg_filters ("seg_filters")
StringOptionKey const	seg_metrics ("seg_metrics")
BooleanOptionKey const	output_elements_opt ("output_elements")

Detailed Description

an app to make segment files

Author

frankdt (frank.nosp@m.dt@e.nosp@m.mail..nosp@m.unc..nosp@m.edu)

Jared Adolf–Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com)

Function Documentation

main()

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

References argv, utility::file::create_directory_recursive(), utility::excn::Exception::display(), utility::options::OptionKeys::options::exit, basic::options::OptionKeys::AnchoredDesign::filters::filters, basic::init(), utility::file::is_directory(), in::file::l(), motifs, jd2::no_output(), option, output_elements_opt, bur_nodon_tyr::pdb_list, in::file::s(), seg_filters, seg_metrics, seg_script_opt, segment_path, utility::string_split(), TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Variable Documentation

motifs

FileOptionKey const motifs("motif_file")

(

"motif_file"

)

Referenced by harvest_motifs(), harvest_scores(), apps::pilot::frankdt::import_motifs(), main(), merge_motifs(), print_motifs(), process_file_list(), and sicdock_thread_num().

output_elements_opt

BooleanOptionKey const output_elements_opt("output_elements")

(

"output_elements"

)

Referenced by main().

pdbs

FileOptionKey const pdbs("pdb_file")

(

"pdb_file"

)

Referenced by main(), and posewrap_from_command_line().

seg_filters

StringOptionKey const seg_filters("seg_filters")

(

"seg_filters"

)

Referenced by main().

seg_metrics

StringOptionKey const seg_metrics("seg_metrics")

(

"seg_metrics"

)

Referenced by main().

seg_script_opt

FileOptionKey const seg_script_opt("seg_xml")

(

"seg_xml"

)

Referenced by main().

segment_path

FileOptionKey const segment_path("segment_path")

(

"segment_path"

)

Referenced by main().

TR

basic::Tracer TR("apps.public.pose_sewing.MakeSegmentFile") ( "apps.public.pose_sewing.MakeSegmentFile"  )

static

Referenced by main().