basic_thread.cc File Reference

#include <core/types.hh>
#include <devel/init.hh>
#include <basic/Tracer.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ResidueType.hh>
#include <basic/options/option.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/sequence/SWAligner.hh>
#include <core/sequence/NWAligner.hh>
#include <core/sequence/ScoringScheme.fwd.hh>
#include <core/sequence/SimpleScoringScheme.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/pose/Pose.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <protocols/comparative_modeling/ThreadingMover.hh>
#include <protocols/comparative_modeling/StealSideChainsMover.hh>
#include <protocols/comparative_modeling/RecoverSideChainsMover.hh>
#include <core/id/AtomID.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID_Mask.fwd.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Residue.functions.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <utility/vector1.hh>
#include <utility/string_util.hh>
#include <core/pack/optimizeH.hh>
#include <string>
#include <basic/options/keys/cm.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/james.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/util.hh>
#include <utility/excn/Exceptions.hh>

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

Detailed Description

Author

James Thompson

Function Documentation

main()

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

References basic::options::OptionKeys::cm::aligner, aln, argv, basic::options::OptionKeys::chemical::chemical, test.T009_Exceptions::e, end, basic::Tracer::Error, basic::options::OptionKeys::in::file::fasta, utility::file_basename(), basic::Tracer::flush(), create_a3b_hbs::ii, basic::init(), beta_sc_scan::name3, basic::options::option, localrmsd::output_name, kic_runner::pdb, pyrosetta.distributed.io::pose_from_file, create_a3b_hbs::prefix, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::relax::sequence, challenge::ss, vancomycin::task, basic::options::OptionKeys::in::file::template_pdb, basic::options::OptionKeys::james::thread_unaligned, and tr.