thread_fast.cc File Reference

#include <core/types.hh>
#include <devel/init.hh>
#include <basic/Tracer.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/scoring/rms_util.hh>
#include <basic/options/option.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/SequenceProfile.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/id/SequenceMapping.hh>
#include <core/sequence/ScoringScheme.hh>
#include <core/sequence/ScoringSchemeFactory.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/conformation/Residue.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/ScoreFileSilentStruct.hh>
#include <protocols/comparative_modeling/ThreadingMover.hh>
#include <protocols/jobdist/not_universal_main.hh>
#include <utility/exit.hh>
#include <utility/vector1.hh>
#include <utility/string_util.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <ObjexxFCL/char.functions.hh>
#include <ObjexxFCL/string.functions.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <numeric/model_quality/rms.hh>
#include <map>
#include <iostream>
#include <string>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/cm.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/annotated_sequence.hh>
#include <protocols/jobdist/Jobs.hh>
#include <utility/io/mpistream.hh>
#include <ObjexxFCL/format.hh>
#include <utility/excn/Exceptions.hh>

Functions
std::map< std::string, core::pose::Pose >	poses_from_cmd_line (utility::vector1< std::string > const &fn_list)
void	print_seq_map (std::ostream &out, std::map< std::string, core::sequence::SequenceOP > const &seqs)
std::map< std::string, core::sequence::SequenceOP >	sequences_from_cmd_line (utility::vector1< std::string > const &fn_list)
int	main (int argc, char *argv[])

Detailed Description

Author

James Thompson

Function Documentation

main()

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

References in::file::alignment(), cm::aln_format(), argv, numeric::model_quality::calc_rms(), utility::io::oc::cerr, basic::options::OptionKeys::chemical::chemical, basic::Tracer::Debug, test.T009_Exceptions::e, end, basic::Tracer::flush(), create_a3b_hbs::ii, basic::init(), subloop_histogram::iterator, beta_nonlocal::jj, cm::min_gap_extend(), cm::min_gap_open(), in::file::native(), docking::native_pose, natoms(), option, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::mp::assembly::poses, poses_from_cmd_line(), print_seq_map(), in::file::pssm(), numeric::model_quality::rms_wrapper(), runtime_assert, cm::seq_score(), sequences_from_cmd_line(), sfd, basic::options::OptionKeys::in::file::silent, out::file::silent(), challenge::ss, in::file::template_pdb(), tr, and basic::options::OptionKeys::inout::dbms::user.

poses_from_cmd_line()

std::map< std::string, core::pose::Pose > poses_from_cmd_line

(

utility::vector1< std::string > const &

fn_list

)

References basic::options::OptionKeys::chemical::chemical, end, utility::file_basename(), utility::file::file_exists(), file_exists(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, and basic::options::OptionKeys::mp::assembly::poses.

Referenced by main().

print_seq_map()

void print_seq_map	(	std::ostream &	out,
		std::map< std::string, core::sequence::SequenceOP > const &	seqs
	)

References end.

Referenced by main().

sequences_from_cmd_line()

std::map< std::string, core::sequence::SequenceOP > sequences_from_cmd_line

(

utility::vector1< std::string > const &

fn_list

)

References end, utility::file_basename(), utility::file::file_exists(), file_exists(), and basic::options::OptionKeys::relax::sequence.

Referenced by main().