partial_thread.cc File Reference

#include <core/types.hh>
#include <devel/init.hh>
#include <basic/Tracer.hh>
#include <core/chemical/util.hh>
#include <core/id/SequenceMapping.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <basic/options/option.hh>
#include <utility/io/ozstream.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <utility/excn/Exceptions.hh>
#include <core/pose/Pose.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/pose/annotated_sequence.hh>
#include <protocols/comparative_modeling/PartialThreadingMover.hh>
#include <utility/vector1.hh>
#include <utility/string_util.hh>
#include <utility/file/file_sys_util.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/partial_thread.OptionKeys.gen.hh>
#include <basic/citation_manager/CitationManager.hh>
#include <basic/citation_manager/CitationCollection.hh>
#include <core/import_pose/import_pose.hh>

Functions
std::map< std::string, core::pose::Pose >	poses_from_cmd_line (utility::vector1< std::string > const &fn_list)
int	main (int argc, char *argv[])

Detailed Description

Author

James Thompson

Ray Wang

Function Documentation

main()

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

References basic::options::OptionKeys::in::file::alignment, aln, basic::options::OptionKeys::cm::aln_format, basic::citation_manager::Application, argv, basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::cm::cm, basic::Tracer::Debug, basic::options::OptionKeys::matdes::dock::dump_pdb, test.T009_Exceptions::e, basic::Tracer::Error, basic::options::OptionKeys::in::file::fasta, basic::Tracer::flush_all_channels(), utility::SingletonBase< CitationManager >::get_instance(), create_a3b_hbs::ii, basic::init(), subloop_histogram::iterator, basic::options::option, bin_torsions::output, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::mp::assembly::poses, poses_from_cmd_line(), basic::options::OptionKeys::relax::sequence, subloop_histogram::size, basic::options::OptionKeys::partial_thread::skip_repack, basic::options::OptionKeys::in::file::template_pdb, and tr.

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, 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().