fix_alignment_to_match_pdb.cc File Reference

#include <core/types.hh>
#include <devel/init.hh>
#include <basic/Tracer.hh>
#include <core/chemical/util.hh>
#include <basic/options/option.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/id/SequenceMapping.hh>
#include <core/sequence/ScoringScheme.hh>
#include <core/sequence/SimpleScoringScheme.hh>
#include <core/sequence/SWAligner.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/Residue.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 <utility/excn/Exceptions.hh>
#include <ObjexxFCL/char.functions.hh>
#include <ObjexxFCL/string.functions.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/io/silent/SilentFileData.fwd.hh>
#include <core/kinematics/Jump.hh>
#include <core/sequence/SequenceProfile.fwd.hh>
#include <utility/io/ozstream.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

TJ Brunette

Function Documentation

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

References in::file::alignment(), out::file::alignment(), cm::aln_format(), basic::options::OptionKeys::chemical::chemical, basic::Tracer::Debug, utility::excn::Exception::display(), test.T009_Exceptions::e, basic::Tracer::Error, devel::init(), option, options, basic::options::OptionKeys::cp::output, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::mp::assembly::poses, poses_from_cmd_line(), basic::options::OptionKeys::mh::path::scores, basic::options::OptionKeys::relax::sequence, basic::options::OptionKeys::in::file::silent, basic::options::OptionKeys::mh::match::ss, in::file::template_pdb(), tr, and basic::Tracer::Warning.

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(), name, options, demo.D010_Pose_structure::pose, pyrosetta.distributed.io::pose_from_file, and basic::options::OptionKeys::mp::assembly::poses.

Referenced by main().