hybrid.cc File Reference

#include <core/types.hh>
#include <devel/init.hh>
#include <basic/Tracer.hh>
#include <core/id/AtomID.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/SequenceMapping.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/SequenceAlignment.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/PartialThreadingMover.hh>
#include <protocols/comparative_modeling/coord_util.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 <utility/io/mpistream.hh>
#include <utility/io/ozstream.hh>
#include <ObjexxFCL/format.hh>
#include <utility/excn/Exceptions.hh>

Functions
void	superimpose_via_alignment (core::pose::Pose &pose1, core::pose::Pose const &pose2, core::sequence::SequenceAlignment aln, std::string const &atom_name="CA")
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)
int	main (int argc, char *argv[])

Detailed Description

Author

James Thompson

Function Documentation

main()

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

References in::file::alignment(), aln, cm::aln_format(), argv, basic::options::OptionKeys::chemical::chemical, basic::Tracer::Debug, dist(), build_jacobian::distance, test.T009_Exceptions::e, end, basic::Tracer::Error, in::file::fasta(), basic::Tracer::flush_all_channels(), create_a3b_hbs::ii, basic::init(), subloop_histogram::iterator, beta_nonlocal::jj, min(), in::file::native(), docking::native_pose, option, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::mp::assembly::poses, poses_from_cmd_line(), basic::options::OptionKeys::relax::sequence, sfd, basic::options::OptionKeys::in::file::silent, out::file::silent(), ObjexxFCL::string_of(), superimpose_via_alignment(), 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, 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.

superimpose_via_alignment()

void superimpose_via_alignment	(	core::pose::Pose &	pose1,
		core::pose::Pose const &	pose2,
		core::sequence::SequenceAlignment	aln,
		std::string const &	atom_name = "CA"
	)

References aln, end, create_a3b_hbs::ii, test.T008_Serialization::pose1, test.T008_Serialization::pose2, execute::residues, and superimpose_pose().

Referenced by main().