incorporate_motifs.cc File Reference

#include <core/types.hh>
#include <devel/init.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <basic/options/util.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/motifs.OptionKeys.gen.hh>
#include <basic/basic.hh>
#include <basic/Tracer.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/motifs/Motif.hh>
#include <protocols/motifs/SingleMotif.hh>
#include <protocols/motifs/MotifLibrary.hh>
#include <protocols/motifs/IRCollection.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <utility/excn/Exceptions.hh>
#include <fstream>
#include <iostream>

Functions
void	identify_targeted_positions (utility::vector1< core::Size > &pos_vec, core::pose::Pose &pose, std::string &source_file)
void	read_in_flexible_regions (protocols::loops::LoopsOP &flex_regions, core::pose::Pose &pose)
void	find_close_motifs ()
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("incorporate_motifs")

Function Documentation

void find_close_motifs

(

)

References basic::options::OptionKeys::motifs::build_residue_file, pyrosetta::create_score_function, identify_targeted_positions(), basic::options::OptionKeys::motifs::motif_filename, motifs::motif_filename(), option, demo.D010_Pose_structure::pose, pyrosetta.distributed.io::pose_from_file, read_in_flexible_regions(), basic::options::OptionKeys::motifs::residue_trim_file, in::file::s(), TR, and basic::options::OptionKeys::optE::weights.

Referenced by main().

void identify_targeted_positions	(	utility::vector1< core::Size > &	pos_vec,
		core::pose::Pose &	pose,
		std::string &	source_file
	)

References basic::options::OptionKeys::run::chain, make_symmdef_file_denovo::pos, and TR.

Referenced by find_close_motifs().

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

References utility::excn::Exception::display(), test.T009_Exceptions::e, find_close_motifs(), basic::Tracer::flush(), devel::init(), and TR.

void read_in_flexible_regions	(	protocols::loops::LoopsOP &	flex_regions,
		core::pose::Pose &	pose
	)

References basic::Tracer::Error, basic::options::OptionKeys::motifs::motif_flexible_loop_file, option, and TR.

Referenced by find_close_motifs().

Variable Documentation

basic::Tracer TR("incorporate_motifs")

static

Referenced by find_close_motifs(), identify_targeted_positions(), main(), and read_in_flexible_regions().