extract_motifs.cc File Reference

Application to extract motifs from a set of pdb files. More...

#include <core/types.hh>
#include <core/conformation/Conformation.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/scoring/ScoreFunction.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/motifs/Motif.hh>
#include <protocols/motifs/SingleMotif.hh>
#include <protocols/motifs/MotifLibrary.hh>
#include <fstream>
#include <protocols/jd2/JobDistributor.hh>
#include <devel/init.hh>
#include <utility/excn/Exceptions.hh>

Functions
Vector const	atom1_vector (1.500, 0.000, 0.000)
Vector const	atom2_vector (0.000, 0.000, 0.000)
Vector const	atom3_vector (0.000, 1.500, 0.000)
static THREAD_LOCAL basic::Tracer	TR ("extract_motifs")
void	fetch_atom_names (core::chemical::AA const &aa, std::string &oa1, std::string &oa2, std::string &oa3)
void	output_single_motif (Pose &src_pose, AA const &target_aa, std::string &pdb_name, int prot_pos, std::vector< Size > &contacts)
void	motif_distances (protocols::motifs::Motif const &m1, protocols::motifs::Motif const &m2, core::Real &dist_diff, core::Real &angl_diff)
Real	get_packing_score (Pose &pose, Size pos1, Size pos2, ScoreFunction &sf)
Real	get_hbond_score (Pose &pose, Size pos1, Size pos2, ScoreFunction &sf)
Real	get_elec_score (Pose &pose, Size pos1, Size pos2, ScoreFunction &sf)
void	process_for_motifs (Pose &pose, std::string &pdb_name, chemical::AA const target_aa, protocols::motifs::MotifLibrary &motif_lib)
int	main (int argc, char *argv[])

Detailed Description

Application to extract motifs from a set of pdb files.

Function Documentation

Vector const atom1_vector	(	1.	500,
		0.	000,
		0.	000
	)

Referenced by output_single_motif().

Vector const atom2_vector	(	0.	000,
		0.	000,
		0.	000
	)

Referenced by output_single_motif().

Vector const atom3_vector	(	0.	000,
		1.	500,
		0.	000
	)

Referenced by output_single_motif().

void fetch_atom_names	(	core::chemical::AA const &	aa,
		std::string &	oa1,
		std::string &	oa2,
		std::string &	oa3
	)

References TR().

Referenced by output_single_motif(), and process_for_motifs().

Real get_elec_score	(	Pose &	pose,
		Size	pos1,
		Size	pos2,
		ScoreFunction &	sf
	)

References app.surface_docking.surface_docking::pose.

Referenced by process_for_motifs().

Real get_hbond_score	(	Pose &	pose,
		Size	pos1,
		Size	pos2,
		ScoreFunction &	sf
	)

References app.surface_docking.surface_docking::pose.

Referenced by process_for_motifs().

Real get_packing_score	(	Pose &	pose,
		Size	pos1,
		Size	pos2,
		ScoreFunction &	sf
	)

References app.surface_docking.surface_docking::pose.

Referenced by process_for_motifs().

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

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, devel::init(), in::file::l(), utility::excn::EXCN_Base::msg(), option, out::path::pdb(), in::path::pdb(), app.surface_docking.surface_docking::pose, process_for_motifs(), motifs::target_aa(), basic::options::OptionKeys::motifs::target_aa, TR(), and ObjexxFCL::uppercase().

void motif_distances	(	protocols::motifs::Motif const &	m1,
		protocols::motifs::Motif const &	m2,
		core::Real &	dist_diff,
		core::Real &	angl_diff
	)

Referenced by process_for_motifs().

void output_single_motif	(	Pose &	src_pose,
		AA const &	target_aa,
		std::string &	pdb_name,
		int	prot_pos,
		std::vector< Size > &	contacts
	)

References atom1_vector(), atom2_vector(), atom3_vector(), basic::options::OptionKeys::matdes::dock::dump_pdb, fetch_atom_names(), option, out::path::pdb(), app.surface_docking.surface_docking::pose, ObjexxFCL::string_of(), and TR().

Referenced by process_for_motifs().

void process_for_motifs	(	Pose &	pose,
		std::string &	pdb_name,
		chemical::AA const	target_aa,
		protocols::motifs::MotifLibrary &	motif_lib
	)

References basic::options::OptionKeys::frags::contacts::contacts, motifs::duplicate_angle_cutoff(), motifs::duplicate_dist_cutoff(), basic::options::OptionKeys::motifs::elec_max_threshold, motifs::elec_max_threshold(), basic::options::OptionKeys::motifs::elec_min_threshold, motifs::elec_min_threshold(), fetch_atom_names(), get_elec_score(), get_hbond_score(), get_packing_score(), basic::options::OptionKeys::motifs::hbond_max_threshold, motifs::hbond_max_threshold(), basic::options::OptionKeys::motifs::hbond_min_threshold, motifs::hbond_min_threshold(), motif_distances(), clean_pdb_keep_ligand::nres, option, output_single_motif(), basic::options::OptionKeys::motifs::pack_max_threshold, motifs::pack_max_threshold(), basic::options::OptionKeys::motifs::pack_min_threshold, motifs::pack_min_threshold(), PyMOL_demo::scorefxn, ObjexxFCL::string_of(), basic::options::OptionKeys::motifs::target_aa, and TR().

Referenced by main().

static THREAD_LOCAL basic::Tracer TR ( "extract_motifs"  )

static

Referenced by fetch_atom_names(), main(), output_single_motif(), and process_for_motifs().