dna_motifs_collector.cc File Reference

app for collection of protein-DNA interaction motifs More...

#include <devel/init.hh>
#include <protocols/dna/util.hh>
#include <protocols/motifs/motif_utils.hh>
#include <protocols/motifs/Motif.hh>
#include <protocols/motifs/MotifLibrary.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/types.hh>
#include <basic/Tracer.hh>
#include <core/pack/task/ResidueLevelTask.hh>
#include <utility/io/ozstream.hh>
#include <utility/string_util.hh>
#include <ObjexxFCL/string.functions.hh>
#include <map>
#include <string>
#include <basic/options/option.hh>
#include <basic/options/util.hh>
#include <basic/options/keys/motifs.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <utility/vector1.hh>

Functions
void	output_single_motif (core::pose::Pose &src_pose, std::string &pdb_prefix, core::Size prot_pos, utility::vector1< core::Size > &contacts, utility::io::ozstream &motif_output_file)
void	place_waters_and_minimize (core::pose::Pose &pose, core::scoring::ScoreFunction &scorefxn, std::string &pdb_prefix)
core::Real	get_packing_score (core::pose::Pose &pose, core::Size pos1, core::Size pos2, core::scoring::ScoreFunction &scorefxn)
core::Real	get_hbond_score (core::pose::Pose &pose, core::Size pos1, core::Size pos2, core::scoring::ScoreFunction &scorefxn)
core::Real	get_water_hbond_score (core::pose::Pose &pose, core::Size pos1, core::Size pos2, core::scoring::ScoreFunction &scorefxn)
void	process_for_motifs (core::pose::Pose &pose, std::string &pdb_prefix, protocols::motifs::MotifLibrary &motifs, utility::io::ozstream &motif_output_file)
void	process_file_list ()
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.pilot.dna_motifs_collector")

Detailed Description

app for collection of protein-DNA interaction motifs

Author

sthyme

Function Documentation

get_hbond_score()

core::Real get_hbond_score	(	core::pose::Pose &	pose,
		core::Size	pos1,
		core::Size	pos2,
		core::scoring::ScoreFunction &	scorefxn
	)

References beta_nonlocal::pose, and oop_conformations::scorefxn.

Referenced by process_for_motifs().

get_packing_score()

core::Real get_packing_score	(	core::pose::Pose &	pose,
		core::Size	pos1,
		core::Size	pos2,
		core::scoring::ScoreFunction &	scorefxn
	)

References beta_nonlocal::pose, and oop_conformations::scorefxn.

Referenced by process_for_motifs().

get_water_hbond_score()

core::Real get_water_hbond_score	(	core::pose::Pose &	pose,
		core::Size	pos1,
		core::Size	pos2,
		core::scoring::ScoreFunction &	scorefxn
	)

References beta_nonlocal::pose, and oop_conformations::scorefxn.

Referenced by process_for_motifs().

main()

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

References argv, test.T009_Exceptions::e, basic::init(), and process_file_list().

output_single_motif()

void output_single_motif	(	core::pose::Pose &	src_pose,
		std::string &	pdb_prefix,
		core::Size	prot_pos,
		utility::vector1< core::Size > &	contacts,
		utility::io::ozstream &	motif_output_file
	)

References contacts(), basic::options::OptionKeys::matdes::dock::dump_pdb, basic::options::OptionKeys::extension, basic::options::OptionKeys::motifs::keep_motif_xtal_location, basic::options::OptionKeys::motifs::motif_output_directory, basic::options::option, beta_nonlocal::pose, basic::options::OptionKeys::in::file::residue_type_set, ObjexxFCL::string_of(), TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by process_for_motifs().

place_waters_and_minimize()

void place_waters_and_minimize	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction &	scorefxn,
		std::string &	pdb_prefix
	)

References basic::options::OptionKeys::matdes::dock::dump_pdb, create_a3b_hbs::i, SmotifHasher::min_score, basic::options::OptionKeys::relax::min_tolerance, basic::options::OptionKeys::run::min_tolerance, basic::options::OptionKeys::dna::specificity::min_type, basic::options::OptionKeys::run::min_type, beta_nonlocal::mm, basic::options::option, options, basic::options::OptionKeys::motifs::place_adduct_waters, beta_nonlocal::pose, basic::options::OptionKeys::motifs::preminimize_motif_pdbs, basic::options::OptionKeys::motifs::preminimize_motif_pdbs_sconly, oop_conformations::scorefxn, vancomycin::task, TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by process_for_motifs().

process_file_list()

void process_file_list

(

)

References motifs, basic::options::option, basic::options::OptionKeys::motifs::output_file, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file(), process_for_motifs(), basic::options::start_files(), utility::string_split(), TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

process_for_motifs()

void process_for_motifs	(	core::pose::Pose &	pose,
		std::string &	pdb_prefix,
		protocols::motifs::MotifLibrary &	motifs,
		utility::io::ozstream &	motif_output_file
	)

References contacts(), basic::options::OptionKeys::motifs::duplicate_motif_cutoff, basic::options::OptionKeys::motifs::eliminate_weak_motifs, end, create_a3b_hbs::first, get_hbond_score(), get_packing_score(), pyrosetta.distributed.io::get_score_function(), get_water_hbond_score(), hb_score(), basic::options::OptionKeys::motifs::hb_score_cutoff, create_a3b_hbs::nres, basic::options::option, output_single_motif(), basic::options::OptionKeys::motifs::pack_score_cutoff, place_waters_and_minimize(), beta_nonlocal::pose, basic::options::OptionKeys::in::file::residue_type_set, oop_conformations::scorefxn, ObjexxFCL::string_of(), TR, and basic::options::OptionKeys::motifs::water_score_cutoff.

Referenced by process_file_list().

Variable Documentation

TR

basic::Tracer TR("apps.pilot.dna_motifs_collector") ( "apps.pilot.dna_motifs_collector"  )

static

Referenced by output_single_motif(), place_waters_and_minimize(), process_file_list(), and process_for_motifs().