#include <devel/dna/protocols.hh>
#include <devel/dna/util.hh>
#include <protocols/viewer/viewers.hh>
#include <utility/excn/Exceptions.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/dna/setup.hh>
#include <core/scoring/dna/BasePartner.hh>
#include <core/scoring/func/Func.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/PDBPoseMap.hh>
#include <basic/options/util.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <utility/vector1.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/random/random.hh>
#include <ObjexxFCL/string.functions.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <set>
#include <cstdlib>
#include <sstream>
#include <basic/Tracer.hh>
#include <basic/options/keys/dna.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>
#include <core/kinematics/Jump.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <protocols/moves/Mover.hh>
#include <ObjexxFCL/format.hh>

Classes
class	MotifScanMover

Typedefs
typedef std::map< char, Real >	MotifColumn

typedef std::map< Size, MotifColumn >	Motif

Functions
void	smooth_motif_column (MotifColumn &C)

Real	motif_column_deviation (MotifColumn P, MotifColumn E)

Real	motif_deviation (Motif const &P, Motif const &E)

vector1< Size >	parse_pdb_pos (pose::Pose const &pose)

void	make_dna_only_pose (pose::Pose const &pose, Pose &dna_pose)

void	single_position_motif_scan (Pose const &start_pose, ScoreFunction const &scorefxn, Size const seqpos, protocols::moves::Mover &complex_mover, protocols::moves::Mover &dna_mover, std::string const &tag, Real const KT, bool const dump_pdbs, MotifColumn &prob)

MotifColumn	contact_model_prediction (Pose const &pose, Size const seqpos)

void	motif_scan ()

void *	my_main (void *)

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

Variables
static basic::Tracer	tw ("demo.phil.motif_scan", basic::t_warning)

static basic::Tracer	tt ("demo.phil.motif_scan", basic::t_trace)

Typedef Documentation

◆ Motif

typedef std::map< Size, MotifColumn > Motif

◆ MotifColumn

typedef std::map< char, Real > MotifColumn

Function Documentation

◆ contact_model_prediction()

MotifColumn contact_model_prediction	(	Pose const &	pose,
		Size const	seqpos
	)

References ObjexxFCL::abs(), C, basic::options::OptionKeys::dna::dna, test.T009_Exceptions::e, create_a3b_hbs::i, create_a3b_hbs::ii, create_a3b_hbs::j, beta_nonlocal::jj, N, beta_nonlocal::pose, create_a3b_hbs::r, test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

Referenced by motif_scan().

◆ main()

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

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

◆ make_dna_only_pose()

void make_dna_only_pose	(	pose::Pose const &	pose,
		Pose &	dna_pose
	)

References create_a3b_hbs::i, and beta_nonlocal::pose.

Referenced by single_position_motif_scan().

◆ motif_column_deviation()

Real motif_column_deviation	(	MotifColumn	P,
		MotifColumn	E
	)

References ObjexxFCL::format::E(), test.T009_Exceptions::e, numeric::log(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, P, and smooth_motif_column().

Referenced by motif_deviation(), and motif_scan().

◆ motif_deviation()

Real motif_deviation	(	Motif const &	P,
		Motif const &	E
	)

References ObjexxFCL::format::E(), motif_column_deviation(), N, and P.

Referenced by motif_scan().

◆ motif_scan()

void motif_scan ( )

References C, predPRE::chain, contact_model_prediction(), utility::io::oc::cout, data, basic::options::OptionKeys::ddg::dump_pdbs, ObjexxFCL::format::F(), lactamize::filename, getline(), create_a3b_hbs::i, create_a3b_hbs::ii, extract_by_sidechain_sasa_score::l, line, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, DRRAFTER_util::matches(), beta_nonlocal::mm, SmotifHasher::mode, motif_column_deviation(), motif_deviation(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, create_a3b_hbs::nres, option, parse_pdb_pos(), basic::options::OptionKeys::dna::specificity::pdb_pos, make_symmdef_file_denovo::pos, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::dna::specificity::pre_minimize, basic::options::OptionKeys::dna::specificity::pre_pack, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::prob, test.T500_Packing::rotamer_trials, test.Workshop4test::score2, test.Workshop4test::score3, basic::options::OptionKeys::dna::specificity::score_function, oop_conformations::scorefxn, MotifScanMover::seqpos(), single_position_motif_scan(), basic::options::start_files(), vancomycin::task, tt, tw, basic::options::OptionKeys::inout::dbms::user, and utility_exit.

Referenced by my_main().

◆ my_main()

void* my_main ( void * )

References motif_scan().

Referenced by main().

◆ parse_pdb_pos()

vector1< Size > parse_pdb_pos ( pose::Pose const & pose )

References predPRE::chain, create_a3b_hbs::i, ObjexxFCL::int_of(), option, basic::options::OptionKeys::dna::specificity::pdb_pos, make_symmdef_file_denovo::pos, and beta_nonlocal::pose.

Referenced by motif_scan().

◆ single_position_motif_scan()

void single_position_motif_scan	(	Pose const &	start_pose,
		ScoreFunction const &	scorefxn,
		Size const	seqpos,
		protocols::moves::Mover &	complex_mover,
		protocols::moves::Mover &	dna_mover,
		std::string const &	tag,
		Real const	KT,
		bool const	dump_pdbs,
		MotifColumn &	prob
	)