ligand_motifs.cc File Reference

#include <sstream>
#include <string>
#include <core/types.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/chemical/MMAtomTypeSet.hh>
#include <core/chemical/AtomType.hh>
#include <basic/Tracer.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueTypeSelector.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/Conformation.hh>
#include <core/chemical/residue_io.hh>
#include <core/chemical/util.hh>
#include <core/chemical/VariantType.hh>
#include <core/scoring/Energies.hh>
#include <devel/init.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/etable/Etable.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/etable/EtableEnergy.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/methods/ShortRangeTwoBodyEnergy.hh>
#include <core/scoring/methods/ShortRangeTwoBodyEnergy.fwd.hh>
#include <core/scoring/Ramachandran.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/scoring/hbonds/HBondEnergy.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/etable/count_pair/CountPairFunction.hh>
#include <core/scoring/LREnergyContainer.hh>
#include <core/scoring/methods/LongRangeTwoBodyEnergy.hh>
#include <core/scoring/TenANeighborGraph.hh>
#include <core/scoring/rms_util.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/pack/rotamer_set/RotamerSet.hh>
#include <core/pack/rotamer_set/RotamerSetFactory.hh>
#include <core/pack/packer_neighbors.hh>
#include <utility/graph/Graph.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/id/AtomID_Map.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/scoring/mm/MMTorsionLibrary.hh>
#include <core/scoring/mm/MMTorsionLibrary.fwd.hh>
#include <core/optimization/types.hh>
#include <core/optimization/Multifunc.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/Minimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/pose/PDBInfo.hh>
#include <basic/options/util.hh>
#include <basic/basic.hh>
#include <basic/database/open.hh>
#include <utility/vector1.hh>
#include <utility/exit.hh>
#include <utility/pointer/owning_ptr.hh>
#include <utility/VirtualBase.hh>
#include <utility/excn/Exceptions.hh>
#include <numeric/xyzVector.hh>
#include <numeric/random/random.hh>
#include <ObjexxFCL/string.functions.hh>
#include <protocols/dna/util.hh>
#include <protocols/motifs/MotifLibrary.hh>
#include <protocols/motifs/Motif.hh>
#include <core/import_pose/import_pose.hh>
#include <core/scoring/hbonds/HBondSet.fwd.hh>
#include <fstream>
#include <iostream>
#include <algorithm>
#include <utility/io/ozstream.hh>
#include <utility/file/FileName.hh>

Functions
core::Real	get_hbond_score (core::pose::Pose &pose, core::Size pos1, core::Size pos2, core::scoring::ScoreFunction &scorefxn)
void	output_single_motif (Pose &src_pose, protocols::motifs::MotifLibrary &motifs, std::string &pdb_name, Size prot_pos, Size lig_pos, utility::vector1< Size > &lig_atoms, Real pack_score, Real hb_score)
core::Real	get_packing_score (core::pose::Pose &pose, core::Size pos1, core::Size pos2, core::scoring::ScoreFunction &scorefxn)
void	process_for_motifs (Pose &pose, std::string &pdb_name, protocols::motifs::MotifLibrary &motifs)
void	process_file_list ()
int	main (int argc, char *argv[])

Variables
static basic::Tracer	ms_tr ("apps.pilot.ligand_motifs", basic::t_info)

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().

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	(	Pose &	src_pose,
		protocols::motifs::MotifLibrary &	motifs,
		std::string &	pdb_name,
		Size	prot_pos,
		Size	lig_pos,
		utility::vector1< Size > &	lig_atoms,
		Real	pack_score,
		Real	hb_score
	)

References basic::options::OptionKeys::matdes::dock::dump_pdb, basic::options::OptionKeys::extension, hb_score(), ms_tr, beta_nonlocal::pose, ObjexxFCL::string_of(), and numeric::interpolation::to_string().

Referenced by process_for_motifs().

process_file_list()

void process_file_list

(

)

References lactamize::filename, motifs, ms_tr, basic::options::OptionKeys::corrections::score::p_aa_pp, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, process_for_motifs(), oop_conformations::scorefxn, and basic::options::start_files().

Referenced by main().

process_for_motifs()

void process_for_motifs	(	Pose &	pose,
		std::string &	pdb_name,
		protocols::motifs::MotifLibrary &	motifs
	)

References contacts(), pyrosetta::create_score_function, end, get_hbond_score(), get_packing_score(), hb_score(), min(), ms_tr, create_a3b_hbs::nres, output_single_motif(), beta_nonlocal::pose, and oop_conformations::scorefxn.

Referenced by process_file_list().

Variable Documentation

ms_tr

basic::Tracer ms_tr("apps.pilot.ligand_motifs", basic::t_info) ( "apps.pilot.ligand_motifs"  , basic::t_info    )

static

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