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 <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 <devel/init.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/etable/Etable.hh>
#include <core/scoring/ScoreType.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/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 <fstream>
#include <iostream>
#include <algorithm>
#include <utility/io/ozstream.hh>
#include <utility/file/FileName.hh>

Functions
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)
void	place_waters_and_minimize (Pose &pose)
Real	get_packing_score (Pose &pose, Size pos1, Size pos2)
void	process_for_motifs (Pose &pose, std::string &pdb_name, protocols::motifs::MotifLibrary &motifs)
void	process_file_list ()
int	main (int argc, char *argv[])

Function Documentation

get_packing_score()

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

References test.T200_Scoring::emap, oop_conformations::energy, beta_nonlocal::pose, and basic::options::OptionKeys::frags::scoring::scoring.

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
	)

References utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, basic::options::OptionKeys::extension, beta_nonlocal::pose, and ObjexxFCL::string_of().

Referenced by process_for_motifs().

place_waters_and_minimize()

void place_waters_and_minimize

(

Pose &

pose

)

References utility::io::oc::cout, create_a3b_hbs::i, beta_nonlocal::mm, beta_nonlocal::pose, oop_conformations::scorefxn, and vancomycin::task.

process_file_list()

void process_file_list

(

)

References utility::io::oc::cout, lactamize::filename, motifs, basic::options::OptionKeys::corrections::score::p_aa_pp, kic_runner::pdb, 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(), utility::io::oc::cout, end, get_packing_score(), min(), create_a3b_hbs::nres, output_single_motif(), and beta_nonlocal::pose.

Referenced by process_file_list().