IdentifyLigandMotifs.cc File Reference

.cc fils for IdentifyLigandMotifs protocol. Protocol object reads in a pdb file(s) and outputs motifs for protein-ligand interactions in .pdb and .motifs format. App originally written by mdsmith, optimized and converted to protocol by Ari Ginsparg. More...

#include <basic/options/option.hh>
#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 <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 <protocols/motifs/IdentifyLigandMotifs.hh>
#include <fstream>
#include <iostream>
#include <algorithm>
#include <utility/io/ozstream.hh>
#include <utility/file/FileName.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/dna.OptionKeys.gen.hh>
#include <basic/options/keys/motifs.OptionKeys.gen.hh>
#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>
#include <core/import_pose/pose_stream/util.hh>
#include <protocols/motifs/motif_utils.hh>
#include <time.h>

Functions
static basic::Tracer	TR ("apps.pilot.ligand_motifs", basic::t_info)

Detailed Description

.cc fils for IdentifyLigandMotifs protocol. Protocol object reads in a pdb file(s) and outputs motifs for protein-ligand interactions in .pdb and .motifs format. App originally written by mdsmith, optimized and converted to protocol by Ari Ginsparg.

Function Documentation

TR()

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

static

Referenced by IdentifyLigandMotifs::get_atom_trios(), IdentifyLigandMotifs::IdentifyLigandMotifs(), IdentifyLigandMotifs::ligand_to_residue_analysis(), IdentifyLigandMotifs::output_single_motif_to_pdb(), and IdentifyLigandMotifs::process_for_motifs().