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Rosetta
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.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/pose/extra_pose_info_util.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 ("protocols.motifs.IdentifyLigandMotifs", basic::t_info) |
.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.
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1.9.1