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LigandAligner.cc File Reference

Align a ligand to a reference ligand or an inferred reference ligand. More...

#include <protocols/ligand_docking/GALigandDock/LigandAligner.hh>
#include <protocols/ligand_docking/GALigandDock/GriddedAtomTreeMultifunc.hh>
#include <protocols/ligand_docking/GALigandDock/util.hh>
#include <core/types.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/optimization/Minimizer.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/scoring/func/SumFunc.hh>
#include <core/scoring/func/TopOutFunc.hh>
#include <core/scoring/func/ConstantFunc.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <core/conformation/residue_datacache.hh>
#include <core/chemical/ChemicalManager.fwd.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueGraphTypes.hh>
#include <core/chemical/Bond.hh>
#include <core/chemical/types.hh>
#include <core/pose/util.hh>
#include <core/pose/extra_pose_info_util.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/id/AtomID.hh>
#include <core/import_pose/import_pose.hh>
#include <basic/options/option.hh>
#include <basic/options/after_opts.hh>
#include <basic/basic.hh>
#include <basic/database/open.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <utility/vector1.hh>
#include <utility/string_util.hh>
#include <numeric/xyzVector.hh>
#include <numeric/random/random_xyz.hh>
#include <numeric/random/random.functions.hh>
#include <numeric/random/random.hh>
#include <numeric/xyz.functions.hh>
#include <protocols/constraint_movers/ConstraintSetMover.hh>
#include <core/scoring/constraints/util.hh>
#include <utility/excn/Exceptions.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <fstream>
#include <iostream>
#include <string>

Namespaces

 protocols
 The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
 
 protocols::ligand_docking
 
 protocols::ligand_docking::ga_ligand_dock
 

Functions

static basic::Tracer protocols::ligand_docking::ga_ligand_dock::TR ("ligand_align")
 

Detailed Description

Align a ligand to a reference ligand or an inferred reference ligand.

Author
Hahnbeom Park and Frank DiMaio