#include <core/chemical/ChemicalManager.hh>
#include <devel/init.hh>
#include <utility/vector1.hh>
#include <basic/options/util.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <core/pose/Pose.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/util.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueType.hh>
#include <protocols/toolbox/pose_manipulation/pose_manipulation.hh>
#include <core/util/disulfide_util.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/pack_rotamers.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/chemical/util.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <protocols/relax/util.hh>
#include <basic/Tracer.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/util.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <utility/excn/Exceptions.hh>