ddG.cc File Reference

implementation of the ddG class for computing interface delta dGs More...

#include <core/types.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/NoRepackDisulfides.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/symmetry/util.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/scoring/methods/PoissonBoltzmannEnergy.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <protocols/simple_moves/DesignRepackMover.hh>
#include <protocols/toolbox/task_operations/RestrictToInterface.hh>
#include <protocols/simple_moves/ddG.hh>
#include <protocols/simple_moves/ddGCreator.hh>
#include <basic/datacache/DataMap.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/Job.hh>
#include <protocols/rosetta_scripts/util.hh>
#include <protocols/filters/Filter.hh>
#include <numeric/xyzVector.hh>
#include <ObjexxFCL/format.hh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>
#include <utility/tag/Tag.hh>
#include <basic/Tracer.hh>
#include <basic/options/keys/pb_potential.OptionKeys.gen.hh>
#include <map>
#include <algorithm>
#include <utility/excn/Exceptions.hh>
#include <boost/functional/hash.hpp>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::simple_moves

Functions
static thread_local basic::Tracer	protocols::simple_moves::TR ("protocols.protein_interface_design.movers.ddG")

Detailed Description

implementation of the ddG class for computing interface delta dGs

Author

Sarel Fleishman (sarel.nosp@m.f@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu)

Sachko Honda (honda.nosp@m.@apl.nosp@m..wash.nosp@m.ingt.nosp@m.on.ed.nosp@m.u) Additional notes by Honda on 12/16/2012 When this mover is called with PB_elec (PB potential energy) in scorefxn, it enables caching poses in two (bound/unbound) states so that subsequent calls can avoid resolving the PDE over and over for the same conformation.

See also core/scoring/methods/PoissonBoltzmannEnergy, core/scoring/PoissonBoltzmannPotential