BuriedUnsatPenalty.cc File Reference

An EnergyMethod that gives a penalty for buried unsatisfied hydrogen bond donors and acceptors. More...

#include <core/pack/guidance_scoreterms/buried_unsat_penalty/BuriedUnsatPenalty.hh>
#include <core/pack/guidance_scoreterms/buried_unsat_penalty/BuriedUnsatPenaltyCreator.hh>
#include <core/pack/guidance_scoreterms/buried_unsat_penalty/graph/BuriedUnsatPenaltyGraph.hh>
#include <core/pack/guidance_scoreterms/buried_unsat_penalty/graph/BuriedUnsatPenaltyGraphContainer.hh>
#include <core/pack/guidance_scoreterms/buried_unsat_penalty/graph/BuriedUnsatPenaltyGraphOptions.hh>
#include <core/scoring/EnergiesCacheableDataType.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/Conformation.hh>
#include <core/scoring/Energies.hh>
#include <core/pose/symmetry/util.hh>
#include <core/conformation/symmetry/SymmetricConformation.fwd.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/pack/rotamer_set/RotamerSets.fwd.hh>
#include <basic/Tracer.hh>
#include <basic/citation_manager/CitationCollection.hh>
#include <basic/citation_manager/CitationManager.hh>
#include <utility/vector1.hh>
#include <utility/pointer/owning_ptr.hh>
#include <utility/graph/Graph.hh>

Namespaces
	core
	A class for reading in the atom type properties.
	core::pack
	core::pack::guidance_scoreterms
	core::pack::guidance_scoreterms::buried_unsat_penalty

Functions
static basic::Tracer	core::pack::guidance_scoreterms::buried_unsat_penalty::TR ("core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty")

Detailed Description

An EnergyMethod that gives a penalty for buried unsatisfied hydrogen bond donors and acceptors.

This energy method is inherently not pairwise decomposible. However, it is intended for very rapid calculation, and has been designed to plug into Alex Ford's modifications to the packer that permit it to work with non-pairwise scoring terms.

Note

This was updated on 21 September 2018 to ensure that, during a packing trajectorym, only buried unsatisfied groups that are (a) on packable rotamers, or (b) that are on non-packable rotamers, but which can hydrogen-bond to at least one packable rotamer are the only ones that count towards the penalty. Without this, "native" buried unsats that are unreachable in a packing problem contribute unreasonably to the total score. (Thanks to Kale Kundert for identifying the problem.)

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).