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BuriedUnsatPenalty.hh File Reference

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

#include <core/pack/guidance_scoreterms/buried_unsat_penalty/BuriedUnsatPenalty.fwd.hh>
#include <core/pack/guidance_scoreterms/buried_unsat_penalty/graph/BuriedUnsatPenaltyGraph.fwd.hh>
#include <core/pack/guidance_scoreterms/buried_unsat_penalty/graph/BuriedUnsatPenaltyGraphOptions.fwd.hh>
#include <core/scoring/annealing/ResidueArrayAnnealableEnergy.hh>
#include <core/scoring/methods/EnergyMethod.hh>
#include <core/scoring/methods/EnergyMethodOptions.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/EnergyMap.fwd.hh>
#include <core/scoring/methods/WholeStructureEnergy.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/chemical/ResidueProperty.hh>
#include <core/scoring/TenANeighborGraph.hh>
#include <core/pack/rotamer_set/RotamerSets.hh>
#include <core/scoring/hbonds/HBondOptions.fwd.hh>
#include <core/kinematics/MinimizerMapBase.fwd.hh>
#include <core/types.hh>
#include <map>
#include <string>
#include <utility/vector1.hh>
#include <core/pack/guidance_scoreterms/buried_unsat_penalty/BuriedUnsatPenaltyTests.fwd.hh>

Classes

class  core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty
 BuriedUnsatPenalty, an EnergyMethod that gives a penalty for buried unsatisfied hydrogen bond donors or acceptors. More...
 

Namespaces

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

Detailed Description

Headers for 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).