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Rosetta 3.4
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Rosetta 3.4
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Defines a (pseudo) context-dependent one-body surface energy. Really, this class is only being used as a hack for the optE protocol so that the non-PD surface energy can be optimized together with the other PD-terms. The difference from this energy method from the plain SurfaceEnergy method is that it calculates the patch area using methods in sasa.cc instead of using average values. This new method also uses a new approach for finding which residues to include in a patch, not just all residues within 10A. More...
#include <HPatchEnergy.hh>
Public Types | |
| typedef scoring::methods::ContextDependentOneBodyEnergy | parent |
Public Member Functions | |
| HPatchEnergy () | |
| virtual scoring::methods::EnergyMethodOP | clone () const |
| virtual void | setup_for_scoring (pose::Pose &pose, scoring::ScoreFunction const &) const |
| virtual void | residue_energy (conformation::Residue const &rsd, pose::Pose const &, scoring::EnergyMap &) const |
| Evaluate the one-body energies for a particular residue, in the context of a given Pose, and increment those energies in the input Emap (do not overwrite them). | |
| virtual void | finalize_total_energy (pose::Pose &pose, scoring::ScoreFunction const &, scoring::EnergyMap &totals) const |
| called by the ScoreFunction at the end of energy evaluation. The derived class has the opportunity to accumulate a score into the pose's total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call. | |
| void | indicate_required_context_graphs (utility::vector1< bool > &) const |
| Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed. | |
| virtual core::Size | version () const |
| Return the version of the energy method. | |
Defines a (pseudo) context-dependent one-body surface energy. Really, this class is only being used as a hack for the optE protocol so that the non-PD surface energy can be optimized together with the other PD-terms. The difference from this energy method from the plain SurfaceEnergy method is that it calculates the patch area using methods in sasa.cc instead of using average values. This new method also uses a new approach for finding which residues to include in a patch, not just all residues within 10A.
| typedef scoring::methods::ContextDependentOneBodyEnergy core::pack::interaction_graph::HPatchEnergy::parent |
Reimplemented from core::scoring::methods::ContextDependentOneBodyEnergy.
| core::pack::interaction_graph::HPatchEnergy::HPatchEnergy | ( | ) |
Referenced by clone().
| scoring::methods::EnergyMethodOP core::pack::interaction_graph::HPatchEnergy::clone | ( | ) | const [virtual] |
Implements core::scoring::methods::EnergyMethod.
References HPatchEnergy().
| void core::pack::interaction_graph::HPatchEnergy::finalize_total_energy | ( | pose::Pose & | pose, |
| scoring::ScoreFunction const & | sfxn, | ||
| scoring::EnergyMap & | total_energy | ||
| ) | const [virtual] |
called by the ScoreFunction at the end of energy evaluation. The derived class has the opportunity to accumulate a score into the pose's total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.
called at the end of energy evaluation
Reimplemented from core::scoring::methods::EnergyMethod.
References core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), core::pose::Pose::energies(), core::pack::interaction_graph::SurfacePotential::get_instance(), core::scoring::hpatch, and core::scoring::Energies::use_nblist().
| void core::pack::interaction_graph::HPatchEnergy::indicate_required_context_graphs | ( | utility::vector1< bool > & | context_graphs_required | ) | const [inline, virtual] |
Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.
Implements core::scoring::methods::EnergyMethod.
| void core::pack::interaction_graph::HPatchEnergy::residue_energy | ( | conformation::Residue const & | rsd, |
| pose::Pose const & | pose, | ||
| scoring::EnergyMap & | emap | ||
| ) | const [virtual] |
Evaluate the one-body energies for a particular residue, in the context of a given Pose, and increment those energies in the input Emap (do not overwrite them).
Implements core::scoring::methods::ContextDependentOneBodyEnergy.
| void core::pack::interaction_graph::HPatchEnergy::setup_for_scoring | ( | pose::Pose & | pose, |
| scoring::ScoreFunction const & | |||
| ) | const [virtual] |
Reimplemented from core::scoring::methods::EnergyMethod.
| core::Size core::pack::interaction_graph::HPatchEnergy::version | ( | ) | const [virtual] |
Return the version of the energy method.
Implements core::scoring::methods::EnergyMethod.
1.7.4
