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Rosetta
2020.50
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base class for the energy method hierarchy More...
#include <EnergyMethod.hh>
Public Types | |
typedef utility::VirtualBase | parent |
Public Member Functions | |
EnergyMethod (EnergyMethodCreatorOP creator) | |
Constructor with EnergyMethodCreator, which lists the score types that this energy method is responsible for. More... | |
virtual EnergyMethodOP | clone () const =0 |
virtual void | setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const |
if an energy method needs to cache data in the Energies object, before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing. More... | |
virtual void | setup_for_packing_with_rotsets (pose::Pose &pose, pack_basic::RotamerSetsBaseOP const &rotsets, ScoreFunction const &sfxn) const |
if an energy method needs to cache data in the Energies object, before packing begins and requires access to the RotamerSets object, then it does so during this function. The default behavior is to do nothing. More... | |
virtual void | prepare_rotamers_for_packing (pose::Pose const &, conformation::RotamerSetBase &) const |
If an energy method needs to cache data in a packing::RotamerSet object before rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing. More... | |
virtual void | update_residue_for_packing (pose::Pose &, Size resid) const |
If the pose changes in the middle of a packing (as happens in rotamer trials) and if an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing. More... | |
virtual void | setup_for_scoring (pose::Pose &, ScoreFunction const &) const |
if an energy method needs to cache something in the pose (e.g. in pose.energies()), before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing. More... | |
virtual bool | requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring (pose::Pose const &pose) const |
Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false. More... | |
virtual void | setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, basic::datacache::BasicDataCache &residue_data_cache) const |
Do any setup work before scoring, caching any slow-to-compute data that will be used during energy evaluation inside of the input Residue object's data cache. (The Residue on the whole is given as a constant reference, but non-constant access to its data cache is granted.) More... | |
virtual void | setup_for_minimizing (pose::Pose &, ScoreFunction const &, kinematics::MinimizerMapBase const &) const |
Called at the beginning of atom tree minimization, this method allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose's Energies object's "use_nblist()" method returns true. More... | |
virtual void | finalize_after_minimizing (pose::Pose &pose) const |
Called after minimization, allowing a derived class to do some teardown steps. More... | |
virtual void | setup_for_derivatives (pose::Pose &pose, ScoreFunction const &sfxn) const |
Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. More... | |
virtual void | finalize_after_derivatives (pose::Pose &, ScoreFunction const &) const |
called at the end of derivatives evaluation More... | |
virtual bool | minimize_in_whole_structure_context (pose::Pose const &) const |
Should this EnergyMethod have score and derivative evaluation evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that's serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return "true" will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction's traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return "true" cannot be included in RTMin. More... | |
virtual bool | defines_high_order_terms (pose::Pose const &) const |
Should this EnergyMethod have score and derivative evaluation evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta's get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns "false". More... | |
virtual void | eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &sfxn, EnergyMap const &emap, Vector &F1, Vector &F2) const |
Evaluate the XYZ derivative for an atom in the pose. Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom's XYZ derivative. More... | |
virtual void | finalize_total_energy (pose::Pose &pose, ScoreFunction const &sfxn, EnergyMap &total_energy) 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. More... | |
ScoreTypes const & | score_types () const |
Returns the score types that this energy method computes. More... | |
virtual EnergyMethodType | method_type () const =0 |
Return one of the 7 kinds of energy methods that exist: e.g. context-dependent-one-body vs whole-structure. More... | |
virtual void | indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const =0 |
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. More... | |
virtual core::Size | version () const =0 |
Return the version of the energy method. More... | |
virtual void | show_additional_info (std::ostream &, pose::Pose &, bool) const |
show additional information of the energy method More... | |
virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Protected Member Functions | |
void | set_score_types (EnergyMethodCreatorOP creator) |
Override the entirety of the score types list if they were initialized incorrectly in a parent's constructor. More... | |
Private Attributes | |
ScoreTypes | score_types_ |
base class for the energy method hierarchy
typedef utility::VirtualBase core::scoring::methods::EnergyMethod::parent |
core::scoring::methods::EnergyMethod::EnergyMethod | ( | EnergyMethodCreatorOP | creator | ) |
Constructor with EnergyMethodCreator, which lists the score types that this energy method is responsible for.
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pure virtual |
Implemented in core::scoring::etable::AnalyticEtableEnergy, core::scoring::etable::TableLookupEtableEnergy, core::energy_methods::CartesianBondedEnergy, core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy, core::energy_methods::ExactOccludedHbondSolEnergy, core::scoring::elec::FA_ElecEnergy, core::energy_methods::GoapEnergy, core::energy_methods::FA_GrpElecEnergy, core::scoring::methods::NMerSVMEnergy, core::energy_methods::MHCEpitopeEnergy, core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty, protocols::nmr::pre::PREEnergy, protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy, protocols::nmr::pcs::PCSEnergy, core::energy_methods::LinearChainbreakEnergy, core::energy_methods::GenBornEnergy, core::energy_methods::PoissonBoltzmannEnergy, core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy, core::scoring::lkball::LK_BallEnergy, protocols::fldsgn::potentials::AACompositionEnergy, protocols::nmr::rdc::RDCEnergy, protocols::scoring::methods::pcs2::PcsEnergy, core::energy_methods::RG_Energy_Fast, core::energy_methods::ElecDensAtomwiseEnergy, core::energy_methods::DEEREnergy, core::energy_methods::DumpTrajectoryEnergy, core::energy_methods::AACompositionEnergy, core::scoring::methods::MMLJEnergyIntra, protocols::scoring::methods::pcs::PCS_Energy, core::scoring::hbonds::HBondEnergy, protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1, protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2, protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3, protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4, core::energy_methods::LinearBranchEnergy, core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy, core::energy_methods::MultipoleElecEnergy, core::energy_methods::NetChargeEnergy, core::energy_methods::SASAEnergy, core::energy_methods::VdWTinkerEnergy, core::energy_methods::NPDHBondEnergy, core::energy_methods::AARepeatEnergy, core::energy_methods::AspartimidePenaltyEnergy, core::energy_methods::MPResidueLipophilicityEnergy, core::scoring::methods::NMerPSSMEnergy, core::energy_methods::FaMPSolvEnergy, core::energy_methods::MPEnvEnergy, core::energy_methods::MPHelicalityEnergy, core::scoring::methods::NMerRefEnergy, core::energy_methods::FaMPEnvSmoothEnergy, core::energy_methods::FiberDiffractionEnergyDens, core::pack::guidance_scoreterms::sap::SapConstraintEnergy, core::energy_methods::FACTSEnergy, core::scoring::rna::RNA_LowResolutionPotential, core::energy_methods::FaMPEnvEnergy, core::energy_methods::RNA_FA_ElecEnergy, core::pack::interaction_graph::SurfaceEnergy, core::scoring::membrane::MPTMProjPenalty, core::scoring::vdwaals::VDW_Energy, protocols::rna::AlignmentEnergy, core::energy_methods::ContextIndependentGeometricSolEnergy, core::energy_methods::RG_LocalEnergy, core::energy_methods::SAXSEnergy, core::energy_methods::XtalMLEnergy, core::pack::interaction_graph::HPatchEnergy, core::scoring::membrane::MPNonHelixPenalty, core::energy_methods::EnvSmoothEnergy, core::energy_methods::FiberDiffractionEnergy, core::energy_methods::ReferenceEnergy, core::energy_methods::ReferenceEnergyNoncanonical, core::scoring::membrane::MPTerminiPenalty, core::scoring::methods::MMBondAngleEnergy, core::energy_methods::FastSAXSEnergy, core::energy_methods::LK_PolarNonPolarEnergy, core::energy_methods::RamaPreProEnergy, core::energy_methods::SequenceDependentRefEnergy, core::scoring::carbon_hbonds::CarbonHBondEnergy, core::scoring::methods::MMLJEnergyInter, core::energy_methods::ContextDependentGeometricSolEnergy, core::energy_methods::MembraneEnvEnergy, core::energy_methods::MPCbetaEnergy, core::energy_methods::SugarBackboneEnergy, core::scoring::packing::HolesEnergyRes, core::energy_methods::DirectReadoutEnergy, core::energy_methods::DNA_ReferenceEnergy, core::energy_methods::FA_ElecEnergyAroAll, core::energy_methods::MotifDockEnergy, core::energy_methods::ProQ_Energy, core::energy_methods::ResidualDipolarCouplingEnergy_Rohl, core::energy_methods::RNA_PartitionEnergy, protocols::scoring::methods::TargetClashEnergy, core::energy_methods::DNATorsionEnergy, core::energy_methods::FA_ElecEnergyAroAro, core::energy_methods::FreeDOF_Energy, core::energy_methods::LoopCloseEnergy, core::energy_methods::MembraneCbetaEnergy, core::energy_methods::MPPairEnergy, core::energy_methods::MPSpanAngleEnergy, core::energy_methods::OccludedHbondSolEnergy, core::energy_methods::PairEnergy, core::energy_methods::PointWaterEnergy, core::energy_methods::ResidualDipolarCouplingEnergy, core::energy_methods::RNA_SugarCloseEnergy, core::energy_methods::SecondaryStructureEnergy, core::energy_methods::SuckerEnergy, core::pack::dunbrack::DunbrackEnergy, core::scoring::methods::MMBondLengthEnergy, protocols::scoring::methods::InterchainEnvEnergy, protocols::scoring::VDW_GridEnergy, core::energy_methods::DNA_BaseEnergy, core::energy_methods::GenericBondedEnergy, core::energy_methods::HolesEnergy, core::energy_methods::MembraneCenPairEnergy, core::energy_methods::PeptideBondEnergy, core::energy_methods::RG_Energy_RNA, core::energy_methods::StackElecEnergy, core::energy_methods::SymmetricLigandEnergy, core::scoring::constraints::ConstraintsEnergy, protocols::membrane::scoring::FaWaterToBilayerEnergy, core::energy_methods::CenHBEnergy, core::energy_methods::ChemicalShiftAnisotropyEnergy, core::energy_methods::CustomAtomPairEnergy, core::energy_methods::DipolarCouplingEnergy, core::energy_methods::LK_hack, core::energy_methods::MembraneEnvSmoothEnergy, core::energy_methods::MgEnergy, core::energy_methods::OccludedHbondSolEnergy_onebody, core::energy_methods::P_AA_pp_Energy, core::energy_methods::PackStatEnergy, core::energy_methods::pHEnergy, core::energy_methods::ProClosureEnergy, core::energy_methods::RNA_FullAtomStackingEnergy, core::energy_methods::RNP_LowResEnergy, core::energy_methods::RNP_LowResPairDistEnergy, core::energy_methods::RNP_LowResStackEnergy, core::energy_methods::WaterAdductHBondEnergy, core::scoring::methods::MMTorsionEnergy, protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments, core::energy_methods::AromaticBackboneRestraintEnergy, core::energy_methods::CenPairEnergy, core::energy_methods::CenRotPairEnergy, core::energy_methods::DistanceChainbreakEnergy, core::energy_methods::Fa_MbsolvEnergy, core::energy_methods::GaussianOverlapEnergy, core::energy_methods::HybridVDW_Energy, core::energy_methods::IntermolEnergy, core::energy_methods::MissingEnergy, core::energy_methods::MPSpanInsertionEnergy, core::energy_methods::RingClosureEnergy, core::energy_methods::RNA_DataBackboneEnergy, core::energy_methods::RNA_PairwiseLowResolutionEnergy, core::energy_methods::SmoothCenPairEnergy, core::energy_methods::SplitUnfoldedTwoBodyEnergy, core::energy_methods::SurfEnergy, core::energy_methods::SurfVolEnergy, protocols::scoring::methods::InterchainPairEnergy, core::energy_methods::CenRotEnvEnergy, core::energy_methods::DNA_EnvPairEnergy, core::energy_methods::EnvEnergy, core::energy_methods::Fa_MbenvEnergy, core::energy_methods::MembraneEnvPenalties, core::energy_methods::RMS_Energy, core::energy_methods::RNA_BulgeEnergy, core::energy_methods::RNA_FullAtomVDW_BasePhosphate, core::energy_methods::RNA_LJ_BaseEnergy, core::energy_methods::RNA_MgPointEnergy, core::energy_methods::SmoothEnvEnergy, core::energy_methods::UnfoldedStateEnergy, core::pack::dunbrack::cenrot::CenRotDunEnergy, core::energy_methods::MembraneLipo, core::energy_methods::OmegaTetherEnergy, core::energy_methods::P_AA_Energy, core::energy_methods::P_AA_ss_Energy, core::energy_methods::RNA_StubCoordinateEnergy, core::energy_methods::RNA_VDW_Energy, core::energy_methods::CenPairMotifEnergy, core::energy_methods::WaterAdductIntraEnergy, core::energy_methods::WaterSpecificEnergy, core::energy_methods::YHHPlanarityEnergy, core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty, core::scoring::nv::NVscore, protocols::scoring::methods::EnsembleEnergy, protocols::scoring::methods::saxs::PDDFEnergy, protocols::scoring::methods::SpecialRotamerEnergy, core::energy_methods::CenPairMotifDegreeEnergy, core::energy_methods::CenPairMotifEnergy, core::energy_methods::D2H_SA_Energy, core::energy_methods::dfire::DFIRE_Energy, core::energy_methods::ElecDensCenEnergy, core::energy_methods::HydroxylTorsionEnergy, core::energy_methods::RNA_ChemicalMappingEnergy, core::energy_methods::RNA_ChemicalShiftEnergy, core::energy_methods::RNA_TorsionEnergy, core::energy_methods::SA_Energy, core::energy_methods::BranchEnergy, core::energy_methods::ChainbreakEnergy, core::energy_methods::ContactOrderEnergy, core::energy_methods::ElecDensAllAtomCenEnergy, core::energy_methods::SSElementMotifContactEnergy, core::energy_methods::DNAChiEnergy, core::energy_methods::RamachandranEnergy, core::scoring::orbitals::OrbitalsScore, core::energy_methods::CentroidDisulfideEnergy, core::energy_methods::FastDensEnergy, core::energy_methods::FullatomDisulfideEnergy, core::energy_methods::RNA_JR_SuiteEnergy, core::energy_methods::Abego, core::energy_methods::CovalentLabelingEnergy, core::energy_methods::CovalentLabelingFAEnergy, core::energy_methods::ElecDensEnergy, core::energy_methods::RamachandranEnergy2B, core::energy_methods::ArgCationPiEnergy, core::energy_methods::DisulfideMatchingEnergy, core::energy_methods::HackAroEnergy, core::energy_methods::Burial_v2Energy, core::energy_methods::BurialEnergy, core::energy_methods::DNA_DihedralEnergy, core::energy_methods::RNA_SuiteEnergy, core::energy_methods::TNA_SuiteEnergy, core::energy_methods::HRF_MSLabelingEnergy, core::energy_methods::HRFDynamicsEnergy, core::energy_methods::OtherPoseEnergy, core::scoring::interface_::DDPscore, and core::scoring::sym_e::symEnergy.
Referenced by core::scoring::ScoreFunction::add_extra_method().
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Should this EnergyMethod have score and derivative evaluation evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta's get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns "false".
Reimplemented in core::scoring::constraints::ConstraintsEnergy.
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Evaluate the XYZ derivative for an atom in the pose. Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom's XYZ derivative.
The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) "Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations" Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.
default implementation does not alter either the F1 or F2 vectors.
Reimplemented in core::scoring::etable::BaseEtableEnergy< Derived >, core::scoring::etable::BaseEtableEnergy< AnalyticEtableEnergy >, core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >, core::scoring::constraints::ConstraintsEnergy, core::scoring::lkball::LK_BallEnergy, core::energy_methods::FA_GrpElecEnergy, core::energy_methods::RNA_FA_ElecEnergy, core::energy_methods::GenBornEnergy, core::energy_methods::FACTSEnergy, core::energy_methods::LK_PolarNonPolarEnergy, core::energy_methods::FA_ElecEnergyAroAll, core::energy_methods::FA_ElecEnergyAroAro, core::energy_methods::ElecDensAtomwiseEnergy, protocols::nmr::pre::PREEnergy, protocols::nmr::pcs::PCSEnergy, protocols::nmr::rdc::RDCEnergy, core::energy_methods::DNATorsionEnergy, core::energy_methods::ElecDensEnergy, core::energy_methods::RG_Energy_Fast, core::scoring::vdwaals::VDW_Energy, core::energy_methods::NPDHBondEnergy, core::energy_methods::ElecDensCenEnergy, core::energy_methods::LinearChainbreakEnergy, core::energy_methods::ElecDensAllAtomCenEnergy, core::scoring::methods::MMLJEnergyInter, core::energy_methods::MPResidueLipophilicityEnergy, core::energy_methods::MPHelicalityEnergy, core::scoring::methods::MMBondAngleEnergy, core::energy_methods::RNA_FullAtomStackingEnergy, core::scoring::methods::MMTorsionEnergy, core::energy_methods::CustomAtomPairEnergy, core::energy_methods::WaterAdductHBondEnergy, core::energy_methods::PeptideBondEnergy, core::scoring::methods::MMBondLengthEnergy, core::energy_methods::DNA_BaseEnergy, core::energy_methods::LinearBranchEnergy, core::energy_methods::ResidualDipolarCouplingEnergy, core::energy_methods::FaMPEnvEnergy, core::energy_methods::HybridVDW_Energy, core::energy_methods::RNA_FullAtomVDW_BasePhosphate, core::energy_methods::ChemicalShiftAnisotropyEnergy, core::energy_methods::DipolarCouplingEnergy, core::energy_methods::StackElecEnergy, core::energy_methods::RG_LocalEnergy, core::energy_methods::RNA_MgPointEnergy, core::energy_methods::RNA_DataBackboneEnergy, core::energy_methods::RNA_PairwiseLowResolutionEnergy, core::energy_methods::RNA_VDW_Energy, core::energy_methods::EnvSmoothEnergy, core::energy_methods::RNA_SugarCloseEnergy, core::scoring::packing::HolesEnergyRes, core::energy_methods::FaMPSolvEnergy, core::energy_methods::MPSpanAngleEnergy, core::energy_methods::RNA_TorsionEnergy, core::energy_methods::HolesEnergy, core::energy_methods::MembraneEnvSmoothEnergy, core::energy_methods::RNA_JR_SuiteEnergy, core::energy_methods::HackAroEnergy, core::energy_methods::LoopCloseEnergy, core::energy_methods::SurfEnergy, core::energy_methods::SurfVolEnergy, core::energy_methods::RG_Energy_RNA, core::energy_methods::MPSpanInsertionEnergy, core::energy_methods::SuckerEnergy, core::energy_methods::XtalMLEnergy, core::energy_methods::RNA_ChemicalShiftEnergy, core::energy_methods::GaussianOverlapEnergy, core::energy_methods::SymmetricLigandEnergy, core::energy_methods::Fa_MbenvEnergy, core::energy_methods::LK_hack, core::energy_methods::FiberDiffractionEnergy, core::energy_methods::FastSAXSEnergy, core::energy_methods::IntermolEnergy, core::energy_methods::RNA_LJ_BaseEnergy, core::energy_methods::Fa_MbsolvEnergy, core::energy_methods::MissingEnergy, core::energy_methods::BranchEnergy, and core::energy_methods::ChainbreakEnergy.
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called at the end of derivatives evaluation
default implementation noop
Reimplemented in core::energy_methods::DNATorsionEnergy, and core::scoring::orbitals::OrbitalsScore.
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Called after minimization, allowing a derived class to do some teardown steps.
Base class function does nothing. Derived classes may override.
Reimplemented in core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty, core::energy_methods::MHCEpitopeEnergy, core::energy_methods::AACompositionEnergy, core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty, core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy, core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy, core::energy_methods::DumpTrajectoryEnergy, and core::pack::guidance_scoreterms::sap::SapConstraintEnergy.
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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 in core::scoring::etable::BaseEtableEnergy< Derived >, core::scoring::etable::BaseEtableEnergy< AnalyticEtableEnergy >, core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >, core::scoring::hbonds::HBondEnergy, core::scoring::lkball::LK_BallEnergy, core::scoring::constraints::ConstraintsEnergy, core::scoring::elec::FA_ElecEnergy, core::energy_methods::FA_GrpElecEnergy, core::energy_methods::LK_PolarNonPolarEnergy, core::energy_methods::ContextIndependentGeometricSolEnergy, core::energy_methods::DEEREnergy, core::energy_methods::ContextDependentGeometricSolEnergy, core::energy_methods::FaMPSolvEnergy, protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy, core::energy_methods::RNA_LJ_BaseEnergy, core::energy_methods::StackElecEnergy, core::energy_methods::Fa_MbsolvEnergy, core::energy_methods::RNA_FullAtomStackingEnergy, core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty, core::energy_methods::MHCEpitopeEnergy, core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty, core::energy_methods::FastDensEnergy, core::energy_methods::DumpTrajectoryEnergy, core::energy_methods::RNA_PairwiseLowResolutionEnergy, protocols::nmr::pre::PREEnergy, core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy, core::energy_methods::DNATorsionEnergy, core::energy_methods::NPDHBondEnergy, protocols::nmr::pcs::PCSEnergy, core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy, protocols::nmr::rdc::RDCEnergy, core::energy_methods::AACompositionEnergy, core::energy_methods::LinearChainbreakEnergy, protocols::scoring::methods::pcs2::PcsEnergy, core::energy_methods::MPEnvEnergy, core::energy_methods::RG_Energy_Fast, core::scoring::orbitals::OrbitalsScore, core::energy_methods::NetChargeEnergy, core::energy_methods::AARepeatEnergy, protocols::scoring::methods::pcs::PCS_Energy, protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1, protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2, protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3, protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4, core::energy_methods::FreeDOF_Energy, core::scoring::membrane::MPNonHelixPenalty, core::energy_methods::CenRotEnvEnergy, core::pack::dunbrack::cenrot::CenRotDunEnergy, core::energy_methods::LinearBranchEnergy, core::energy_methods::SmoothEnvEnergy, core::scoring::membrane::MPTerminiPenalty, core::energy_methods::MembraneEnvEnergy, core::energy_methods::ResidualDipolarCouplingEnergy, core::energy_methods::RNA_FA_ElecEnergy, core::energy_methods::MPPairEnergy, protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments, core::energy_methods::ChemicalShiftAnisotropyEnergy, core::energy_methods::DipolarCouplingEnergy, core::pack::guidance_scoreterms::sap::SapConstraintEnergy, core::energy_methods::MembraneCenPairEnergy, protocols::rna::AlignmentEnergy, protocols::scoring::methods::InterchainEnvEnergy, core::energy_methods::FaMPEnvEnergy, core::energy_methods::MembraneCbetaEnergy, core::energy_methods::CenPairEnergy, core::energy_methods::MPCbetaEnergy, core::energy_methods::SmoothCenPairEnergy, core::energy_methods::CenRotPairEnergy, protocols::scoring::methods::InterchainPairEnergy, core::pack::interaction_graph::SurfaceEnergy, core::energy_methods::EnvEnergy, core::energy_methods::SAXSEnergy, core::pack::interaction_graph::HPatchEnergy, core::energy_methods::LoopCloseEnergy, core::energy_methods::RG_Energy_RNA, core::energy_methods::RG_LocalEnergy, core::scoring::packing::HolesEnergyRes, core::energy_methods::RNA_BulgeEnergy, core::energy_methods::SecondaryStructureEnergy, protocols::membrane::scoring::FaWaterToBilayerEnergy, protocols::scoring::VDW_GridEnergy, core::energy_methods::FiberDiffractionEnergyDens, core::energy_methods::ProQ_Energy, core::scoring::membrane::MPTMProjPenalty, protocols::scoring::methods::TargetClashEnergy, core::energy_methods::CovalentLabelingEnergy, core::energy_methods::CovalentLabelingFAEnergy, core::energy_methods::HolesEnergy, core::energy_methods::MPSpanAngleEnergy, core::energy_methods::ResidualDipolarCouplingEnergy_Rohl, core::energy_methods::RNA_ChemicalShiftEnergy, core::energy_methods::RNA_PartitionEnergy, core::energy_methods::BurialEnergy, core::energy_methods::SurfEnergy, core::energy_methods::SurfVolEnergy, core::energy_methods::XtalMLEnergy, core::energy_methods::FiberDiffractionEnergy, core::energy_methods::RNA_ChemicalMappingEnergy, core::energy_methods::SSElementMotifContactEnergy, core::energy_methods::DNA_EnvPairEnergy, core::energy_methods::FastSAXSEnergy, core::energy_methods::HRF_MSLabelingEnergy, core::energy_methods::HRFDynamicsEnergy, core::energy_methods::MPSpanInsertionEnergy, core::energy_methods::PackStatEnergy, core::energy_methods::DistanceChainbreakEnergy, core::energy_methods::IntermolEnergy, core::energy_methods::MembraneEnvPenalties, core::energy_methods::RMS_Energy, core::energy_methods::MembraneLipo, protocols::scoring::methods::EnsembleEnergy, core::energy_methods::D2H_SA_Energy, core::energy_methods::Fa_MbenvEnergy, core::energy_methods::SA_Energy, core::energy_methods::ContactOrderEnergy, core::energy_methods::MissingEnergy, core::energy_methods::CenPairMotifEnergy, core::energy_methods::CenPairMotifDegreeEnergy, core::energy_methods::CenPairMotifEnergy, core::energy_methods::Abego, core::energy_methods::BranchEnergy, core::energy_methods::ChainbreakEnergy, protocols::scoring::methods::saxs::PDDFEnergy, core::energy_methods::Burial_v2Energy, and core::energy_methods::OtherPoseEnergy.
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pure 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.
Implemented in core::scoring::etable::BaseEtableEnergy< Derived >, core::scoring::etable::BaseEtableEnergy< AnalyticEtableEnergy >, core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >, core::energy_methods::CartesianBondedEnergy, core::scoring::elec::FA_ElecEnergy, core::scoring::hbonds::HBondEnergy, core::scoring::constraints::ConstraintsEnergy, core::scoring::lkball::LK_BallEnergy, core::energy_methods::FA_GrpElecEnergy, core::energy_methods::MultipoleElecEnergy, core::energy_methods::VdWTinkerEnergy, core::energy_methods::SASAEnergy, core::energy_methods::ContextIndependentGeometricSolEnergy, core::energy_methods::RNA_FA_ElecEnergy, core::energy_methods::GenBornEnergy, core::energy_methods::PairEnergy, core::energy_methods::DEEREnergy, core::energy_methods::LK_PolarNonPolarEnergy, core::energy_methods::ContextDependentGeometricSolEnergy, core::energy_methods::StackElecEnergy, core::energy_methods::FACTSEnergy, core::energy_methods::ProClosureEnergy, core::scoring::carbon_hbonds::CarbonHBondEnergy, core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty, core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy, core::energy_methods::ExactOccludedHbondSolEnergy, core::energy_methods::FA_ElecEnergyAroAll, core::energy_methods::FA_ElecEnergyAroAro, core::energy_methods::PoissonBoltzmannEnergy, core::scoring::methods::MMLJEnergyInter, core::energy_methods::FullatomDisulfideEnergy, core::energy_methods::DNATorsionEnergy, core::energy_methods::DNA_ReferenceEnergy, core::scoring::orbitals::OrbitalsScore, core::scoring::methods::MMLJEnergyIntra, core::energy_methods::GoapEnergy, protocols::nmr::pre::PREEnergy, protocols::nmr::rdc::RDCEnergy, protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy, protocols::nmr::pcs::PCSEnergy, core::energy_methods::MgEnergy, core::energy_methods::AspartimidePenaltyEnergy, core::energy_methods::OccludedHbondSolEnergy, core::energy_methods::DNA_DihedralEnergy, core::scoring::vdwaals::VDW_Energy, core::energy_methods::GenericBondedEnergy, core::scoring::methods::NMerSVMEnergy, core::energy_methods::PointWaterEnergy, core::energy_methods::MPResidueLipophilicityEnergy, core::energy_methods::NPDHBondEnergy, core::energy_methods::RG_Energy_Fast, core::pack::dunbrack::cenrot::CenRotDunEnergy, core::energy_methods::FaMPSolvEnergy, core::energy_methods::ElecDensEnergy, core::scoring::methods::MMTorsionEnergy, protocols::fldsgn::potentials::AACompositionEnergy, core::energy_methods::MPSpanInsertionEnergy, core::energy_methods::RNA_FullAtomStackingEnergy, core::energy_methods::WaterAdductHBondEnergy, core::energy_methods::HybridVDW_Energy, core::energy_methods::RNP_LowResStackEnergy, core::energy_methods::RNP_LowResEnergy, core::energy_methods::RNP_LowResPairDistEnergy, core::energy_methods::RamaPreProEnergy, core::scoring::methods::MMBondAngleEnergy, core::energy_methods::FastDensEnergy, core::energy_methods::MPHelicalityEnergy, core::energy_methods::ElecDensCenEnergy, core::energy_methods::CustomAtomPairEnergy, core::energy_methods::ElecDensAllAtomCenEnergy, core::energy_methods::RNA_DataBackboneEnergy, core::energy_methods::MPSpanAngleEnergy, core::energy_methods::RNA_PairwiseLowResolutionEnergy, core::scoring::methods::MMBondLengthEnergy, core::energy_methods::CenHBEnergy, core::energy_methods::LinearChainbreakEnergy, core::energy_methods::SmoothCenPairEnergy, core::energy_methods::CenRotPairEnergy, core::energy_methods::DNA_BaseEnergy, core::energy_methods::LK_hack, core::energy_methods::P_AA_pp_Energy, core::scoring::methods::NMerRefEnergy, core::energy_methods::FaMPEnvSmoothEnergy, core::energy_methods::PeptideBondEnergy, core::energy_methods::RNA_LJ_BaseEnergy, core::energy_methods::RNA_MgPointEnergy, core::energy_methods::Fa_MbsolvEnergy, core::energy_methods::RNA_FullAtomVDW_BasePhosphate, core::energy_methods::RNA_VDW_Energy, core::scoring::methods::NMerPSSMEnergy, core::energy_methods::FaMPEnvEnergy, core::energy_methods::RNA_SuiteEnergy, core::energy_methods::TNA_SuiteEnergy, core::energy_methods::EnvSmoothEnergy, core::energy_methods::ReferenceEnergy, core::energy_methods::RNA_TorsionEnergy, core::energy_methods::MPPairEnergy, core::energy_methods::RG_LocalEnergy, core::pack::dunbrack::DunbrackEnergy, core::energy_methods::LinearBranchEnergy, core::energy_methods::RNA_SugarCloseEnergy, core::energy_methods::ArgCationPiEnergy, core::energy_methods::RamachandranEnergy, core::energy_methods::dfire::DFIRE_Energy, core::energy_methods::MembraneCenPairEnergy, core::energy_methods::MHCEpitopeEnergy, core::energy_methods::MPEnvEnergy, core::energy_methods::RNA_JR_SuiteEnergy, core::energy_methods::CenPairEnergy, core::energy_methods::MembraneEnvSmoothEnergy, core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty, protocols::membrane::scoring::FaWaterToBilayerEnergy, core::energy_methods::HackAroEnergy, core::energy_methods::SuckerEnergy, core::energy_methods::YHHPlanarityEnergy, core::scoring::packing::HolesEnergyRes, protocols::scoring::methods::InterchainPairEnergy, core::energy_methods::GaussianOverlapEnergy, core::energy_methods::HolesEnergy, core::energy_methods::OmegaTetherEnergy, core::energy_methods::RamachandranEnergy2B, core::energy_methods::SequenceDependentRefEnergy, core::energy_methods::SurfEnergy, core::energy_methods::SurfVolEnergy, core::scoring::membrane::MPNonHelixPenalty, core::energy_methods::DirectReadoutEnergy, core::energy_methods::CenRotEnvEnergy, core::energy_methods::LoopCloseEnergy, core::energy_methods::ReferenceEnergyNoncanonical, core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy, core::scoring::membrane::MPTerminiPenalty, core::energy_methods::RG_Energy_RNA, core::energy_methods::SmoothEnvEnergy, protocols::scoring::methods::pcs2::PcsEnergy, core::energy_methods::MembraneEnvEnergy, core::energy_methods::ResidualDipolarCouplingEnergy, core::energy_methods::AromaticBackboneRestraintEnergy, core::energy_methods::ElecDensAtomwiseEnergy, core::energy_methods::RingClosureEnergy, protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments, core::energy_methods::ChemicalShiftAnisotropyEnergy, core::energy_methods::DipolarCouplingEnergy, core::energy_methods::DumpTrajectoryEnergy, core::energy_methods::FiberDiffractionEnergyDens, core::energy_methods::SymmetricLigandEnergy, core::energy_methods::XtalMLEnergy, core::energy_methods::AACompositionEnergy, core::energy_methods::MotifDockEnergy, core::energy_methods::RNA_ChemicalShiftEnergy, core::energy_methods::Fa_MbenvEnergy, core::energy_methods::SecondaryStructureEnergy, protocols::scoring::methods::InterchainEnvEnergy, protocols::scoring::methods::pcs::PCS_Energy, core::energy_methods::MembraneCbetaEnergy, core::energy_methods::MPCbetaEnergy, protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1, protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2, protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3, protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4, core::energy_methods::FiberDiffractionEnergy, core::energy_methods::P_AA_ss_Energy, core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy, core::energy_methods::FastSAXSEnergy, core::energy_methods::IntermolEnergy, core::energy_methods::NetChargeEnergy, core::energy_methods::ProQ_Energy, core::energy_methods::WaterAdductIntraEnergy, core::energy_methods::WaterSpecificEnergy, protocols::scoring::methods::SpecialRotamerEnergy, core::energy_methods::FreeDOF_Energy, core::energy_methods::HydroxylTorsionEnergy, core::energy_methods::AARepeatEnergy, core::energy_methods::EnvEnergy, core::energy_methods::pHEnergy, core::energy_methods::DNAChiEnergy, core::energy_methods::RNA_BulgeEnergy, protocols::scoring::VDW_GridEnergy, core::energy_methods::CovalentLabelingEnergy, core::energy_methods::CovalentLabelingFAEnergy, core::energy_methods::MissingEnergy, protocols::scoring::methods::TargetClashEnergy, core::pack::interaction_graph::SurfaceEnergy, core::scoring::membrane::MPTMProjPenalty, core::energy_methods::BurialEnergy, core::energy_methods::SAXSEnergy, core::pack::interaction_graph::HPatchEnergy, core::energy_methods::ResidualDipolarCouplingEnergy_Rohl, core::energy_methods::RNA_ChemicalMappingEnergy, core::energy_methods::RNA_PartitionEnergy, core::energy_methods::HRF_MSLabelingEnergy, core::energy_methods::HRFDynamicsEnergy, core::energy_methods::OccludedHbondSolEnergy_onebody, core::energy_methods::DNA_EnvPairEnergy, core::energy_methods::PackStatEnergy, core::energy_methods::BranchEnergy, core::energy_methods::ChainbreakEnergy, core::energy_methods::SugarBackboneEnergy, core::pack::guidance_scoreterms::sap::SapConstraintEnergy, core::scoring::interface_::DDPscore, protocols::rna::AlignmentEnergy, core::energy_methods::ContactOrderEnergy, core::energy_methods::DistanceChainbreakEnergy, core::energy_methods::P_AA_Energy, core::scoring::nv::NVscore, protocols::scoring::methods::EnsembleEnergy, core::energy_methods::MembraneEnvPenalties, core::energy_methods::MembraneLipo, core::energy_methods::RMS_Energy, core::energy_methods::RNA_StubCoordinateEnergy, core::energy_methods::D2H_SA_Energy, core::energy_methods::SA_Energy, core::energy_methods::SSElementMotifContactEnergy, core::scoring::rna::RNA_LowResolutionPotential, core::energy_methods::UnfoldedStateEnergy, core::energy_methods::SplitUnfoldedTwoBodyEnergy, core::energy_methods::CenPairMotifEnergy, core::energy_methods::CenPairMotifDegreeEnergy, core::energy_methods::CenPairMotifEnergy, core::energy_methods::OtherPoseEnergy, core::energy_methods::Burial_v2Energy, protocols::scoring::methods::saxs::PDDFEnergy, core::energy_methods::CentroidDisulfideEnergy, core::energy_methods::Abego, core::energy_methods::DisulfideMatchingEnergy, and core::scoring::sym_e::symEnergy.
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Return one of the 7 kinds of energy methods that exist: e.g. context-dependent-one-body vs whole-structure.
Implemented in core::scoring::methods::ContextDependentTwoBodyEnergy, core::scoring::methods::ContextDependentOneBodyEnergy, core::scoring::methods::WholeStructureEnergy, core::scoring::methods::ContextIndependentOneBodyEnergy, core::scoring::methods::ContextIndependentTwoBodyEnergy, core::scoring::methods::ContextDependentLRTwoBodyEnergy, and core::scoring::methods::ContextIndependentLRTwoBodyEnergy.
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Should this EnergyMethod have score and derivative evaluation evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that's serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return "true" will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction's traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return "true" cannot be included in RTMin.
Reimplemented in core::energy_methods::CartesianBondedEnergy, core::scoring::lkball::LK_BallEnergy, core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy, core::energy_methods::ContextIndependentGeometricSolEnergy, core::scoring::elec::FA_ElecEnergy, core::energy_methods::FA_GrpElecEnergy, core::scoring::orbitals::OrbitalsScore, core::energy_methods::RNA_FA_ElecEnergy, core::energy_methods::AspartimidePenaltyEnergy, core::energy_methods::GoapEnergy, core::scoring::hbonds::HBondEnergy, core::scoring::carbon_hbonds::CarbonHBondEnergy, core::energy_methods::MPResidueLipophilicityEnergy, core::energy_methods::PointWaterEnergy, core::energy_methods::RamaPreProEnergy, core::energy_methods::MPHelicalityEnergy, core::energy_methods::NPDHBondEnergy, core::scoring::methods::NMerSVMEnergy, core::energy_methods::FastDensEnergy, core::scoring::etable::BaseEtableEnergy< Derived >, core::scoring::etable::BaseEtableEnergy< AnalyticEtableEnergy >, core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >, core::energy_methods::FA_ElecEnergyAroAll, core::energy_methods::FA_ElecEnergyAroAro, core::energy_methods::PairEnergy, core::scoring::methods::NMerRefEnergy, core::energy_methods::RNA_SuiteEnergy, core::energy_methods::TNA_SuiteEnergy, core::scoring::methods::NMerPSSMEnergy, core::energy_methods::ReferenceEnergy, core::scoring::constraints::ConstraintsEnergy, core::energy_methods::OccludedHbondSolEnergy, core::scoring::methods::MMLJEnergyIntra, core::energy_methods::ContextDependentGeometricSolEnergy, core::energy_methods::ProClosureEnergy, core::energy_methods::FullatomDisulfideEnergy, core::energy_methods::SequenceDependentRefEnergy, core::pack::dunbrack::DunbrackEnergy, core::energy_methods::P_AA_pp_Energy, core::pack::dunbrack::cenrot::CenRotDunEnergy, core::energy_methods::AromaticBackboneRestraintEnergy, core::energy_methods::GenericBondedEnergy, core::energy_methods::RingClosureEnergy, core::energy_methods::StackElecEnergy, core::energy_methods::OmegaTetherEnergy, core::energy_methods::YHHPlanarityEnergy, core::energy_methods::RamachandranEnergy, core::energy_methods::SugarBackboneEnergy, core::energy_methods::DNA_ReferenceEnergy, core::energy_methods::UnfoldedStateEnergy, core::energy_methods::HydroxylTorsionEnergy, core::energy_methods::SplitUnfoldedTwoBodyEnergy, and core::scoring::methods::MMTorsionEnergy.
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If an energy method needs to cache data in a packing::RotamerSet object before rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.
default implementation noop
Reimplemented in core::energy_methods::MultipoleElecEnergy, core::energy_methods::SASAEnergy, core::energy_methods::VdWTinkerEnergy, core::scoring::orbitals::OrbitalsScore, core::scoring::elec::FA_ElecEnergy, core::scoring::etable::BaseEtableEnergy< Derived >, core::scoring::etable::BaseEtableEnergy< AnalyticEtableEnergy >, core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >, core::energy_methods::FA_GrpElecEnergy, core::energy_methods::GenBornEnergy, core::scoring::lkball::LK_BallEnergy, core::energy_methods::RNA_FA_ElecEnergy, core::scoring::hbonds::HBondEnergy, core::energy_methods::FACTSEnergy, core::scoring::methods::MMLJEnergyInter, core::scoring::vdwaals::VDW_Energy, core::energy_methods::FA_ElecEnergyAroAll, core::energy_methods::FA_ElecEnergyAroAro, core::energy_methods::PairEnergy, and core::energy_methods::CustomAtomPairEnergy.
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Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by energy methods wishing to provide citation information.
The default implementation of this function does nothing. It may be overriden by simple metrics wishing to provide citation information.
Reimplemented in core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty, core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty, core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy, core::energy_methods::AACompositionEnergy, core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy, and core::energy_methods::NetChargeEnergy.
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Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false.
Reimplemented in core::scoring::lkball::LK_BallEnergy.
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Returns the score types that this energy method computes.
References score_types_.
Referenced by core::scoring::ScoreFunction::add_extra_method(), core::scoring::methods::ShortRangeTwoBodyEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::ShortRangeTwoBodyEnergy::evaluate_rotamer_pair_energies(), core::scoring::methods::OneBodyEnergy::setup_for_derivatives_for_residue(), and core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue().
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Override the entirety of the score types list if they were initialized incorrectly in a parent's constructor.
References score_types_.
Referenced by core::energy_methods::FA_ElecEnergyAroAll::FA_ElecEnergyAroAll(), core::energy_methods::FA_ElecEnergyAroAro::FA_ElecEnergyAroAro(), and core::energy_methods::RNA_FA_ElecEnergy::RNA_FA_ElecEnergy().
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Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls.
default implementation noop
Reimplemented in core::energy_methods::CartesianBondedEnergy, core::scoring::constraints::ConstraintsEnergy, core::energy_methods::DEEREnergy, core::energy_methods::ExactOccludedHbondSolEnergy, core::scoring::elec::FA_ElecEnergy, core::scoring::etable::BaseEtableEnergy< Derived >, core::scoring::etable::BaseEtableEnergy< AnalyticEtableEnergy >, core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >, core::energy_methods::GoapEnergy, core::energy_methods::FA_GrpElecEnergy, core::energy_methods::DumpTrajectoryEnergy, core::scoring::lkball::LK_BallEnergy, core::energy_methods::RG_Energy_Fast, core::energy_methods::GenBornEnergy, core::energy_methods::MultipoleElecEnergy, core::energy_methods::SASAEnergy, core::energy_methods::VdWTinkerEnergy, core::energy_methods::FastDensEnergy, core::energy_methods::RG_LocalEnergy, core::energy_methods::FaMPEnvEnergy, core::energy_methods::MPResidueLipophilicityEnergy, core::energy_methods::RNA_SugarCloseEnergy, core::energy_methods::MPHelicalityEnergy, core::energy_methods::NPDHBondEnergy, core::energy_methods::FACTSEnergy, core::energy_methods::FaMPEnvSmoothEnergy, core::energy_methods::MPEnvEnergy, core::scoring::packing::HolesEnergyRes, protocols::membrane::scoring::FaWaterToBilayerEnergy, core::energy_methods::EnvSmoothEnergy, core::energy_methods::FaMPSolvEnergy, core::energy_methods::HolesEnergy, core::energy_methods::RNA_FA_ElecEnergy, core::scoring::methods::MMBondAngleEnergy, core::scoring::vdwaals::VDW_Energy, core::energy_methods::MPSpanAngleEnergy, core::energy_methods::RNA_FullAtomStackingEnergy, core::energy_methods::SurfEnergy, core::energy_methods::SurfVolEnergy, core::scoring::membrane::MPNonHelixPenalty, core::scoring::methods::MMTorsionEnergy, core::energy_methods::CenHBEnergy, core::energy_methods::ElecDensCenEnergy, core::energy_methods::MembraneEnvEnergy, core::energy_methods::MPSpanInsertionEnergy, core::energy_methods::PairEnergy, core::scoring::membrane::MPTerminiPenalty, core::scoring::methods::MMBondLengthEnergy, core::energy_methods::DNATorsionEnergy, core::energy_methods::ElecDensAllAtomCenEnergy, core::energy_methods::ElecDensEnergy, core::energy_methods::HybridVDW_Energy, core::energy_methods::MembraneEnvSmoothEnergy, core::energy_methods::PointWaterEnergy, core::energy_methods::XtalMLEnergy, core::energy_methods::CustomAtomPairEnergy, core::energy_methods::FiberDiffractionEnergy, core::energy_methods::LoopCloseEnergy, core::energy_methods::FastSAXSEnergy, core::energy_methods::GenericBondedEnergy, core::energy_methods::RG_Energy_RNA, core::energy_methods::Fa_MbenvEnergy, core::energy_methods::LK_PolarNonPolarEnergy, core::energy_methods::StackElecEnergy, core::energy_methods::RNA_DataBackboneEnergy, core::energy_methods::RNA_PairwiseLowResolutionEnergy, core::energy_methods::CenRotEnvEnergy, core::energy_methods::OccludedHbondSolEnergy, core::energy_methods::RNA_MgPointEnergy, core::energy_methods::RNA_VDW_Energy, core::energy_methods::SmoothEnvEnergy, core::energy_methods::WaterAdductHBondEnergy, core::energy_methods::FA_ElecEnergyAroAll, core::energy_methods::OccludedHbondSolEnergy_onebody, core::energy_methods::RNA_ChemicalShiftEnergy, core::energy_methods::FA_ElecEnergyAroAro, core::energy_methods::LK_hack, core::energy_methods::DNA_BaseEnergy, core::energy_methods::RNA_LJ_BaseEnergy, core::scoring::nv::NVscore, core::energy_methods::Fa_MbsolvEnergy, core::energy_methods::HackAroEnergy, core::scoring::orbitals::OrbitalsScore, and core::scoring::interface_::DDPscore.
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Called at the beginning of atom tree minimization, this method allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose's Energies object's "use_nblist()" method returns true.
default implementation noop
Reimplemented in core::energy_methods::ExactOccludedHbondSolEnergy, core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty, core::energy_methods::DEEREnergy, core::energy_methods::MHCEpitopeEnergy, core::energy_methods::AACompositionEnergy, core::energy_methods::StackElecEnergy, core::scoring::elec::FA_ElecEnergy, core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy, core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty, core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy, core::scoring::etable::BaseEtableEnergy< Derived >, protocols::nmr::pre::PREEnergy, core::scoring::etable::BaseEtableEnergy< AnalyticEtableEnergy >, core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >, protocols::nmr::pcs::PCSEnergy, protocols::nmr::rdc::RDCEnergy, core::energy_methods::FA_GrpElecEnergy, core::energy_methods::DumpTrajectoryEnergy, core::pack::guidance_scoreterms::sap::SapConstraintEnergy, core::scoring::orbitals::OrbitalsScore, core::energy_methods::LK_PolarNonPolarEnergy, core::energy_methods::ResidualDipolarCouplingEnergy, core::energy_methods::XtalMLEnergy, core::energy_methods::ChemicalShiftAnisotropyEnergy, core::energy_methods::DipolarCouplingEnergy, core::energy_methods::RNA_FA_ElecEnergy, core::energy_methods::RNA_FullAtomStackingEnergy, core::energy_methods::OccludedHbondSolEnergy_onebody, core::scoring::methods::MMLJEnergyInter, core::energy_methods::PointWaterEnergy, core::energy_methods::P_AA_ss_Energy, and core::scoring::nv::NVscore.
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if an energy method needs to cache data in the Energies object, before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.
default implementation noop
Reimplemented in core::scoring::constraints::ConstraintsEnergy, core::energy_methods::StackElecEnergy, core::energy_methods::ExactOccludedHbondSolEnergy, core::scoring::elec::FA_ElecEnergy, core::scoring::etable::BaseEtableEnergy< Derived >, core::scoring::etable::BaseEtableEnergy< AnalyticEtableEnergy >, core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >, core::energy_methods::FA_GrpElecEnergy, core::energy_methods::GoapEnergy, core::scoring::lkball::LK_BallEnergy, core::energy_methods::GenBornEnergy, core::energy_methods::RNA_FA_ElecEnergy, core::scoring::hbonds::HBondEnergy, core::energy_methods::MultipoleElecEnergy, core::energy_methods::SASAEnergy, core::energy_methods::VdWTinkerEnergy, core::energy_methods::RNA_FullAtomStackingEnergy, core::scoring::methods::MMLJEnergyInter, core::energy_methods::ContextIndependentGeometricSolEnergy, core::energy_methods::FACTSEnergy, core::energy_methods::FA_ElecEnergyAroAll, core::energy_methods::WaterAdductHBondEnergy, core::energy_methods::FA_ElecEnergyAroAro, core::energy_methods::RNA_DataBackboneEnergy, core::energy_methods::RNA_PairwiseLowResolutionEnergy, core::energy_methods::RNA_MgPointEnergy, core::energy_methods::DNA_BaseEnergy, core::energy_methods::RNA_VDW_Energy, core::scoring::methods::MMBondAngleEnergy, core::energy_methods::ContextDependentGeometricSolEnergy, core::energy_methods::FullatomDisulfideEnergy, core::scoring::methods::MMTorsionEnergy, core::energy_methods::PairEnergy, core::scoring::methods::MMBondLengthEnergy, core::energy_methods::CustomAtomPairEnergy, core::energy_methods::OccludedHbondSolEnergy_onebody, core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty, core::scoring::nv::NVscore, core::scoring::interface_::DDPscore, and core::scoring::sym_e::symEnergy.
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if an energy method needs to cache data in the Energies object, before packing begins and requires access to the RotamerSets object, then it does so during this function. The default behavior is to do nothing.
The exact order of events when setting up for packing are as follows:
Reimplemented in core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty.
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if an energy method needs to cache something in the pose (e.g. in pose.energies()), before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.
Reimplemented in core::energy_methods::CartesianBondedEnergy, core::scoring::constraints::ConstraintsEnergy, core::energy_methods::ExactOccludedHbondSolEnergy, core::energy_methods::ElecDensAtomwiseEnergy, core::scoring::elec::FA_ElecEnergy, protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy, core::energy_methods::FaMPSolvEnergy, core::scoring::etable::BaseEtableEnergy< Derived >, core::scoring::etable::BaseEtableEnergy< AnalyticEtableEnergy >, core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >, core::energy_methods::GoapEnergy, core::energy_methods::DEEREnergy, core::energy_methods::FA_GrpElecEnergy, core::energy_methods::Fa_MbsolvEnergy, core::energy_methods::FaMPEnvEnergy, core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty, core::energy_methods::PoissonBoltzmannEnergy, core::scoring::hbonds::HBondEnergy, protocols::membrane::scoring::FaWaterToBilayerEnergy, core::energy_methods::DumpTrajectoryEnergy, core::energy_methods::GenBornEnergy, core::scoring::lkball::LK_BallEnergy, core::energy_methods::Fa_MbenvEnergy, core::energy_methods::MultipoleElecEnergy, core::energy_methods::SASAEnergy, core::energy_methods::VdWTinkerEnergy, core::energy_methods::MPSpanAngleEnergy, core::energy_methods::MPResidueLipophilicityEnergy, core::energy_methods::NPDHBondEnergy, core::energy_methods::AspartimidePenaltyEnergy, core::energy_methods::ContextIndependentGeometricSolEnergy, core::energy_methods::FACTSEnergy, core::energy_methods::MPHelicalityEnergy, core::energy_methods::RNA_FA_ElecEnergy, core::energy_methods::FaMPEnvSmoothEnergy, core::energy_methods::MPEnvEnergy, protocols::scoring::methods::TargetClashEnergy, core::energy_methods::LK_PolarNonPolarEnergy, core::energy_methods::PointWaterEnergy, core::energy_methods::ContextDependentGeometricSolEnergy, core::energy_methods::EnvSmoothEnergy, core::scoring::vdwaals::VDW_Energy, core::energy_methods::FiberDiffractionEnergyDens, core::scoring::methods::MMBondAngleEnergy, core::energy_methods::dfire::DFIRE_Energy, core::energy_methods::ElecDensCenEnergy, core::scoring::membrane::MPNonHelixPenalty, core::energy_methods::CenHBEnergy, core::energy_methods::ElecDensAllAtomCenEnergy, core::energy_methods::FastDensEnergy, core::energy_methods::MembraneEnvEnergy, core::energy_methods::XtalMLEnergy, core::pack::interaction_graph::SurfaceEnergy, core::scoring::methods::MMTorsionEnergy, protocols::rna::AlignmentEnergy, core::energy_methods::ElecDensEnergy, core::energy_methods::FiberDiffractionEnergy, core::energy_methods::HybridVDW_Energy, core::energy_methods::MembraneLipo, core::energy_methods::PairEnergy, core::energy_methods::WaterAdductHBondEnergy, core::pack::interaction_graph::HPatchEnergy, core::scoring::membrane::MPTerminiPenalty, core::scoring::methods::MMBondLengthEnergy, core::energy_methods::DNATorsionEnergy, core::energy_methods::FA_ElecEnergyAroAll, core::energy_methods::FastSAXSEnergy, core::energy_methods::LoopCloseEnergy, core::energy_methods::MembraneCbetaEnergy, core::energy_methods::MembraneEnvSmoothEnergy, core::energy_methods::MPCbetaEnergy, core::energy_methods::ProQ_Energy, core::energy_methods::SecondaryStructureEnergy, core::scoring::carbon_hbonds::CarbonHBondEnergy, protocols::scoring::VDW_GridEnergy, core::energy_methods::CustomAtomPairEnergy, core::energy_methods::FA_ElecEnergyAroAro, core::energy_methods::GenericBondedEnergy, core::energy_methods::MembraneCenPairEnergy, core::energy_methods::MPPairEnergy, core::energy_methods::RamaPreProEnergy, core::energy_methods::ResidualDipolarCouplingEnergy, core::energy_methods::RG_Energy_RNA, core::energy_methods::DNA_BaseEnergy, core::energy_methods::RNA_FullAtomStackingEnergy, core::energy_methods::RNP_LowResEnergy, core::energy_methods::RNP_LowResPairDistEnergy, core::energy_methods::StackElecEnergy, core::energy_methods::CenPairEnergy, core::energy_methods::CenRotPairEnergy, core::energy_methods::ChemicalShiftAnisotropyEnergy, core::energy_methods::CovalentLabelingEnergy, core::energy_methods::CovalentLabelingFAEnergy, core::energy_methods::DipolarCouplingEnergy, core::energy_methods::FreeDOF_Energy, core::energy_methods::MgEnergy, core::energy_methods::RNA_DataBackboneEnergy, core::energy_methods::RNA_PairwiseLowResolutionEnergy, core::energy_methods::SmoothCenPairEnergy, protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments, core::energy_methods::CenRotEnvEnergy, core::energy_methods::EnvEnergy, core::energy_methods::OccludedHbondSolEnergy, core::energy_methods::RNA_MgPointEnergy, core::energy_methods::SmoothEnvEnergy, core::pack::dunbrack::cenrot::CenRotDunEnergy, protocols::scoring::methods::InterchainEnvEnergy, core::energy_methods::BurialEnergy, core::energy_methods::RNA_VDW_Energy, core::energy_methods::FullatomDisulfideEnergy, core::energy_methods::RNA_ChemicalShiftEnergy, core::energy_methods::HRF_MSLabelingEnergy, core::energy_methods::HRFDynamicsEnergy, core::energy_methods::OccludedHbondSolEnergy_onebody, protocols::scoring::methods::InterchainPairEnergy, core::energy_methods::RNA_StubCoordinateEnergy, core::energy_methods::P_AA_ss_Energy, core::scoring::nv::NVscore, core::energy_methods::Abego, core::energy_methods::HackAroEnergy, core::energy_methods::CentroidDisulfideEnergy, core::energy_methods::DNA_DihedralEnergy, core::scoring::orbitals::OrbitalsScore, core::energy_methods::DisulfideMatchingEnergy, core::energy_methods::RNA_SuiteEnergy, core::energy_methods::TNA_SuiteEnergy, core::scoring::interface_::DDPscore, and core::scoring::sym_e::symEnergy.
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Do any setup work before scoring, caching any slow-to-compute data that will be used during energy evaluation inside of the input Residue object's data cache. (The Residue on the whole is given as a constant reference, but non-constant access to its data cache is granted.)
Reimplemented in core::scoring::lkball::LK_BallEnergy.
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show additional information of the energy method
Reimplemented in protocols::nmr::pre::PREEnergy, protocols::nmr::pcs::PCSEnergy, protocols::nmr::rdc::RDCEnergy, protocols::scoring::methods::pcs::PCS_Energy, protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1, protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2, protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3, and protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4.
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If the pose changes in the middle of a packing (as happens in rotamer trials) and if an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.
default implementation noop
Reimplemented in core::energy_methods::MultipoleElecEnergy, core::energy_methods::SASAEnergy, core::energy_methods::VdWTinkerEnergy, core::scoring::orbitals::OrbitalsScore, core::scoring::elec::FA_ElecEnergy, core::scoring::etable::BaseEtableEnergy< Derived >, core::scoring::etable::BaseEtableEnergy< AnalyticEtableEnergy >, core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >, core::energy_methods::FA_GrpElecEnergy, core::energy_methods::GenBornEnergy, core::scoring::lkball::LK_BallEnergy, core::energy_methods::RNA_FA_ElecEnergy, core::scoring::hbonds::HBondEnergy, core::energy_methods::FACTSEnergy, core::scoring::methods::MMLJEnergyInter, core::energy_methods::FA_ElecEnergyAroAll, core::energy_methods::FA_ElecEnergyAroAro, core::energy_methods::PairEnergy, and core::energy_methods::CustomAtomPairEnergy.
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Return the version of the energy method.
Implemented in core::scoring::etable::AnalyticEtableEnergy, core::scoring::etable::TableLookupEtableEnergy, core::energy_methods::CartesianBondedEnergy, core::scoring::lkball::LK_BallEnergy, core::scoring::elec::FA_ElecEnergy, core::scoring::hbonds::HBondEnergy, core::energy_methods::FA_GrpElecEnergy, core::scoring::constraints::ConstraintsEnergy, core::energy_methods::MultipoleElecEnergy, core::energy_methods::VdWTinkerEnergy, core::energy_methods::SASAEnergy, core::scoring::methods::MMLJEnergyInter, core::scoring::carbon_hbonds::CarbonHBondEnergy, core::scoring::orbitals::OrbitalsScore, core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy, core::energy_methods::RNA_FA_ElecEnergy, core::energy_methods::LK_PolarNonPolarEnergy, core::energy_methods::ProClosureEnergy, core::energy_methods::StackElecEnergy, core::energy_methods::GenBornEnergy, core::energy_methods::ContextIndependentGeometricSolEnergy, core::energy_methods::PairEnergy, core::energy_methods::FACTSEnergy, core::energy_methods::ExactOccludedHbondSolEnergy, core::energy_methods::DEEREnergy, core::energy_methods::ContextDependentGeometricSolEnergy, core::energy_methods::OccludedHbondSolEnergy, core::energy_methods::RNA_FullAtomStackingEnergy, core::scoring::methods::NMerSVMEnergy, core::energy_methods::MgEnergy, core::energy_methods::MPResidueLipophilicityEnergy, core::energy_methods::Fa_MbsolvEnergy, core::energy_methods::MPHelicalityEnergy, core::energy_methods::PoissonBoltzmannEnergy, core::energy_methods::FullatomDisulfideEnergy, core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty, core::energy_methods::FaMPSolvEnergy, protocols::scoring::methods::pcs2::PcsEnergy, core::energy_methods::FA_ElecEnergyAroAll, core::scoring::methods::MMLJEnergyIntra, core::energy_methods::FA_ElecEnergyAroAro, core::energy_methods::RNA_PairwiseLowResolutionEnergy, core::energy_methods::LK_hack, core::energy_methods::GoapEnergy, core::energy_methods::ElecDensAtomwiseEnergy, protocols::nmr::pre::PREEnergy, core::energy_methods::AspartimidePenaltyEnergy, core::energy_methods::EnvSmoothEnergy, protocols::nmr::pcs::PCSEnergy, core::energy_methods::RNA_LJ_BaseEnergy, core::energy_methods::FaMPEnvSmoothEnergy, core::energy_methods::SAXSEnergy, core::energy_methods::DNATorsionEnergy, core::scoring::vdwaals::VDW_Energy, core::energy_methods::DNA_ReferenceEnergy, protocols::nmr::rdc::RDCEnergy, core::energy_methods::NPDHBondEnergy, core::energy_methods::MembraneEnvSmoothEnergy, core::scoring::methods::MMBondAngleEnergy, core::energy_methods::LinearChainbreakEnergy, core::energy_methods::ResidualDipolarCouplingEnergy_Rohl, protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy, core::energy_methods::RNA_SugarCloseEnergy, core::energy_methods::RNA_VDW_Energy, core::energy_methods::CustomAtomPairEnergy, core::energy_methods::RNA_DataBackboneEnergy, core::energy_methods::RNA_MgPointEnergy, core::energy_methods::PointWaterEnergy, core::energy_methods::ElecDensEnergy, core::pack::dunbrack::cenrot::CenRotDunEnergy, core::scoring::methods::NMerPSSMEnergy, core::energy_methods::DNA_DihedralEnergy, core::energy_methods::HybridVDW_Energy, protocols::scoring::methods::pcs::PCS_Energy, core::energy_methods::GenericBondedEnergy, core::energy_methods::HackAroEnergy, core::scoring::methods::NMerRefEnergy, protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1, protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2, protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3, protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4, core::energy_methods::CenHBEnergy, core::energy_methods::RamaPreProEnergy, core::energy_methods::RNP_LowResStackEnergy, core::energy_methods::WaterAdductHBondEnergy, core::energy_methods::RNP_LowResEnergy, core::energy_methods::RNP_LowResPairDistEnergy, core::energy_methods::RNA_PartitionEnergy, core::scoring::methods::MMTorsionEnergy, core::energy_methods::FastDensEnergy, protocols::membrane::scoring::FaWaterToBilayerEnergy, core::energy_methods::ElecDensCenEnergy, core::energy_methods::ElecDensAllAtomCenEnergy, protocols::fldsgn::potentials::AACompositionEnergy, core::energy_methods::FaMPEnvEnergy, core::energy_methods::ResidualDipolarCouplingEnergy, core::energy_methods::RG_Energy_Fast, core::energy_methods::SmoothCenPairEnergy, core::energy_methods::CenRotPairEnergy, core::energy_methods::OccludedHbondSolEnergy_onebody, core::energy_methods::SuckerEnergy, core::energy_methods::DNA_BaseEnergy, core::energy_methods::MPSpanInsertionEnergy, core::energy_methods::ChemicalShiftAnisotropyEnergy, core::energy_methods::DipolarCouplingEnergy, core::energy_methods::Fa_MbenvEnergy, core::energy_methods::MPEnvEnergy, core::pack::dunbrack::DunbrackEnergy, core::scoring::methods::MMBondLengthEnergy, core::energy_methods::GaussianOverlapEnergy, protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments, core::energy_methods::PeptideBondEnergy, core::energy_methods::P_AA_pp_Energy, core::energy_methods::RNA_TorsionEnergy, core::energy_methods::FiberDiffractionEnergyDens, core::energy_methods::MembraneCenPairEnergy, core::energy_methods::LinearBranchEnergy, core::energy_methods::RNA_SuiteEnergy, core::energy_methods::TNA_SuiteEnergy, core::energy_methods::dfire::DFIRE_Energy, core::energy_methods::MPSpanAngleEnergy, core::energy_methods::ReferenceEnergy, protocols::scoring::methods::InterchainPairEnergy, core::energy_methods::CenPairEnergy, core::energy_methods::RNA_FullAtomVDW_BasePhosphate, core::energy_methods::LoopCloseEnergy, core::energy_methods::MPPairEnergy, core::energy_methods::RamachandranEnergy, core::energy_methods::RNA_JR_SuiteEnergy, core::energy_methods::MHCEpitopeEnergy, core::scoring::membrane::MPNonHelixPenalty, core::scoring::packing::HolesEnergyRes, core::energy_methods::CenRotEnvEnergy, core::energy_methods::FiberDiffractionEnergy, core::energy_methods::DirectReadoutEnergy, core::energy_methods::SmoothEnvEnergy, core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty, core::scoring::membrane::MPTerminiPenalty, core::energy_methods::HolesEnergy, core::energy_methods::MembraneEnvEnergy, core::energy_methods::SugarBackboneEnergy, core::energy_methods::XtalMLEnergy, protocols::scoring::methods::saxs::PDDFEnergy, core::energy_methods::SequenceDependentRefEnergy, core::energy_methods::FastSAXSEnergy, core::energy_methods::YHHPlanarityEnergy, protocols::scoring::methods::InterchainEnvEnergy, core::energy_methods::ArgCationPiEnergy, core::energy_methods::OmegaTetherEnergy, core::energy_methods::RamachandranEnergy2B, core::energy_methods::ReferenceEnergyNoncanonical, core::energy_methods::RG_Energy_RNA, core::energy_methods::RingClosureEnergy, core::energy_methods::MembraneCbetaEnergy, core::energy_methods::SecondaryStructureEnergy, core::energy_methods::RNA_StubCoordinateEnergy, core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy, core::energy_methods::RNA_ChemicalShiftEnergy, core::energy_methods::IntermolEnergy, core::energy_methods::AromaticBackboneRestraintEnergy, core::scoring::membrane::MPTMProjPenalty, core::energy_methods::CentroidDisulfideEnergy, core::energy_methods::DumpTrajectoryEnergy, core::energy_methods::EnvEnergy, core::energy_methods::AACompositionEnergy, core::energy_methods::DisulfideMatchingEnergy, core::energy_methods::SurfEnergy, core::energy_methods::SurfVolEnergy, core::energy_methods::P_AA_ss_Energy, protocols::scoring::methods::TargetClashEnergy, core::energy_methods::MotifDockEnergy, core::energy_methods::pHEnergy, core::energy_methods::SymmetricLigandEnergy, core::energy_methods::MPCbetaEnergy, core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy, core::energy_methods::NetChargeEnergy, core::energy_methods::AARepeatEnergy, core::energy_methods::MissingEnergy, core::pack::interaction_graph::SurfaceEnergy, core::energy_methods::FreeDOF_Energy, core::energy_methods::HydroxylTorsionEnergy, core::energy_methods::WaterAdductIntraEnergy, core::energy_methods::WaterSpecificEnergy, protocols::scoring::methods::SpecialRotamerEnergy, core::energy_methods::DNAChiEnergy, core::scoring::nv::NVscore, core::energy_methods::RNA_BulgeEnergy, protocols::scoring::VDW_GridEnergy, core::scoring::interface_::DDPscore, core::energy_methods::DNA_EnvPairEnergy, core::energy_methods::MembraneEnvPenalties, core::energy_methods::MembraneLipo, core::energy_methods::P_AA_Energy, core::energy_methods::RMS_Energy, core::energy_methods::RNA_ChemicalMappingEnergy, core::pack::interaction_graph::HPatchEnergy, core::pack::guidance_scoreterms::sap::SapConstraintEnergy, core::energy_methods::CovalentLabelingEnergy, core::energy_methods::CovalentLabelingFAEnergy, core::energy_methods::ProQ_Energy, protocols::rna::AlignmentEnergy, core::energy_methods::BranchEnergy, core::energy_methods::ChainbreakEnergy, core::energy_methods::BurialEnergy, core::energy_methods::DistanceChainbreakEnergy, core::energy_methods::SSElementMotifContactEnergy, core::energy_methods::HRF_MSLabelingEnergy, core::energy_methods::HRFDynamicsEnergy, core::energy_methods::SplitUnfoldedTwoBodyEnergy, core::energy_methods::UnfoldedStateEnergy, core::scoring::rna::RNA_LowResolutionPotential, core::energy_methods::PackStatEnergy, core::energy_methods::ContactOrderEnergy, protocols::scoring::methods::EnsembleEnergy, core::energy_methods::D2H_SA_Energy, core::energy_methods::SA_Energy, core::energy_methods::CenPairMotifEnergy, core::energy_methods::CenPairMotifDegreeEnergy, core::energy_methods::CenPairMotifEnergy, core::scoring::sym_e::symEnergy, core::energy_methods::Abego, core::energy_methods::Burial_v2Energy, and core::energy_methods::OtherPoseEnergy.
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Referenced by score_types(), and set_score_types().