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| | BaseEtableEnergy (methods::EnergyMethodCreatorOP creator, Etable const &etable_in, methods::EnergyMethodOptions const &options, bool const do_classic_intrares_=false) |
| | construction with an etable More...
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| | BaseEtableEnergy (BaseEtableEnergy< Derived > const &) |
| | explicit copy constructor, since the BaseEtableEnergy now contains OP data More...
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| bool | minimize_in_whole_structure_context (pose::Pose const &) const override |
| | The neighborlist-autoupdate algorithm requires that the EtableEnergy be able to control the definition and update for its atom-neighbors. This will bypass the standard neighborlist evaluation inside the ScoreFunction, avoiding the use the MinimizationGraph. More...
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| void | setup_for_minimizing (pose::Pose &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map) const override |
| | stashes nblist if pose.energies().use_nblist_auto_update() is true This is only invoked, now, if the neighborlist-autoupdate flag is on. More...
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| void | setup_for_scoring (pose::Pose &pose, ScoreFunction const &scfxn) const override |
| | check compatibility with atomtypeset More...
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| void | setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) const override |
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| void | setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const override |
| | 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...
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| void | prepare_rotamers_for_packing (pose::Pose const &pose, conformation::RotamerSetBase &set) const override |
| | 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...
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| void | update_residue_for_packing (pose::Pose &pose, Size resid) const override |
| | 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...
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| count_pair::CountPairFunctionCOP | get_count_pair_function (Size res1, Size res2, pose::Pose const &pose, ScoreFunction const &sfxn) const |
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| count_pair::CountPairFunctionCOP | get_count_pair_function (conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &pose, ScoreFunction const &sfxn) const |
| | and gets duplicated in a handful of other places within this class... this NEEDS to be reworked. More...
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| count_pair::CountPairFunctionOP | get_intrares_countpair (conformation::Residue const &res, pose::Pose const &pose, ScoreFunction const &sfxn) const |
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| void | residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const override |
| | Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap. More...
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| bool | use_extended_residue_pair_energy_interface () const override |
| | APL – note, new. More...
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| void | residue_pair_energy_ext (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResPairMinimizationData const &min_data, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const override |
| | APL – note, new. More...
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| void | setup_for_minimizing_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, ResSingleMinimizationData const &res1_data_cache, ResSingleMinimizationData const &res2_data_cache, ResPairMinimizationData &min_data) const override |
| | APL – note, new. More...
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| bool | requires_a_setup_for_scoring_for_residue_opportunity_during_minimization (pose::Pose const &pose) const override |
| | Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. More...
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| void | setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &, ResSingleMinimizationData &min_data) const override |
| | Do any setup work should the coordinates of this residue (who is still guaranteed to be of the same residue type as when setup_for_minimizing_for_residue was called) have changed so dramatically as to possibly require some amount of setup work before scoring should proceed. This function is used for both intra-residue setup and pre-inter-residue setup. More...
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| bool | requires_a_setup_for_derivatives_for_residue_opportunity (pose::Pose const &pose) const override |
| | Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so. More...
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| void | setup_for_derivatives_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &, ResSingleMinimizationData &min_data, basic::datacache::BasicDataCache &) const override |
| | Do any setup work necessary before evaluating the derivatives for this residue. More...
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| bool | requires_a_setup_for_scoring_for_residue_pair_opportunity (pose::Pose const &pose) const override |
| | Does this EnergyMethod require the opportunity to examine each residue pair before scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so. More...
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| void | setup_for_scoring_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &minsingle_data1, ResSingleMinimizationData const &minsingle_data2, pose::Pose const &pose, ScoreFunction const &, ResPairMinimizationData &data_cache) const override |
| | Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed. More...
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| bool | requires_a_setup_for_derivatives_for_residue_pair_opportunity (pose::Pose const &pose) const override |
| | Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so. More...
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| void | setup_for_derivatives_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &minsingle_data1, ResSingleMinimizationData const &minsingle_data2, pose::Pose const &pose, ScoreFunction const &, ResPairMinimizationData &data_cache) const override |
| | Do any setup work necessary before evaluating the derivatives for this residue pair. More...
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| void | eval_residue_pair_derivatives (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &, ResSingleMinimizationData const &, ResPairMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_at_derivs, utility::vector1< DerivVectorPair > &r2_at_derivs) const override |
| | APL – note, new. More...
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| void | backbone_backbone_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const override |
| | Evaluates the interaction between the backbone of rsd1 and the backbone of rsd2 and accumulates the unweighted energy. More...
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| void | backbone_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const override |
| | Evaluates the interaction between the backbone of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy. More...
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| void | sidechain_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const override |
| | Evaluates the interaction between the sidechain of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy. More...
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| void | evaluate_rotamer_pair_energies (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const override |
| | Batch computation of rotamer pair energies. Need not be overriden in derived class – by default, iterates over all pairs of rotamers, and calls the derived class's residue_pair_energy method. More...
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| void | evaluate_rotamer_background_energies (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< core::PackerEnergy > &energy_vector) const override |
| | Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamr. More...
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| bool | use_extended_intrares_energy_interface () const override |
| | APL – note, new. More...
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| void | eval_intrares_energy_ext (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const override |
| | APL – note, new. More...
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| void | setup_for_minimizing_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, basic::datacache::BasicDataCache &, ResSingleMinimizationData &min_data) const override |
| | APL – note, new. More...
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| void | eval_intrares_derivatives (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &atom_derivs) const override |
| | Evaluate the derivative for the intra-residue component of this energy method for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd. More...
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| void | bump_energy_full (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const override |
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| void | bump_energy_backbone (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const override |
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| void | finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) const override |
| | called at the end of energy evaluation More...
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| void | eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &, ScoreFunction const &sfxn, EnergyMap const &weights, Vector &F1, Vector &F2) const override |
| | called during gradient-based minimization inside dfunc More...
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| bool | has_atomistic_pairwise_energies () const override |
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| void | atomistic_pair_energy (core::Size, conformation::Residue const &, core::Size, conformation::Residue const &, pose::Pose const &, ScoreFunction const &sfxn, EnergyMap &) const override |
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| void | prepare_for_residue_pair (Size const res1, Size const res2, pose::Pose const &pose) const |
| | Should/Could these inlined" in a separate .inline.hh? More...
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| void | atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, EnergyMap &emap, Real &dsq) const |
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| void | atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb, Real &dsq) const |
| | for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication. More...
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| void | atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, AtomPairEnergy &ape) const |
| | APL – consider reinstating this function! More...
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| void | pair_energy_H (conformation::Atom const &atom1, conformation::Atom const &atom2, Real weight, EnergyMap &emap) const |
| | APL – Consider reinstating this function! More...
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| Real | hydrogen_interaction_cutoff2 () const |
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| Distance | atomic_interaction_cutoff () const override |
| | Etable atomic distance cutoff is 5.5 A. More...
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| bool | divides_backbone_and_sidechain_energetics () const override |
| | A derived class should return true for this function if it implements its own versions of the backbone_backbone_energy, backbone_sidechain_energy and sidechain_sidechain_energy functions. The default sidechain_sidechain_energy implemented by the TwoBodyEnergy base class calls residue_pair_energy. If the derived class implements its own versions of these functions, then calling code may avoid calling it on pairs of residues that are "provably distant" based on a pair of bounding spheres for a sidechains and backbones and this method's atomic_interaction_cutoff energy method. More...
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| void | indicate_required_context_graphs (utility::vector1< bool > &) const override |
| | 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...
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| EnergiesCacheableDataType::Enum | nblist_type () const |
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| min_single_data | min_single_data_type () const |
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| min_pair_data | min_pair_data_type () const |
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| bool | calculate_interres (core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2) const |
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| bool | calculate_intrares (core::conformation::Residue const &rsd) const |
| |
 Public Member Functions inherited from core::scoring::methods::ContextIndependentTwoBodyEnergy |
| | ContextIndependentTwoBodyEnergy (EnergyMethodCreatorOP) |
| | Constructor with an EnergyMethodCreator to inform the ancestor EnergyMethod class which ScoreTypes this EnergyMethod is responsible for computing. More...
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| | ~ContextIndependentTwoBodyEnergy () override |
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| EnergyMethodType | method_type () const override |
| | Return one of the 7 kinds of energy methods that exist: e.g. context-dependent-one-body vs whole-structure. More...
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| Public Member Functions inherited from core::scoring::methods::ShortRangeTwoBodyEnergy |
| | ShortRangeTwoBodyEnergy (EnergyMethodCreatorOP) |
| | Constructor with EnergyMethodCreator to provide to the EnergyMethod grandparent the list of the ScoreTypes this EnergyMethod is responsible for computing. More...
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| | ~ShortRangeTwoBodyEnergy () override |
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| void | evaluate_rotamer_pair_energies (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const override |
| | Batch computation of rotamer pair energies. Need not be overriden in derived class – by default, iterates over all pairs of rotamers, and calls derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...
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| void | evaluate_rotamer_background_energies (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< core::PackerEnergy > &energy_vector) const override |
| | Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...
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| void | evaluate_rotamer_background_energy_maps (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< EnergyMap > &emaps) const override |
| | Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...
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| Public Member Functions inherited from core::scoring::methods::TwoBodyEnergy |
| | TwoBodyEnergy (EnergyMethodCreatorOP) |
| | Constructor, requiring an EnergyMethodCreator. No default constructor provided to force EnergyMethod writers to provide an energy-method-creator at construction time. More...
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| | ~TwoBodyEnergy () override |
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| virtual bool | defines_score_for_residue_pair (conformation::Residue const &res1, conformation::Residue const &res2, bool res_moving_wrt_eachother) const |
| | During minimization, energy methods are allowed to decide that they say nothing about a particular residue pair (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default implementation returns "true" for all residue pairs. Context-dependent two-body energies have the option of behaving as if they are context-independent by returning "false" for residue pairs that do no move wrt each other. More...
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| virtual bool | defines_intrares_energy (EnergyMap const &weights) const =0 |
| | Two body energies are able to define intra-residue energies, and to do so only in the presence of certain non-zero weights. The ScoreFunction will hand over its weight set as it asks whether the energy method defines an intraresidue energy or not. More...
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| virtual void | eval_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const =0 |
| | Evaluate the intra-residue energy for a given residue. More...
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| virtual bool | defines_intrares_energy_for_residue (conformation::Residue const &res) const |
| | If a score function defines no intra-residue scores for a particular residue, then it may opt-out of being asked during minimization to evaluate the score for this residue. More...
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| virtual bool | defines_intrares_dof_derivatives (pose::Pose const &p) const |
| | Use the dof_derivative interface for this energy method when calculating derivatives? It is possible to define both dof_derivatives and atom-derivatives; they are not mutually exclusive. More...
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| virtual utility::vector1< id::PartialAtomID > | atoms_with_dof_derivatives (conformation::Residue const &res, pose::Pose const &p) const |
| | For a particular residue, list which atoms go into defining the DOF derivatives, including any atoms on adjacent residues. The Pose is provided for context, but there is no requirement that res be a member of that Pose. More...
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| virtual Real | eval_intraresidue_dof_derivative (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights) const |
| | Evaluate the DOF derivative for a particular residue. The Pose merely serves as context, and the input residue is not required to be a member of the Pose. More...
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| virtual void | evaluate_rotamer_intrares_energies (conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< core::PackerEnergy > &energies) const |
| | Batch computation of rotamer intrares energies. Need not be overriden in derived class – by default, iterates over all rotamers, and calls derived class's intrares _energy method. More...
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| virtual void | evaluate_rotamer_intrares_energy_maps (conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< EnergyMap > &emaps) const |
| | Batch computation of rotamer intrares energy map. Need not be overriden in derived class – by default, iterates over all rotamers, and calls derived class's intrares _energy method. More...
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| 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...
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| | EnergyMethod (EnergyMethodCreatorOP creator) |
| | Constructor with EnergyMethodCreator, which lists the score types that this energy method is responsible for. More...
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| virtual EnergyMethodOP | clone () const =0 |
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| 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...
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| 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...
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| 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...
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| virtual void | finalize_after_minimizing (pose::Pose &pose) const |
| | Called after minimization, allowing a derived class to do some teardown steps. More...
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| virtual void | finalize_after_derivatives (pose::Pose &, ScoreFunction const &) const |
| | called at the end of derivatives evaluation More...
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| 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...
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| virtual bool | has_atomistic_energies () const |
| | Does this EnergyMethod have a non-trivial implementation of the (one body) atomistic energy method? Note that this may return false even if the score term theoretically could support atomistic energies. And even if this function returns true, it's not necessarily the case that all atoms will get assigned an energy, or that the sum over all atoms (or atom pairs) will result in the same energy as the residue-level approach. The atomistic functions are intended for supplemental informational purposes only. The residue-level energies are the main interface for EnergyMethods. More...
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| virtual void | atomistic_energy (core::Size atmno, conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &scorefxn, EnergyMap &emap) const |
| | Evaluate the (one body) energy associated with a particular atom This may be a "self" energy, or it may be the single atom contribution from a whole structure term. NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_energies() More...
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| ScoreTypes const & | score_types () const |
| | Returns the score types that this energy method computes. More...
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| virtual core::Size | version () const =0 |
| | Return the version of the energy method. More...
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| virtual void | show_additional_info (std::ostream &, pose::Pose &, bool) const |
| | show additional information of the energy method More...
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| 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...
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