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Rosetta
2020.11
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Rosetta
2020.11
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#include <FullatomDisulfideEnergy.hh>
Public Member Functions | |
| FullatomDisulfideEnergy (FullatomDisulfidePotential const &potential) | |
| ~FullatomDisulfideEnergy () override | |
| methods::EnergyMethodOP | clone () const override |
| void | ensure_lrenergy_container_is_up_to_date (pose::Pose &pose) const |
| check that the fullatom disulfid energy container is the right size, and the set of disulfides it holds corresponds correctly to the set of disulfides in the Pose. More... | |
| void | setup_for_scoring (pose::Pose &, ScoreFunction const &) const override |
| 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... | |
| void | setup_for_packing (pose::Pose &pose, utility::vector1< bool > const &residues_repacking, utility::vector1< bool > const &residues_designing) const override |
| Make sure that the FullatomDisulfideEnergyContainer is ready for packing. More... | |
| bool | defines_score_for_residue_pair (conformation::Residue const &res1, conformation::Residue const &res2, bool res_moving_wrt_eachother) const override |
| Returns true only for disulfide-bonded residue pairs. More... | |
| bool | minimize_in_whole_structure_context (pose::Pose const &) const override |
| 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... | |
| bool | use_extended_residue_pair_energy_interface () const override |
| During minimization, access atom-index information from the ResPairMinimizationData. More... | |
| 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 |
| Pull the atom-index information out of min_data object, and use those indices to score the disulfide bond. More... | |
| 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 &data_cache) const override |
| Initialize the atom-index information for a particular residue pair and store those indices in the ResPairMinimizationData data_cache. More... | |
| 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_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const override |
| Retrieve the atom-index information for this residue pair from the minpair_data object and evaluate the derivatives for a particular atom. More... | |
| virtual void | old_eval_atom_derivative (id::AtomID const &, pose::Pose const &, kinematics::DomainMap const &, ScoreFunction const &, EnergyMap const &, Vector &, Vector &) const |
| virtual Real | eval_dof_derivative (id::DOF_ID const &, id::TorsionID const &, pose::Pose const &, ScoreFunction const &, EnergyMap const &) const |
| 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... | |
| 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... | |
| bool | defines_intrares_energy (EnergyMap const &weights) const override |
| 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... | |
| void | eval_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const override |
| Evaluate the intra-residue energy for a given residue. More... | |
| methods::LongRangeEnergyType | long_range_type () const override |
| bool | defines_residue_pair_energy (pose::Pose const &pose, Size res1, Size res2) const override |
 Public Member Functions inherited from core::scoring::methods::ContextIndependentLRTwoBodyEnergy | |
| ContextIndependentLRTwoBodyEnergy (EnergyMethodCreatorOP) | |
| ~ContextIndependentLRTwoBodyEnergy () override | |
| 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... | |
| Public Member Functions inherited from core::scoring::methods::LongRangeTwoBodyEnergy | |
| LongRangeTwoBodyEnergy (EnergyMethodCreatorOP creator) | |
| Constructor with an EnergyMethodCreator to inform the grandparent EnergyMethod class which ScoreTypes this EnergyMethod computes. More... | |
| ~LongRangeTwoBodyEnergy () override | |
| virtual bool | defines_residue_pair_energy (pose::Pose const &pose, Size res1, Size res2) const =0 |
| 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... | |
| ~TwoBodyEnergy () override | |
| virtual void | setup_for_minimizing_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, basic::datacache::BasicDataCache &residue_data_cache, ResSingleMinimizationData &res_data_cache) const |
| Called at the beginning of minimization, allowing this energy method to cache data pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. More... | |
| virtual bool | requires_a_setup_for_scoring_for_residue_opportunity_during_minimization (pose::Pose const &pose) const |
| 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... | |
| virtual void | setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data) const |
| 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... | |
| virtual bool | requires_a_setup_for_derivatives_for_residue_opportunity (pose::Pose const &pose) const |
| 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... | |
| virtual void | setup_for_derivatives_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data, basic::datacache::BasicDataCache &res_data_cache) const |
| Do any setup work necessary before evaluating the derivatives for this residue. More... | |
| virtual bool | requires_a_setup_for_scoring_for_residue_pair_opportunity (pose::Pose const &pose) const |
| 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... | |
| virtual 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 &sfxn, ResPairMinimizationData &data_cache) const |
| 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... | |
| virtual bool | requires_a_setup_for_derivatives_for_residue_pair_opportunity (pose::Pose const &pose) const |
| 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... | |
| virtual 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 &sfxn, ResPairMinimizationData &data_cache) const |
| Do any setup work necessary before evaluating the derivatives for this residue pair. More... | |
| virtual void | backbone_backbone_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const |
| Evaluate the interaction between the backbone of rsd1 and the backbone of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the weighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy. More... | |
| virtual void | backbone_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const |
| Evaluate the interaction between the backbone of rsd1 and the sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy. More... | |
| virtual void | sidechain_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const |
| Evaluate the interaction between the sidechain of rsd1 and the sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy. More... | |
| 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... | |
| virtual bool | use_extended_intrares_energy_interface () const |
| Derived classes wishing to invoke the alternate, extended interface for eval_intrares_energy during minimization routines should return "true" when this function is invoked on them. This class provides a default "return false" implementation so that classes not desiring to take advantage of this alternate interface need to do nothing. More... | |
| virtual void | eval_intrares_energy_ext (conformation::Residue const &rsd, ResSingleMinimizationData const &data_cache, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const |
| Evaluate the intra-residue energy for a given residue using the data held within the ResSingleMinimizationData object. This function should be invoked only on derived instances of this class if they return "true" in a call to their use_extended_intrares_energy_interface method. This base class provides a noop implementation for classes that do not implement this interface, or that do not define intrares energies. More... | |
| virtual 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 |
| 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... | |
| 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... | |
| 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... | |
| virtual void | bump_energy_full (conformation::Residue const &, conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const |
| virtual void | bump_energy_backbone (conformation::Residue const &, conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const |
| 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... | |
| 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... | |
| virtual 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 |
| 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... | |
| virtual 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 |
| 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... | |
| virtual 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 |
| 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... | |
| Public Member Functions inherited from core::scoring::methods::EnergyMethod | |
| EnergyMethod (EnergyMethodCreatorOP creator) | |
| Constructor with EnergyMethodCreator, which lists the score types that this energy method is responsible for. 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 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 | 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 void | show_additional_info (std::ostream &, pose::Pose &, bool) const |
| show additional information of the energy method More... | |
| virtual bool | energy_method_provides_citation_info () const |
| Does this energy method provide information about how to cite it? More... | |
| virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP > | provide_citation_info () const |
| Provide the citation. More... | |
| virtual bool | energy_method_is_unpublished () const |
| Does this energy method indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More... | |
| virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP > | provide_authorship_info_for_unpublished () const |
| Provide a list of authors and their e-mail addresses, as strings. More... | |
Public Attributes | |
| __pad0__:ContextIndependentLRTwoBodyEnergy parent | |
Private Member Functions | |
| core::Size | version () const override |
| Return the version of the energy method. More... | |
Private Attributes | |
| FullatomDisulfidePotential const & | potential_ |
Additional Inherited Members | |
| Public Types inherited from core::scoring::methods::ContextIndependentLRTwoBodyEnergy | |
| typedef LongRangeTwoBodyEnergy | parent |
| Public Types inherited from core::scoring::methods::LongRangeTwoBodyEnergy | |
| typedef TwoBodyEnergy | parent |
| Public Types inherited from core::scoring::methods::TwoBodyEnergy | |
| typedef EnergyMethod | parent |
| Public Types inherited from core::scoring::methods::EnergyMethod | |
| typedef utility::pointer::ReferenceCount | parent |
| Protected Member Functions inherited from core::scoring::methods::EnergyMethod | |
| 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... | |
| core::scoring::disulfides::FullatomDisulfideEnergy::FullatomDisulfideEnergy | ( | FullatomDisulfidePotential const & | potential | ) |
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Implements core::scoring::methods::EnergyMethod.
References potential_.
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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.
For example, the Etable method defines intra-residue energies only when one or more of the fa_intra_{atr,rep,sol} weights are non-zero.
Implements core::scoring::methods::TwoBodyEnergy.
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Returns true only for disulfide-bonded residue pairs.
returns true if both residues are cys, if both are disulfide-cys, and then if all of these conditions have been satisfied, if residue1's SG atom connects to residue 2, and if residue 2's SG atom connects to residue 1
Reimplemented from core::scoring::methods::TwoBodyEnergy.
References core::conformation::Residue::atom_index(), core::conformation::Residue::connect_map(), core::chemical::DISULFIDE, core::chemical::ResidueTypeBase::get_disulfide_atom_name(), core::conformation::Residue::has_variant_type(), core::chemical::ResConnID::resid(), core::chemical::ResidueType::residue_connection_id_for_atom(), core::conformation::Residue::seqpos(), and core::conformation::Residue::type().
| void core::scoring::disulfides::FullatomDisulfideEnergy::ensure_lrenergy_container_is_up_to_date | ( | pose::Pose & | pose | ) | const |
check that the fullatom disulfid energy container is the right size, and the set of disulfides it holds corresponds correctly to the set of disulfides in the Pose.
References core::pose::Pose::conformation(), core::pose::Pose::energies(), core::scoring::methods::fa_disulfide_energy, core::scoring::Energies::long_range_container(), core::scoring::Energies::nonconst_long_range_container(), core::scoring::Energies::set_long_range_container(), and core::conformation::Conformation::size().
Referenced by setup_for_packing(), and setup_for_scoring().
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Evaluate the intra-residue energy for a given residue.
Implements core::scoring::methods::TwoBodyEnergy.
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Retrieve the atom-index information for this residue pair from the minpair_data object and evaluate the derivatives for a particular atom.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
References core::scoring::disulfides::DisulfideAtomIndices::c_alpha_index(), core::scoring::disulfides::DisulfideAtomIndices::c_beta_index(), core::scoring::disulfides::DisulfideAtomIndices::disulf_atom_index(), core::scoring::dslf_ca_dih, core::scoring::dslf_cs_ang, core::scoring::dslf_fa13, core::scoring::dslf_ss_dih, core::scoring::dslf_ss_dst, core::scoring::fa_dslf_respair_data, core::scoring::ResPairMinimizationData::get_data(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives_old(), core::conformation::Residue::has_variant_type(), potential_, core::chemical::REPLONLY, and core::scoring::disulfides::DisulfMinData::res_inds().
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Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.
Implements core::scoring::methods::EnergyMethod.
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Implements core::scoring::methods::LongRangeTwoBodyEnergy.
References core::scoring::methods::fa_disulfide_energy.
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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 from core::scoring::methods::EnergyMethod.
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References core::id::AtomID::atomno(), core::scoring::dslf_fa13, core::pose::Pose::energies(), core::scoring::methods::fa_disulfide_energy, core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives_old(), core::scoring::ScoreFunction::has_nonzero_weight(), core::scoring::Energies::long_range_container(), potential_, core::chemical::REPLONLY, core::pose::Pose::residue(), and core::id::AtomID::rsd().
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Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap.
Implements core::scoring::methods::TwoBodyEnergy.
References core::scoring::dslf_ca_dih, core::scoring::dslf_cs_ang, core::scoring::dslf_fa13, core::scoring::dslf_ss_dih, core::scoring::dslf_ss_dst, core::pose::Pose::energies(), core::scoring::methods::fa_disulfide_energy, core::scoring::ScoreFunction::has_nonzero_weight(), core::conformation::Residue::has_variant_type(), core::chemical::ResidueType::is_disulfide_bonded(), core::chemical::ResidueType::is_sidechain_thiol(), core::scoring::Energies::long_range_container(), potential_, core::chemical::REPLONLY, core::scoring::disulfides::FullatomDisulfidePotential::score_this_disulfide(), core::scoring::disulfides::FullatomDisulfidePotential::score_this_disulfide_old(), core::conformation::Residue::seqpos(), and core::conformation::Residue::type().
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overridevirtual |
Pull the atom-index information out of min_data object, and use those indices to score the disulfide bond.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
References core::scoring::dslf_ca_dih, core::scoring::dslf_cs_ang, core::scoring::dslf_fa13, core::scoring::dslf_ss_dih, core::scoring::dslf_ss_dst, core::scoring::fa_dslf_respair_data, core::scoring::ResPairMinimizationData::get_data(), core::scoring::ScoreFunction::has_nonzero_weight(), core::conformation::Residue::has_variant_type(), potential_, core::chemical::REPLONLY, core::scoring::disulfides::DisulfMinData::res_inds(), core::scoring::disulfides::FullatomDisulfidePotential::score_this_disulfide(), core::scoring::disulfides::FullatomDisulfidePotential::score_this_disulfide_old(), and core::conformation::Residue::seqpos().
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overridevirtual |
Initialize the atom-index information for a particular residue pair and store those indices in the ResPairMinimizationData data_cache.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
References core::scoring::fa_dslf_respair_data, core::conformation::Residue::has_variant_type(), core::chemical::REPLONLY, core::conformation::Residue::seqpos(), and core::scoring::ResPairMinimizationData::set_data().
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overridevirtual |
Make sure that the FullatomDisulfideEnergyContainer is ready for packing.
Reimplemented from core::scoring::methods::EnergyMethod.
References ensure_lrenergy_container_is_up_to_date().
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overridevirtual |
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 from core::scoring::methods::EnergyMethod.
References ensure_lrenergy_container_is_up_to_date().
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overridevirtual |
During minimization, access atom-index information from the ResPairMinimizationData.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
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overrideprivatevirtual |
Return the version of the energy method.
Implements core::scoring::methods::EnergyMethod.
| core::scoring::disulfides::FullatomDisulfideEnergy::__pad0__ |
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private |
1.8.7