#include <ConstraintsEnergy.hh>
Public Member Functions | |
| ConstraintsEnergy () | |
| ~ConstraintsEnergy () override | |
| EnergyMethodOP | clone () const override |
| methods::LongRangeEnergyType | long_range_type () const override |
| Identification for this LR2B energy that links it with the long-range energy container that it stores in the Energies object. More... | |
| bool | defines_residue_pair_energy (pose::Pose const &pose, Size res1, Size res2) const override |
| Interface from the LongRangeTwoBodyEnergy base class; returns "true" if there's any non-zero or potentially non-zero interaction between a pair of residues in a pose. 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 constraint residue_pair_energy. Defers entirely to cst_set. 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 |
| Returns true as the ConstraintsEnergy caches its residue pair constraints in the ResPairMinimicationData objects stored on edges in the MinimizationGraph. 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 |
| The ConstraintsEnergy caches all residue-pair constraints operating between a particular pair of residues in the min_data object so that it does not need to search for those constraints when scoring during minimization. More... | |
| bool | defines_score_for_residue_pair (conformation::Residue const &res1, conformation::Residue const &res2, bool res_moving_wrt_eachother) const override |
| Returns false if residue1 and residue2 have no inter-residue pair constraints or if the two residues are not moving wrt each other. More... | |
| 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 &res_data_cache) const override |
| Cache the intra-residue constraints in the ResSingleMinimizationData object for rapid retrieval during minimization and allow the constraints to store data in the res_data_cache if they need to. 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 &respair_data_cache) const override |
| Cache the residue-pair constraints in the ResPairMinimizationData object for rapid retrieval during minimization and allow constraints to cache useful data in the respair_data_cache if they need to. More... | |
| bool | requires_a_setup_for_scoring_for_residue_pair_opportunity (pose::Pose const &pose) const override |
| Request the opportunity to setup for scoring. More... | |
| 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 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... | |
| bool | requires_a_setup_for_derivatives_for_residue_pair_opportunity (pose::Pose const &pose) const override |
| Ask for the opportunity to setup for derivative evaluation. More... | |
| 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 override |
| Do any setup work necessary before evaluating the derivatives for this residue pair. 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 |
| Evaluate the derivative for an atom in rsd1 with respect to rsd2 in the context of a particular pose, and increment the F1 and F2 vectors. More... | |
| void | prepare_constraints_energy_container (pose::Pose &pose) const |
| void | setup_for_scoring (pose::Pose &pose, ScoreFunction const &scfxn) 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 ConstraintsEnergyContainer is ready for packing. More... | |
| void | setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) const override |
| Setup constraint-set specific derivatives. More... | |
| bool | defines_high_order_terms (pose::Pose const &) const override |
| Returns true if there are three-body or higher-body constraints that the user has defined. High-order terms will not be correctly evaluated in RTMin or other extra-pose techniques for minimization (but will work correctly when minimizing an entire Pose). More... | |
| bool | defines_intrares_energy (EnergyMap const &weights) const override |
| Intraresidue constraints can exist; the ConstraintsEnergy class cannot tell whether or not any intraresidue constraints exist when only given the weight set, so for safety it says "yes, I define intraresidue
energies" and guarantees they will be evaluated properly if they do exist. More... | |
| void | eval_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const override |
| Evaluate the intra-residue constraint energy for a given residue. More... | |
| bool | use_extended_intrares_energy_interface () const override |
| request of minimization routines that they use the extended intraresidue energy interface More... | |
| void | eval_intrares_energy_ext (conformation::Residue const &rsd, ResSingleMinimizationData const &data_cache, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const override |
| Evaluate the intra-residue energies using ConstraintCOPs cached in the data_cache object. More... | |
| bool | requires_a_setup_for_scoring_for_residue_opportunity_during_minimization (pose::Pose const &pose) const override |
| Ask for the opportunity to setup for scoring for evaluating 1-body constraints. More... | |
| void | setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data) const override |
| Allow the component constraints to setup for scoring for a particular residue. More... | |
| 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... | |
| 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 override |
| Do any setup work necessary before evaluating the derivatives for this residue. More... | |
| 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... | |
| bool | defines_intrares_dof_derivatives (pose::Pose const &p) const override |
| The DunbrackConstraint, which adds a "constant term" to the energy for a particular rotamer so that the particular rotamer matches the score of the best rotamer at a particular phi/psi, defines derivatives for phi and psi. or rather – it doesn't, but it should. More... | |
| 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 override |
| 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... | |
| void | finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) const override |
| called at the end of energy evaluation More... | |
| 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... | |
| Real | eval_dof_derivative (id::DOF_ID const &id, id::TorsionID const &tor, pose::Pose const &pose, ScoreFunction const &scorefxn, EnergyMap const &weights) const |
| Evaluate dof derivatives when DOF_constraints are in use. More... | |
| void | indicate_required_context_graphs (utility::vector1< bool > &) const override |
| constraints are context independent More... | |
| core::Size | version () const override |
| Return the version of the energy method. More... | |
 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 | |
| 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 | 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 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... | |
| 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... | |
| 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... | |
| 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 | finalize_after_derivatives (pose::Pose &, ScoreFunction const &) const |
| called at the end of derivatives evaluation More... | |
| 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... | |
| virtual bool | has_atomistic_pairwise_energies () const |
| Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method? NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. More... | |
| 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... | |
| virtual void | atomistic_pair_energy (core::Size atmno1, conformation::Residue const &rsd1, core::Size atomno2, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &scorefxn, EnergyMap &emap) const |
| Evaluate the energy for a particular pair of atoms This function may be fed the same residue with different atom numbers 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_pairwise_energies() 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 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... | |
Public Attributes | |
| __pad0__:ContextIndependentLRTwoBodyEnergy parent | |
| __pad1__:EnergyMethodOP EnergyMethodOP | |
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::VirtualBase | 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... | |
Constructor & Destructor Documentation
◆ ConstraintsEnergy()
| core::scoring::constraints::ConstraintsEnergy::ConstraintsEnergy | ( | ) |
◆ ~ConstraintsEnergy()
|
overridedefault |
Member Function Documentation
◆ clone()
|
overridevirtual |
Implements core::scoring::methods::EnergyMethod.
◆ defines_high_order_terms()
|
overridevirtual |
Returns true if there are three-body or higher-body constraints that the user has defined. High-order terms will not be correctly evaluated in RTMin or other extra-pose techniques for minimization (but will work correctly when minimizing an entire Pose).
Reimplemented from core::scoring::methods::EnergyMethod.
References core::pose::Pose::constraint_set().
◆ defines_intrares_dof_derivatives()
|
overridevirtual |
The DunbrackConstraint, which adds a "constant term" to the energy for a particular rotamer so that the particular rotamer matches the score of the best rotamer at a particular phi/psi, defines derivatives for phi and psi. or rather – it doesn't, but it should.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
◆ defines_intrares_energy()
|
overridevirtual |
Intraresidue constraints can exist; the ConstraintsEnergy class cannot tell whether or not any intraresidue constraints exist when only given the weight set, so for safety it says "yes, I define intraresidue energies" and guarantees they will be evaluated properly if they do exist.
Implements core::scoring::methods::TwoBodyEnergy.
◆ defines_residue_pair_energy()
|
overridevirtual |
Interface from the LongRangeTwoBodyEnergy base class; returns "true" if there's any non-zero or potentially non-zero interaction between a pair of residues in a pose.
Implements core::scoring::methods::LongRangeTwoBodyEnergy.
References core::pose::Pose::constraint_set().
◆ defines_score_for_residue_pair()
|
overridevirtual |
Returns false if residue1 and residue2 have no inter-residue pair constraints or if the two residues are not moving wrt each other.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
◆ eval_atom_derivative()
|
overridevirtual |
called during gradient-based minimization inside dfunc
F1 and F2 are not zeroed – contributions from this atom are just summed in
Reimplemented from core::scoring::methods::EnergyMethod.
References core::pose::Pose::constraint_set().
◆ eval_dof_derivative()
| Real core::scoring::constraints::ConstraintsEnergy::eval_dof_derivative | ( | id::DOF_ID const & | id, |
| id::TorsionID const & | tor, | ||
| pose::Pose const & | pose, | ||
| ScoreFunction const & | scorefxn, | ||
| EnergyMap const & | weights | ||
| ) | const |
Evaluate dof derivatives when DOF_constraints are in use.
uses the dof constraints – depricated interface
◆ eval_intrares_derivatives()
|
overridevirtual |
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.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
References core::scoring::cst_res_data, core::scoring::ResSingleMinimizationData::get_data(), core::conformation::Residue::natoms(), and core::conformation::Residue::seqpos().
◆ eval_intrares_energy()
|
overridevirtual |
Evaluate the intra-residue constraint energy for a given residue.
Implements core::scoring::methods::TwoBodyEnergy.
References core::pose::Pose::constraint_set().
◆ eval_intrares_energy_ext()
|
overridevirtual |
Evaluate the intra-residue energies using ConstraintCOPs cached in the data_cache object.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
References core::scoring::cst_res_data, core::scoring::ResSingleMinimizationData::get_data(), and core::scoring::ScoreFunction::weights().
◆ eval_intraresidue_dof_derivative()
|
overridevirtual |
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.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
◆ eval_residue_pair_derivatives()
|
overridevirtual |
Evaluate the derivative for an atom in rsd1 with respect to rsd2 in the context of a particular pose, and increment the F1 and F2 vectors.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
References core::scoring::cst_respair_data, core::scoring::ResPairMinimizationData::get_data(), core::conformation::Residue::natoms(), and core::conformation::Residue::seqpos().
◆ finalize_total_energy()
|
overridevirtual |
called at the end of energy evaluation
called at the end of energy evaluation; allows for the evaluation of constraints that cannot be decomposed into residue pairs. Defers entirely to cst_set.
Reimplemented from core::scoring::methods::EnergyMethod.
References core::pose::Pose::constraint_set().
◆ indicate_required_context_graphs()
|
overridevirtual |
constraints are context independent
Implements core::scoring::methods::EnergyMethod.
◆ long_range_type()
|
overridevirtual |
Identification for this LR2B energy that links it with the long-range energy container that it stores in the Energies object.
Implements core::scoring::methods::LongRangeTwoBodyEnergy.
References core::scoring::methods::constraints_lr.
◆ minimize_in_whole_structure_context()
|
overridevirtual |
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.
◆ prepare_constraints_energy_container()
| void core::scoring::constraints::ConstraintsEnergy::prepare_constraints_energy_container | ( | pose::Pose & | pose | ) | const |
References core::pose::Pose::constraint_set(), core::scoring::methods::constraints_lr, core::pose::Pose::energies(), core::scoring::Energies::long_range_container(), core::scoring::Energies::nonconst_long_range_container(), and core::scoring::Energies::set_long_range_container().
Referenced by setup_for_packing(), and setup_for_scoring().
◆ requires_a_setup_for_derivatives_for_residue_opportunity()
|
overridevirtual |
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.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
◆ requires_a_setup_for_derivatives_for_residue_pair_opportunity()
|
overridevirtual |
Ask for the opportunity to setup for derivative evaluation.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
◆ requires_a_setup_for_scoring_for_residue_opportunity_during_minimization()
|
overridevirtual |
Ask for the opportunity to setup for scoring for evaluating 1-body constraints.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
◆ requires_a_setup_for_scoring_for_residue_pair_opportunity()
|
overridevirtual |
Request the opportunity to setup for scoring.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
◆ residue_pair_energy()
|
overridevirtual |
Evaluate constraint residue_pair_energy. Defers entirely to cst_set.
Implements core::scoring::methods::TwoBodyEnergy.
References core::pose::Pose::constraint_set().
◆ residue_pair_energy_ext()
|
overridevirtual |
The ConstraintsEnergy caches all residue-pair constraints operating between a particular pair of residues in the min_data object so that it does not need to search for those constraints when scoring during minimization.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
References core::scoring::cst_respair_data, core::scoring::ResPairMinimizationData::get_data(), and core::scoring::ScoreFunction::weights().
◆ setup_for_derivatives()
|
overridevirtual |
Setup constraint-set specific derivatives.
Reimplemented from core::scoring::methods::EnergyMethod.
References core::pose::Pose::constraint_set().
◆ setup_for_derivatives_for_residue()
|
overridevirtual |
Do any setup work necessary before evaluating the derivatives for this residue.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
References core::scoring::cst_res_data, and core::scoring::ResSingleMinimizationData::get_data().
◆ setup_for_derivatives_for_residue_pair()
|
overridevirtual |
Do any setup work necessary before evaluating the derivatives for this residue pair.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
References core::scoring::cst_respair_data, and core::scoring::ResPairMinimizationData::get_data().
◆ setup_for_minimizing_for_residue()
|
overridevirtual |
Cache the intra-residue constraints in the ResSingleMinimizationData object for rapid retrieval during minimization and allow the constraints to store data in the res_data_cache if they need to.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
References core::pose::Pose::constraint_set().
◆ setup_for_minimizing_for_residue_pair()
|
overridevirtual |
Cache the residue-pair constraints in the ResPairMinimizationData object for rapid retrieval during minimization and allow constraints to cache useful data in the respair_data_cache if they need to.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
References core::pose::Pose::constraint_set().
◆ setup_for_packing()
|
overridevirtual |
Make sure that the ConstraintsEnergyContainer is ready for packing.
Reimplemented from core::scoring::methods::EnergyMethod.
References prepare_constraints_energy_container().
◆ setup_for_scoring()
|
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 core::pose::Pose::constraint_set(), and prepare_constraints_energy_container().
◆ setup_for_scoring_for_residue()
|
overridevirtual |
Allow the component constraints to setup for scoring for a particular residue.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
References core::scoring::cst_res_data, and core::scoring::ResSingleMinimizationData::get_data().
◆ setup_for_scoring_for_residue_pair()
|
overridevirtual |
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.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
References core::scoring::cst_respair_data, and core::scoring::ResPairMinimizationData::get_data().
◆ use_extended_intrares_energy_interface()
|
overridevirtual |
request of minimization routines that they use the extended intraresidue energy interface
Reimplemented from core::scoring::methods::TwoBodyEnergy.
◆ use_extended_residue_pair_energy_interface()
|
overridevirtual |
Returns true as the ConstraintsEnergy caches its residue pair constraints in the ResPairMinimicationData objects stored on edges in the MinimizationGraph.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
◆ version()
|
overridevirtual |
Return the version of the energy method.
Implements core::scoring::methods::EnergyMethod.
Member Data Documentation
◆ __pad0__
| core::scoring::constraints::ConstraintsEnergy::__pad0__ |
◆ __pad1__
| core::scoring::constraints::ConstraintsEnergy::__pad1__ |
The documentation for this class was generated from the following files:
- src/core/scoring/constraints/ConstraintsEnergy.hh
- src/core/scoring/constraints/ConstraintsEnergy.cc
