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core::scoring::constraints::ConstraintsEnergy Class Reference

#include <ConstraintsEnergy.hh>

Inheritance diagram for core::scoring::constraints::ConstraintsEnergy:
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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
 
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 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 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 finalize_after_derivatives (pose::Pose &, ScoreFunction const &) const
 called at the end of derivatives evaluation 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
 
 __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

core::scoring::constraints::ConstraintsEnergy::ConstraintsEnergy ( )
core::scoring::constraints::ConstraintsEnergy::~ConstraintsEnergy ( )
overridedefault

Member Function Documentation

methods::EnergyMethodOP core::scoring::constraints::ConstraintsEnergy::clone ( ) const
overridevirtual
bool core::scoring::constraints::ConstraintsEnergy::defines_high_order_terms ( pose::Pose const &  pose) const
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().

bool core::scoring::constraints::ConstraintsEnergy::defines_intrares_dof_derivatives ( pose::Pose const &  p) const
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.

bool core::scoring::constraints::ConstraintsEnergy::defines_intrares_energy ( EnergyMap const &  weights) const
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.

bool core::scoring::constraints::ConstraintsEnergy::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.

References core::pose::Pose::constraint_set().

bool core::scoring::constraints::ConstraintsEnergy::defines_score_for_residue_pair ( conformation::Residue const &  res1,
conformation::Residue const &  res2,
bool  res_moving_wrt_eachother 
) const
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.

void core::scoring::constraints::ConstraintsEnergy::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
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().

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

void core::scoring::constraints::ConstraintsEnergy::eval_intrares_derivatives ( conformation::Residue const &  rsd,
ResSingleMinimizationData const &  min_data,
pose::Pose const &  pose,
EnergyMap const &  weights,
utility::vector1< DerivVectorPair > &  atom_derivs 
) const
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::constraints::CstMinimizationData::constraints(), core::scoring::cst_res_data, core::scoring::constraints::Constraints::eval_intrares_atom_derivative(), core::scoring::ResSingleMinimizationData::get_data(), core::conformation::Residue::natoms(), and core::conformation::Residue::seqpos().

void core::scoring::constraints::ConstraintsEnergy::eval_intrares_energy ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const
overridevirtual

Evaluate the intra-residue constraint energy for a given residue.

Implements core::scoring::methods::TwoBodyEnergy.

References core::pose::Pose::constraint_set().

void core::scoring::constraints::ConstraintsEnergy::eval_intrares_energy_ext ( conformation::Residue const &  rsd,
ResSingleMinimizationData const &  data_cache,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const
overridevirtual
Real core::scoring::constraints::ConstraintsEnergy::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
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.

void core::scoring::constraints::ConstraintsEnergy::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
overridevirtual
void core::scoring::constraints::ConstraintsEnergy::finalize_total_energy ( pose::Pose pose,
ScoreFunction const &  sfxn,
EnergyMap totals 
) const
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().

void core::scoring::constraints::ConstraintsEnergy::indicate_required_context_graphs ( utility::vector1< bool > &  ) const
overridevirtual

constraints are context independent

Implements core::scoring::methods::EnergyMethod.

methods::LongRangeEnergyType core::scoring::constraints::ConstraintsEnergy::long_range_type ( ) const
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.

bool core::scoring::constraints::ConstraintsEnergy::minimize_in_whole_structure_context ( pose::Pose const &  ) const
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.

void core::scoring::constraints::ConstraintsEnergy::prepare_constraints_energy_container ( pose::Pose pose) const
bool core::scoring::constraints::ConstraintsEnergy::requires_a_setup_for_derivatives_for_residue_opportunity ( pose::Pose const &  pose) const
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.

bool core::scoring::constraints::ConstraintsEnergy::requires_a_setup_for_derivatives_for_residue_pair_opportunity ( pose::Pose const &  pose) const
overridevirtual

Ask for the opportunity to setup for derivative evaluation.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

bool core::scoring::constraints::ConstraintsEnergy::requires_a_setup_for_scoring_for_residue_opportunity_during_minimization ( pose::Pose const &  pose) const
overridevirtual

Ask for the opportunity to setup for scoring for evaluating 1-body constraints.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

bool core::scoring::constraints::ConstraintsEnergy::requires_a_setup_for_scoring_for_residue_pair_opportunity ( pose::Pose const &  pose) const
overridevirtual

Request the opportunity to setup for scoring.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

void core::scoring::constraints::ConstraintsEnergy::residue_pair_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const
overridevirtual

Evaluate constraint residue_pair_energy. Defers entirely to cst_set.

Implements core::scoring::methods::TwoBodyEnergy.

References core::pose::Pose::constraint_set().

void core::scoring::constraints::ConstraintsEnergy::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
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::constraints::CstMinimizationData::constraints(), core::scoring::cst_respair_data, core::scoring::ResPairMinimizationData::get_data(), core::scoring::constraints::Constraints::residue_pair_energy(), and core::scoring::ScoreFunction::weights().

void core::scoring::constraints::ConstraintsEnergy::setup_for_derivatives ( pose::Pose pose,
ScoreFunction const &  scfxn 
) const
overridevirtual

Setup constraint-set specific derivatives.

Reimplemented from core::scoring::methods::EnergyMethod.

References core::pose::Pose::constraint_set().

void core::scoring::constraints::ConstraintsEnergy::setup_for_derivatives_for_residue ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
scoring::ScoreFunction const &  sfxn,
ResSingleMinimizationData min_data,
basic::datacache::BasicDataCache &  res_data_cache 
) const
overridevirtual
void core::scoring::constraints::ConstraintsEnergy::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
overridevirtual
void core::scoring::constraints::ConstraintsEnergy::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
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().

void core::scoring::constraints::ConstraintsEnergy::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
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().

void core::scoring::constraints::ConstraintsEnergy::setup_for_packing ( pose::Pose pose,
utility::vector1< bool > const &  residues_repacking,
utility::vector1< bool > const &  residues_designing 
) const
overridevirtual

Make sure that the ConstraintsEnergyContainer is ready for packing.

Reimplemented from core::scoring::methods::EnergyMethod.

References prepare_constraints_energy_container().

void core::scoring::constraints::ConstraintsEnergy::setup_for_scoring ( pose::Pose ,
ScoreFunction const &   
) const
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().

void core::scoring::constraints::ConstraintsEnergy::setup_for_scoring_for_residue ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
scoring::ScoreFunction const &  sfxn,
ResSingleMinimizationData min_data 
) const
overridevirtual
void core::scoring::constraints::ConstraintsEnergy::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
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::constraints::CstMinimizationData::constraints(), core::scoring::cst_respair_data, core::scoring::ResPairMinimizationData::get_data(), and core::scoring::constraints::Constraints::setup_for_scoring().

bool core::scoring::constraints::ConstraintsEnergy::use_extended_intrares_energy_interface ( ) const
overridevirtual

request of minimization routines that they use the extended intraresidue energy interface

Reimplemented from core::scoring::methods::TwoBodyEnergy.

bool core::scoring::constraints::ConstraintsEnergy::use_extended_residue_pair_energy_interface ( ) const
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.

core::Size core::scoring::constraints::ConstraintsEnergy::version ( ) const
overridevirtual

Return the version of the energy method.

Implements core::scoring::methods::EnergyMethod.

Member Data Documentation

core::scoring::constraints::ConstraintsEnergy::__pad0__
core::scoring::constraints::ConstraintsEnergy::__pad1__

The documentation for this class was generated from the following files: