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core::scoring::etable::AnalyticEtableEnergy Class Reference

#include <EtableEnergy.hh>

Inheritance diagram for core::scoring::etable::AnalyticEtableEnergy:
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Public Types

typedef BaseEtableEnergy
< AnalyticEtableEnergy
parent
 
typedef AnalyticEtableEvaluator Evaluator
 

Public Member Functions

 AnalyticEtableEnergy (Etable const &etable_in, methods::EnergyMethodOptions const &options)
 construction with an etable More...
 
 AnalyticEtableEnergy (AnalyticEtableEnergy const &)
 explicit copy constructor More...
 
EnergyMethodOP clone () const
 clone More...
 
void setup_for_scoring_ (pose::Pose const &pose, scoring::ScoreFunction const &) const
 
virtual bool defines_intrares_energy (EnergyMap const &) const
 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...
 
virtual void eval_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluate the intra-residue energy for a given residue. More...
 
AnalyticEtableEvaluator const & intrares_evaluator () const
 
AnalyticEtableEvaluator const & interres_evaluator () const
 
AnalyticEtableEvaluatorintrares_evaluator ()
 
AnalyticEtableEvaluatorinterres_evaluator ()
 
- Public Member Functions inherited from core::scoring::etable::BaseEtableEnergy< AnalyticEtableEnergy >
 BaseEtableEnergy (methods::EnergyMethodCreatorOP creator, Etable const &etable_in, methods::EnergyMethodOptions const &options)
 construction with an etable More...
 
 BaseEtableEnergy (BaseEtableEnergy< AnalyticEtableEnergy > const &)
 explicit copy constructor, since the BaseEtableEnergy now contains OP data More...
 
 BaseEtableEnergy (Etable const &etable_in, methods::EnergyMethodOptions const &options, ScoreType st_atr, ScoreType st_rep, ScoreType st_sol)
 construction with an etable More...
 
 BaseEtableEnergy (Etable const &etable_in, methods::EnergyMethodOptions const &options, ScoreType st_atr, ScoreType st_rep, ScoreType st_sol)
 construction with an etable More...
 
virtual bool minimize_in_whole_structure_context (pose::Pose const &) const
 NO! friend class core::scoring::rna::RNA_FullAtomVDW_BasePhosphateCreator;. More...
 
virtual void setup_for_minimizing (pose::Pose &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map) const
 stashes nblist if pose.energies().use_nblist_auto_update() is true This is only invoked, now, if the neighborlist-autoupdate flag is on. More...
 
virtual void setup_for_minimizing (pose::Pose &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map) const
 stashes nblist if use_nblist is true More...
 
virtual void setup_for_minimizing (pose::Pose &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map) const
 stashes nblist if use_nblist is true More...
 
virtual void setup_for_scoring (pose::Pose &pose, ScoreFunction const &scfxn) const
 check compatibility with atomtypeset More...
 
virtual void setup_for_scoring (pose::Pose &pose, ScoreFunction const &scfxn) const
 check compatibility with atomtypeset More...
 
virtual void setup_for_scoring (pose::Pose &pose, ScoreFunction const &scfxn) const
 check compatibility with atomtypeset More...
 
virtual void setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) const
 Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. More...
 
virtual void setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) const
 Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. More...
 
virtual void setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) const
 Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. More...
 
virtual void setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const
 
virtual void setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const
 
virtual void setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const
 
virtual void prepare_rotamers_for_packing (pose::Pose const &pose, conformation::RotamerSetBase &set) const
 
virtual void prepare_rotamers_for_packing (pose::Pose const &pose, conformation::RotamerSetBase &set) const
 
virtual void prepare_rotamers_for_packing (pose::Pose const &pose, conformation::RotamerSetBase &set) const
 
virtual void update_residue_for_packing (pose::Pose &pose, Size resid) const
 
virtual void update_residue_for_packing (pose::Pose &pose, Size resid) const
 
virtual void update_residue_for_packing (pose::Pose &pose, Size resid) const
 
count_pair::CountPairFunctionCOP get_count_pair_function (Size res1, Size res2, pose::Pose const &pose, ScoreFunction const &sfxn) const
 
count_pair::CountPairFunctionCOP get_count_pair_function (conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &pose, ScoreFunction const &sfxn) const
 
count_pair::CountPairFunctionCOP get_count_pair_function (Size res1, Size res2, pose::Pose const &pose, ScoreFunction const &sfxn) const
 
count_pair::CountPairFunctionCOP get_count_pair_function (conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &pose, ScoreFunction const &sfxn) const
 
count_pair::CountPairFunctionCOP get_count_pair_function (Size res1, Size res2, pose::Pose const &pose, ScoreFunction const &sfxn) const
 
count_pair::CountPairFunctionCOP get_count_pair_function (conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &pose, ScoreFunction const &sfxn) const
 
count_pair::CountPairFunctionOP get_intrares_countpair (conformation::Residue const &res, pose::Pose const &pose, ScoreFunction const &sfxn) const
 
count_pair::CountPairFunctionOP get_intrares_countpair (conformation::Residue const &res, pose::Pose const &pose, ScoreFunction const &sfxn) const
 
count_pair::CountPairFunctionOP get_intrares_countpair (conformation::Residue const &res, pose::Pose const &pose, ScoreFunction const &sfxn) const
 
virtual void residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap. More...
 
virtual void residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap. More...
 
virtual void residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap. More...
 
virtual bool use_extended_residue_pair_energy_interface () const
 APL – note, new. More...
 
virtual 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
 APL – note, new. More...
 
virtual void setup_for_minimizing_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, ResSingleMinimizationData const &res1_data_cache, ResSingleMinimizationData const &res2_data_cache, ResPairMinimizationData &min_data) const
 APL – note, new. More...
 
virtual bool requires_a_setup_for_scoring_for_residue_opportunity (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 &, 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 &, ResSingleMinimizationData &min_data) 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 &, 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 &, ResPairMinimizationData &data_cache) const
 Do any setup work necessary before evaluating the derivatives for this residue pair. More...
 
virtual void eval_residue_pair_derivatives (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &, ResSingleMinimizationData const &, ResPairMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_at_derivs, utility::vector1< DerivVectorPair > &r2_at_derivs) const
 APL – note, new. More...
 
virtual void backbone_backbone_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluates the interaction between the backbone of rsd1 and the backbone of rsd2 and accumulates the unweighted energy. More...
 
virtual void backbone_backbone_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluates the interaction between the backbone of rsd1 and the backbone of rsd2 and accumulates the unweighted energy. More...
 
virtual void backbone_backbone_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluates the interaction between the backbone of rsd1 and the backbone of rsd2 and accumulates the unweighted 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
 Evaluates the interaction between the backbone of rsd1 and the sidechain of rsd2 and accumulates the unweighted 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
 Evaluates the interaction between the backbone of rsd1 and the sidechain of rsd2 and accumulates the unweighted 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
 Evaluates the interaction between the backbone of rsd1 and the sidechain of rsd2 and accumulates the unweighted 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
 Evaluates the interaction between the sidechain of rsd1 and the sidechain of rsd2 and accumulates the unweighted 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
 Evaluates the interaction between the sidechain of rsd1 and the sidechain of rsd2 and accumulates the unweighted 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
 Evaluates the interaction between the sidechain of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy. 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 derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...
 
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 derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...
 
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 derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...
 
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 rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...
 
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 rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...
 
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 rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...
 
virtual bool use_extended_intrares_energy_interface () const
 APL – note, new. More...
 
virtual void eval_intrares_energy_ext (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 APL – note, new. More...
 
virtual void setup_for_minimizing_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, ResSingleMinimizationData &min_data) const
 APL – note, new. 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
 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 void bump_energy_full (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 
virtual void bump_energy_full (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 
virtual void bump_energy_full (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 
virtual void bump_energy_backbone (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 
virtual void bump_energy_backbone (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 
virtual void bump_energy_backbone (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 
virtual void finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) const
 called at the end of energy evaluation More...
 
virtual void finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) const
 called at the end of energy evaluation More...
 
virtual void finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) const
 called at the end of energy evaluation More...
 
virtual 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
 called during gradient-based minimization inside dfunc More...
 
virtual 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
 called during gradient-based minimization inside dfunc More...
 
virtual 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
 called during gradient-based minimization inside dfunc More...
 
void prepare_for_residue_pair (Size const res1, Size const res2, pose::Pose const &pose) const
 Should/Could these inlined" in a separate .inline.hh? More...
 
void prepare_for_residue_pair (Size const res1, Size const res2, pose::Pose const &pose) const
 Should/Could these inlined" in a separate .inline.hh? More...
 
void prepare_for_residue_pair (Size const res1, Size const res2, pose::Pose const &pose) const
 Should/Could these inlined" in a separate .inline.hh? More...
 
void atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, EnergyMap &emap, Real &dsq) const
 
void atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb, Real &dsq) const
 for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication. More...
 
void atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, AtomPairEnergy &ape) const
 APL – consider reinstating this function! More...
 
void atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, EnergyMap &emap, Real &dsq) const
 
void atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb, Real &dsq) const
 for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication. More...
 
void atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, EnergyMap &emap, Real &dsq) const
 
void atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb, Real &dsq) const
 for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication. More...
 
void pair_energy_H (conformation::Atom const &atom1, conformation::Atom const &atom2, Real weight, EnergyMap &emap) const
 APL – Consider reinstating this function! More...
 
void pair_energy_H (conformation::Atom const &atom1, conformation::Atom const &atom2, Real weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb) const
 
void pair_energy_H (conformation::Atom const &atom1, conformation::Atom const &atom2, Real weight, EnergyMap &emap) const
 
void pair_energy_H (conformation::Atom const &atom1, conformation::Atom const &atom2, Real weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb) const
 
void pair_energy_H (conformation::Atom const &atom1, conformation::Atom const &atom2, Real weight, EnergyMap &emap) const
 
Real hydrogen_interaction_cutoff2 () const
 
Real hydrogen_interaction_cutoff2 () const
 
Real hydrogen_interaction_cutoff2 () const
 
virtual Distance atomic_interaction_cutoff () const
 Etable atomic distance cutoff is 5.5 A. More...
 
virtual Distance atomic_interaction_cutoff () const
 Etable atomic distance cutoff is 5.5 A. More...
 
virtual Distance atomic_interaction_cutoff () const
 Etable atomic distance cutoff is 5.5 A. More...
 
virtual bool divides_backbone_and_sidechain_energetics () const
 A derived class should return true for this function if it implements its own versions of the backbone_backbone_energy, backbone_sidechain_energy and sidechain_sidechain_energy functions. The default sidechain_sidechain_energy implemented by the TwoBodyEnergy base class calls residue_pair_energy. If the derived class implements its own versions of these functions, then calling code may avoid calling it on pairs of residues that are "provably distant" based on a pair of bounding spheres for a sidechains and backbones and this method's atomic_interaction_cutoff energy method. More...
 
virtual bool divides_backbone_and_sidechain_energetics () const
 A derived class should return true for this function if it implements its own versions of the backbone_backbone_energy, backbone_sidechain_energy and sidechain_sidechain_energy functions. The default sidechain_sidechain_energy implemented by the TwoBodyEnergy base class calls residue_pair_energy. If the derived class implements its own versions of these functions, then calling code may avoid calling it on pairs of residues that are "provably distant" based on a pair of bounding spheres for a sidechains and backbones and this method's atomic_interaction_cutoff energy method. More...
 
virtual void indicate_required_context_graphs (utility::vector1< bool > &) const
 Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed. More...
 
virtual void indicate_required_context_graphs (utility::vector1< bool > &) const
 Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed. More...
 
virtual void indicate_required_context_graphs (utility::vector1< bool > &) const
 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 memb_atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, EnergyMap &emap, Real &dsq) const
 pba More...
 
void memb_atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb, Real &dsq) const
 for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication. More...
 
void memb_atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, EnergyMap &emap, Real &dsq) const
 pba More...
 
void memb_atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb, Real &dsq) const
 for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication. More...
 
void fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const
 pba More...
 
void fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const
 
void fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const
 pba More...
 
void fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const
 
Real eval_dE_dR_over_r (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
 
Real eval_dE_dR_over_r (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
 
Real memb_eval_dE_dR_over_r (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
 pba More...
 
Real memb_eval_dE_dR_over_r (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
 pba More...
 
Energy sum_energies (Real atr, Real rep, Real solv, Real bb) const
 Inline Methods For Trie-vs-Trie Algorithm. More...
 
Energy sum_energies (Real atr, Real rep, Real solv, Real bb) const
 Inline Methods For Trie-vs-Trie Algorithm. More...
 
Energy heavyatom_heavyatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2, DistanceSquared &d2) const
 
Energy heavyatom_heavyatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2, DistanceSquared &d2) const
 
Energy heavyatom_hydrogenatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2) const
 
Energy heavyatom_hydrogenatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2) const
 
Energy hydrogenatom_heavyatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2) const
 
Energy hydrogenatom_heavyatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2) const
 
Energy hydrogenatom_hydrogenatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2) const
 
Energy hydrogenatom_hydrogenatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2) const
 
- Public Member Functions inherited from core::scoring::methods::ContextIndependentTwoBodyEnergy
 ContextIndependentTwoBodyEnergy (EnergyMethodCreatorOP)
 Constructor with an EnergyMethodCreator to inform the ancestor EnergyMethod class which ScoreTypes this EnergyMethod is responsible for computing. More...
 
virtual ~ContextIndependentTwoBodyEnergy ()
 
EnergyMethodType method_type () const
 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::ShortRangeTwoBodyEnergy
 ShortRangeTwoBodyEnergy (EnergyMethodCreatorOP)
 Constructor with EnergyMethodCreator to provide to the EnergyMethod grandparent the list of the ScoreTypes this EnergyMethod is responsible for computing. More...
 
virtual ~ShortRangeTwoBodyEnergy ()
 
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 rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...
 
- 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...
 
virtual ~TwoBodyEnergy ()
 
virtual bool defines_score_for_residue_pair (conformation::Residue const &res1, conformation::Residue const &res2, bool res_moving_wrt_eachother) const
 During minimization, energy methods are allowed to decide that they say nothing about a particular residue pair (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default implementation returns "true" for all residue pairs. Context-dependent two-body energies have the option of behaving as if they are context-independent by returning "false" for residue pairs that do no move wrt each other. More...
 
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 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 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...
 
- 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...
 
 EnergyMethod (EnergyMethod const &src)
 Copy constructor copies over the score types of the source. More...
 
virtual ~EnergyMethod ()
 
virtual void update_residue_for_packing (pose::Pose &, Size resid) const
 ensure this function gets called. The default behavior is to do nothing. 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...
 
ScoreTypes const & score_types () const
 Returns the score types that this energy method computes. More...
 

Private Member Functions

virtual core::Size version () const
 Return the version of the energy method. More...
 

Private Attributes

AnalyticEtableEvaluator intrares_evaluator_
 
AnalyticEtableEvaluator interres_evaluator_
 

Additional Inherited Members

- Public Attributes inherited from core::scoring::etable::BaseEtableEnergy< AnalyticEtableEnergy >
 __pad0__
 
 __pad1__
 
- Protected Member Functions inherited from core::scoring::etable::BaseEtableEnergy< AnalyticEtableEnergy >
trie::TrieCountPairBaseOP get_count_pair_function_trie (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn) const
 Inline Methods For Trie-vs-Trie Algorithm. More...
 
trie::TrieCountPairBaseOP get_count_pair_function_trie (conformation::Residue const &res1, conformation::Residue const &res2, trie::RotamerTrieBaseCOP trie1, trie::RotamerTrieBaseCOP trie2, pose::Pose const &pose, ScoreFunction const &sfxn) const
 
trie::TrieCountPairBaseOP get_count_pair_function_trie (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn) const
 
trie::TrieCountPairBaseOP get_count_pair_function_trie (conformation::Residue const &res1, conformation::Residue const &res2, trie::RotamerTrieBaseCOP trie1, trie::RotamerTrieBaseCOP trie2, pose::Pose const &pose, ScoreFunction const &sfxn) const
 
trie::TrieCountPairBaseOP get_count_pair_function_trie (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn) const
 
trie::TrieCountPairBaseOP get_count_pair_function_trie (conformation::Residue const &res1, conformation::Residue const &res2, trie::RotamerTrieBaseCOP trie1, trie::RotamerTrieBaseCOP trie2, pose::Pose const &pose, ScoreFunction const &sfxn) const
 
count_pair::CPCrossoverBehavior determine_crossover_behavior (conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &, ScoreFunction const &sfxn) const
 
count_pair::CPCrossoverBehavior determine_crossover_behavior (conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &, ScoreFunction const &sfxn) const
 
count_pair::CPCrossoverBehavior determine_crossover_behavior (conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &, ScoreFunction const &sfxn) const
 
etrie::EtableRotamerTrieOP create_rotamer_trie (conformation::RotamerSetBase const &rotset, pose::Pose const &pose) const
 
etrie::EtableRotamerTrieOP create_rotamer_trie (conformation::Residue const &residue, pose::Pose const &) const
 
etrie::EtableRotamerTrieOP create_rotamer_trie (conformation::RotamerSetBase const &rotset, pose::Pose const &pose) const
 
etrie::EtableRotamerTrieOP create_rotamer_trie (conformation::RotamerSetBase const &rotset, pose::Pose const &pose) const
 
etrie::EtableRotamerTrieOP create_rotamer_trie_2 (conformation::RotamerSetBase const &rotset) const
 
etrie::EtableRotamerTrieOP create_rotamer_trie_2 (conformation::RotamerSetBase const &rotset) const
 
etrie::EtableRotamerTrieOP create_rotamer_trie_2 (conformation::RotamerSetBase const &rotset) const
 
etrie::EtableRotamerTrieOP create_rotamer_trie_1 (conformation::RotamerSetBase const &rotset, Size connection_type) const
 
etrie::EtableRotamerTrieOP create_rotamer_trie_1 (conformation::RotamerSetBase const &rotset, Size connection_type) const
 
etrie::EtableRotamerTrieOP create_rotamer_trie_1 (conformation::RotamerSetBase const &rotset, Size connection_type) const
 
Real eval_dE_dR_over_r_ (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
 
Real eval_dE_dR_over_r_ (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
 
Real eval_dE_dR_over_r_ (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
 
void derived_prepare_for_residue_pair (Size const, Size const, pose::Pose const &) const
 
void derived_prepare_for_residue_pair (Size const res1, Size const res2, pose::Pose const &) const
 
void derived_prepare_for_residue_pair (Size const res1, Size const res2, pose::Pose const &) const
 
bool interpolate_bins (conformation::Atom const &atom1, conformation::Atom const &atom2, Real &d2, int &disbin, Real &frac) const
 
bool interpolate_bins (conformation::Atom const &atom1, conformation::Atom const &atom2, Real &d2, int &disbin, Real &frac) const
 
bool interpolate_bins (conformation::Atom const &atom1, conformation::Atom const &atom2, Real &d2, int &disbin, Real &frac) const
 
ScoreType rep_scoretype () const
 
ScoreType rep_scoretype () const
 
ScoreType rep_scoretype () const
 
Etable const & etable () const
 
void fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const
 
void fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const
 
void atom_pair_energy_ (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Real &atr, Real &rep, Real &solv, Real &bb, Real &dsq) const
 
void atom_pair_energy_ (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Real &atr, Real &rep, Real &solv, Real &bb, Real &dsq) const
 
void memb_atom_pair_energy_ (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Real &atr, Real &rep, Real &solv, Real &bb, Real &dsq) const
 
void memb_atom_pair_energy_ (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Real &atr, Real &rep, Real &solv, Real &bb, Real &dsq) const
 
void pair_energy_H_ (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Real &atr, Real &rep, Real &solv, Real &bb) const
 
void pair_energy_H_ (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Real &atr, Real &rep, Real &solv, Real &bb) const
 
Real memb_eval_dE_dR_over_r_ (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
 pba More...
 
Real memb_eval_dE_dR_over_r_ (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
 pba More...
 
void set_scoretypes (ScoreType atr_type, ScoreType rep_type, ScoreType sol_type) const
 
void set_scoretypes (ScoreType atr_type, ScoreType rep_type, ScoreType sol_type) const
 

Member Typedef Documentation

Constructor & Destructor Documentation

core::scoring::etable::AnalyticEtableEnergy::AnalyticEtableEnergy ( Etable const &  etable_in,
methods::EnergyMethodOptions const &  options 
)
core::scoring::etable::AnalyticEtableEnergy::AnalyticEtableEnergy ( AnalyticEtableEnergy const &  src)

explicit copy constructor

Member Function Documentation

methods::EnergyMethodOP core::scoring::etable::AnalyticEtableEnergy::clone ( ) const
virtual
bool core::scoring::etable::AnalyticEtableEnergy::defines_intrares_energy ( EnergyMap const &  weights) const
virtual

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.

References core::scoring::fa_intra_atr, core::scoring::fa_intra_rep, and core::scoring::fa_intra_sol.

void core::scoring::etable::AnalyticEtableEnergy::eval_intrares_energy ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const
virtual
AnalyticEtableEvaluator const& core::scoring::etable::AnalyticEtableEnergy::interres_evaluator ( ) const
inline

References interres_evaluator_.

AnalyticEtableEvaluator& core::scoring::etable::AnalyticEtableEnergy::interres_evaluator ( )
inline

References interres_evaluator_.

AnalyticEtableEvaluator const& core::scoring::etable::AnalyticEtableEnergy::intrares_evaluator ( ) const
inline

References intrares_evaluator_.

AnalyticEtableEvaluator& core::scoring::etable::AnalyticEtableEnergy::intrares_evaluator ( )
inline

References intrares_evaluator_.

void core::scoring::etable::AnalyticEtableEnergy::setup_for_scoring_ ( pose::Pose const &  pose,
scoring::ScoreFunction const &   
) const
core::Size core::scoring::etable::AnalyticEtableEnergy::version ( ) const
privatevirtual

Return the version of the energy method.

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

Member Data Documentation

AnalyticEtableEvaluator core::scoring::etable::AnalyticEtableEnergy::interres_evaluator_
mutableprivate
AnalyticEtableEvaluator core::scoring::etable::AnalyticEtableEnergy::intrares_evaluator_
mutableprivate

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