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Rosetta 3.5
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Rosetta 3.5
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#include <EtableEnergy.hh>
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 |
| AnalyticEtableEvaluator & | intrares_evaluator () |
| AnalyticEtableEvaluator & | interres_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_ |
Definition at line 631 of file EtableEnergy.hh.
Definition at line 634 of file EtableEnergy.hh.
| typedef BaseEtableEnergy< AnalyticEtableEnergy > core::scoring::etable::AnalyticEtableEnergy::parent |
Definition at line 633 of file EtableEnergy.hh.
| core::scoring::etable::AnalyticEtableEnergy::AnalyticEtableEnergy | ( | Etable const & | etable_in, |
| methods::EnergyMethodOptions const & | options | ||
| ) |
construction with an etable
Definition at line 162 of file EtableEnergy.cc.
References core::scoring::fa_atr, core::scoring::fa_intra_atr, core::scoring::fa_intra_rep, core::scoring::fa_intra_sol, core::scoring::fa_rep, core::scoring::fa_sol, interres_evaluator_, intrares_evaluator_, and core::scoring::etable::EtableEvaluator::set_scoretypes().
Referenced by clone().
| core::scoring::etable::AnalyticEtableEnergy::AnalyticEtableEnergy | ( | AnalyticEtableEnergy const & | src) |
explicit copy constructor
Definition at line 174 of file EtableEnergy.cc.
|
virtual |
clone
Implements core::scoring::methods::EnergyMethod.
Definition at line 184 of file EtableEnergy.cc.
References AnalyticEtableEnergy().
|
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.
Definition at line 199 of file EtableEnergy.cc.
References core::scoring::fa_intra_atr, core::scoring::fa_intra_rep, and core::scoring::fa_intra_sol.
|
virtual |
Evaluate the intra-residue energy for a given residue.
Implements core::scoring::methods::TwoBodyEnergy.
Definition at line 210 of file EtableEnergy.cc.
References core::pose::Pose::energies(), core::scoring::etable::BaseEtableEnergy< AnalyticEtableEnergy >::get_intrares_countpair(), core::conformation::Residue::has_variant_type(), intrares_evaluator_, core::chemical::REPLONLY, core::scoring::etable::AnalyticEtableEvaluator::residue_atom_pair_energy(), core::scoring::etable::EtableEvaluator::st_atr(), core::scoring::etable::EtableEvaluator::st_rep(), core::scoring::etable::EtableEvaluator::st_sol(), and core::scoring::Energies::use_nblist().
|
inline |
Definition at line 689 of file EtableEnergy.hh.
References interres_evaluator_.
|
inline |
Definition at line 692 of file EtableEnergy.hh.
References interres_evaluator_.
|
inline |
Definition at line 688 of file EtableEnergy.hh.
References intrares_evaluator_.
|
inline |
Definition at line 691 of file EtableEnergy.hh.
References intrares_evaluator_.
| void core::scoring::etable::AnalyticEtableEnergy::setup_for_scoring_ | ( | pose::Pose const & | pose, |
| scoring::ScoreFunction const & | |||
| ) | const |
Definition at line 189 of file EtableEnergy.cc.
References core::scoring::etable::Etable::atom_set(), core::chemical::ResidueType::atom_type_set_ptr(), core::scoring::etable::BaseEtableEnergy< AnalyticEtableEnergy >::etable(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::type().
|
privatevirtual |
Return the version of the energy method.
Implements core::scoring::methods::EnergyMethod.
Definition at line 233 of file EtableEnergy.cc.
|
mutableprivate |
Definition at line 703 of file EtableEnergy.hh.
Referenced by AnalyticEtableEnergy(), and interres_evaluator().
|
mutableprivate |
Definition at line 702 of file EtableEnergy.hh.
Referenced by AnalyticEtableEnergy(), eval_intrares_energy(), and intrares_evaluator().
1.8.4