Rosetta 3.4
Public Member Functions | Public Attributes | Protected Member Functions | Protected Attributes | Friends
core::scoring::etable::BaseEtableEnergy< Derived > Class Template Reference

#include <BaseMembEtableEnergy.hh>

Inheritance diagram for core::scoring::etable::BaseEtableEnergy< Derived >:
Inheritance graph
[legend]
Collaboration diagram for core::scoring::etable::BaseEtableEnergy< Derived >:
Collaboration graph
[legend]

List of all members.

Public Member Functions

 BaseEtableEnergy (methods::EnergyMethodCreatorOP creator, Etable const &etable_in, methods::EnergyMethodOptions const &options, ScoreType st_atr, ScoreType st_rep, ScoreType st_sol)
 construction with an etable
virtual bool minimize_in_whole_structure_context (pose::Pose const &) const
 The neighborlist-autoupdate algorithm requires that the EtableEnergy be able to control the definition and update for its atom-neighbors. This will bypass the standard neighborlist evaluation inside the ScoreFunction, avoiding the use the MinimizationGraph.
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.
virtual void setup_for_scoring (pose::Pose &pose, ScoreFunction const &scfxn) const
 check compatibility with atomtypeset
virtual void setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) 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 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
 and gets duplicated in a handful of other places within this class... this NEEDS to be reworked.
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.
virtual bool use_extended_residue_pair_energy_interface () const
 APL -- note, new.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
virtual bool use_extended_intrares_energy_interface () const
 APL -- note, new.
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.
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.
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.
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 finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) const
 called at the end of energy evaluation
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
void prepare_for_residue_pair (Size const res1, Size const res2, pose::Pose const &pose) const
void virtual_atom_pair_energy (EnergyMap &emap) const
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.
void atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, AtomPairEnergy &ape) 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, AtomPairEnergy &ape) const
void pair_energy_H (conformation::Atom const &atom1, conformation::Atom const &atom2, Real weight, EnergyMap &emap) const
Real eval_dE_dR_over_r (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
Real hydrogen_interaction_cutoff2 () const
virtual Distance atomic_interaction_cutoff () const
 Etable atomic distance cutoff is 5.5 A.
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.
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.
Energy sum_energies (Real atr, Real rep, Real solv, Real bb) const
 Inline Methods For Trie-vs-Trie Algorithm.
Energy heavyatom_heavyatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2, DistanceSquared &d2, Size &) const
Energy heavyatom_hydrogenatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2, Size &) const
Energy hydrogenatom_heavyatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2, Size &) const
Energy hydrogenatom_hydrogenatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2, Size &) const
 BaseEtableEnergy (Etable const &etable_in, methods::EnergyMethodOptions const &options, ScoreType st_atr, ScoreType st_rep, ScoreType st_sol)
 construction with an etable
virtual void setup_for_minimizing (pose::Pose &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map) const
 stashes nblist if use_nblist is true
virtual void setup_for_scoring (pose::Pose &pose, ScoreFunction const &scfxn) const
 check compatibility with atomtypeset
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.
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 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::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.
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.
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.
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.
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.
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.
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 finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) const
 called at the end of energy evaluation
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
void prepare_for_residue_pair (Size const res1, Size const res2, pose::Pose const &pose) const
void atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, EnergyMap &emap, Real &dsq) const
void memb_atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, EnergyMap &emap, Real &dsq) const
 pba
void fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const
 pba
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.
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.
void fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) 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 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
Real hydrogen_interaction_cutoff2 () const
virtual Distance atomic_interaction_cutoff () const
 Etable atomic distance cutoff is 5.5 A.
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.
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.
Energy sum_energies (Real atr, Real rep, Real solv, Real bb) const
 Inline Methods For Trie-vs-Trie Algorithm.
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 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
 BaseEtableEnergy (Etable const &etable_in, methods::EnergyMethodOptions const &options, ScoreType st_atr, ScoreType st_rep, ScoreType st_sol)
 construction with an etable
virtual void setup_for_minimizing (pose::Pose &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map) const
 stashes nblist if use_nblist is true
virtual void setup_for_scoring (pose::Pose &pose, ScoreFunction const &scfxn) const
 check compatibility with atomtypeset
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.
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 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::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.
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.
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.
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.
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.
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.
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 finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) const
 called at the end of energy evaluation
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
void prepare_for_residue_pair (Size const res1, Size const res2, pose::Pose const &pose) const
void atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, EnergyMap &emap, Real &dsq) const
void memb_atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, EnergyMap &emap, Real &dsq) const
 pba
void fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const
 pba
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.
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.
void fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) 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 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
Real hydrogen_interaction_cutoff2 () const
virtual Distance atomic_interaction_cutoff () const
 Etable atomic distance cutoff is 5.5 A.
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.
Energy sum_energies (Real atr, Real rep, Real solv, Real bb) const
 Inline Methods For Trie-vs-Trie Algorithm.
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 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

Public Attributes

 __pad0__:ContextIndependentTwoBodyEnergy parent
 __pad1__:EnergyMethodOP EnergyMethodOP

Protected Member Functions

trie::TrieCountPairBaseOP get_count_pair_function_trie (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn) const
 figure out the trie count pair function to use Need to refactor this so that the decision "what kind of count pair behavior should I use" can be decoupled from class instantiation, and therefore shared between the creation of the trie count pair classes and the regular count pair classes
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
etrie::EtableRotamerTrieOP create_rotamer_trie (conformation::RotamerSetBase const &rotset, pose::Pose const &pose) const
 create a rotamer trie for a particular set, deciding upon the kind of count pair data that needs to be contained by the trie.
etrie::EtableRotamerTrieOP create_rotamer_trie (conformation::Residue const &residue, pose::Pose const &) 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
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 pair_energy_H_ (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Real &atr, Real &rep, Real &solv, Real &bb) 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 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
void set_scoretypes (ScoreType atr_type, ScoreType rep_type, ScoreType sol_type) const
ScoreType rep_scoretype () 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
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_1 (conformation::RotamerSetBase const &rotset, Size connection_type) 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 fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) 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 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
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
void set_scoretypes (ScoreType atr_type, ScoreType rep_type, ScoreType sol_type) const
ScoreType rep_scoretype () 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
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_1 (conformation::RotamerSetBase const &rotset, Size connection_type) 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 fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) 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 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
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
void set_scoretypes (ScoreType atr_type, ScoreType rep_type, ScoreType sol_type) const
ScoreType rep_scoretype () const

Protected Attributes

Etable const & etable_

Friends

class core::scoring::rna::RNA_FullAtomVDW_BasePhosphateCreator

template<class Derived>
class core::scoring::etable::BaseEtableEnergy< Derived >


Constructor & Destructor Documentation

template<class Derived >
core::scoring::etable::BaseEtableEnergy< Derived >::BaseEtableEnergy ( methods::EnergyMethodCreatorOP  creator,
Etable const &  etable_in,
methods::EnergyMethodOptions const &  options,
ScoreType  st_atr,
ScoreType  st_rep,
ScoreType  st_sol 
)

construction with an etable

template<class Derived>
core::scoring::etable::BaseEtableEnergy< Derived >::BaseEtableEnergy ( Etable const &  etable_in,
methods::EnergyMethodOptions const &  options,
ScoreType  st_atr,
ScoreType  st_rep,
ScoreType  st_sol 
)

construction with an etable

template<class Derived>
core::scoring::etable::BaseEtableEnergy< Derived >::BaseEtableEnergy ( Etable const &  etable_in,
methods::EnergyMethodOptions const &  options,
ScoreType  st_atr,
ScoreType  st_rep,
ScoreType  st_sol 
)

construction with an etable


Member Function Documentation

template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::atom_pair_energy ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
Real const  weight,
EnergyMap emap,
Real dsq 
) const [inline]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::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 [inline]

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.

template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::atom_pair_energy ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
Real const  weight,
EnergyMap emap,
Real dsq 
) const [inline]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::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 [inline]

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.

template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::atom_pair_energy ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
Real const  weight,
AtomPairEnergy ape 
) const [inline]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::atom_pair_energy ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
Real const  weight,
EnergyMap emap,
Real dsq 
) const [inline]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::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 [inline]

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.

template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::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 [inline, protected]
template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::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 [inline, protected]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::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 [inline, protected]
template<class Derived>
virtual Distance core::scoring::etable::BaseEtableEnergy< Derived >::atomic_interaction_cutoff ( ) const [virtual]

Etable atomic distance cutoff is 5.5 A.

Implements core::scoring::methods::ShortRangeTwoBodyEnergy.

template<class Derived >
Distance core::scoring::etable::BaseEtableEnergy< Derived >::atomic_interaction_cutoff ( ) const [virtual]

Etable atomic distance cutoff is 5.5 A.

return the Etables atomic distance cutoff

Implements core::scoring::methods::ShortRangeTwoBodyEnergy.

References core::chemical::MAX_CHEMICAL_BOND_TO_HYDROGEN_LENGTH.

template<class Derived>
virtual Distance core::scoring::etable::BaseEtableEnergy< Derived >::atomic_interaction_cutoff ( ) const [virtual]

Etable atomic distance cutoff is 5.5 A.

Implements core::scoring::methods::ShortRangeTwoBodyEnergy.

template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::backbone_backbone_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]

Evaluates the interaction between the backbone of rsd1 and the backbone of rsd2 and accumulates the unweighted energy.

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

template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::backbone_backbone_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]

Evaluates the interaction between the backbone of rsd1 and the backbone of rsd2 and accumulates the unweighted energy.

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

template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::backbone_backbone_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]
template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::backbone_sidechain_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]

Evaluates the interaction between the backbone of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy.

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

template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::backbone_sidechain_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]

Evaluates the interaction between the backbone of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy.

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

template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::backbone_sidechain_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]
template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::bump_energy_backbone ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]
template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::bump_energy_backbone ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]
template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::bump_energy_backbone ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]
template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::bump_energy_full ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]
template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::bump_energy_full ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]
template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::bump_energy_full ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]
template<class Derived>
etrie::EtableRotamerTrieOP core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie ( conformation::RotamerSetBase const &  rotset,
pose::Pose const &  pose 
) const [protected]
template<class Derived>
etrie::EtableRotamerTrieOP core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie ( conformation::RotamerSetBase const &  rotset,
pose::Pose const &  pose 
) const [protected]
template<class Derived >
EtableRotamerTrieOP core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie ( conformation::Residue const &  residue,
pose::Pose const &   
) const [protected]
template<class Derived >
EtableRotamerTrieOP core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie ( conformation::RotamerSetBase const &  rotset,
pose::Pose const &  pose 
) const [protected]
template<class Derived>
etrie::EtableRotamerTrieOP core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie_1 ( conformation::RotamerSetBase const &  rotset,
Size  connection_type 
) const [protected]
template<class Derived>
etrie::EtableRotamerTrieOP core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie_1 ( conformation::RotamerSetBase const &  rotset,
Size  connection_type 
) const [protected]
template<class Derived>
etrie::EtableRotamerTrieOP core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie_1 ( conformation::RotamerSetBase const &  rotset,
Size  connection_type 
) const [protected]
template<class Derived>
etrie::EtableRotamerTrieOP core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie_2 ( conformation::RotamerSetBase const &  rotset) const [protected]
template<class Derived>
etrie::EtableRotamerTrieOP core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie_2 ( conformation::RotamerSetBase const &  rotset) const [protected]
template<class Derived>
etrie::EtableRotamerTrieOP core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie_2 ( conformation::RotamerSetBase const &  rotset) const [protected]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::derived_prepare_for_residue_pair ( Size const  res1,
Size const  res2,
pose::Pose const &   
) const [inline, protected]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::derived_prepare_for_residue_pair ( Size const  res1,
Size const  res2,
pose::Pose const &   
) const [inline, protected]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::derived_prepare_for_residue_pair ( Size const  res1,
Size const  res2,
pose::Pose const &   
) const [inline, protected]
template<class Derived>
count_pair::CPCrossoverBehavior core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior ( conformation::Residue const &  res1,
conformation::Residue const &  res2,
pose::Pose const &  ,
ScoreFunction const &  sfxn 
) const [protected]
template<class Derived>
count_pair::CPCrossoverBehavior core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior ( conformation::Residue const &  res1,
conformation::Residue const &  res2,
pose::Pose const &  ,
ScoreFunction const &  sfxn 
) const [protected]
template<class Derived >
count_pair::CPCrossoverBehavior core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior ( conformation::Residue const &  res1,
conformation::Residue const &  res2,
pose::Pose const &  ,
ScoreFunction const &  sfxn 
) const [protected]
template<class Derived>
virtual bool core::scoring::etable::BaseEtableEnergy< Derived >::divides_backbone_and_sidechain_energetics ( ) const [inline, virtual]

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.

Reimplemented from core::scoring::methods::ShortRangeTwoBodyEnergy.

template<class Derived>
virtual bool core::scoring::etable::BaseEtableEnergy< Derived >::divides_backbone_and_sidechain_energetics ( ) const [inline, virtual]

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.

Reimplemented from core::scoring::methods::ShortRangeTwoBodyEnergy.

template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::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 [virtual]

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.

template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::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 [virtual]
template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::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 [virtual]

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.

template<class Derived>
Real core::scoring::etable::BaseEtableEnergy< Derived >::eval_dE_dR_over_r ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
EnergyMap const &  weights,
Vector f1,
Vector f2 
) const [inline]
template<class Derived>
Real core::scoring::etable::BaseEtableEnergy< Derived >::eval_dE_dR_over_r ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
EnergyMap const &  weights,
Vector f1,
Vector f2 
) const [inline]
template<class Derived>
Real core::scoring::etable::BaseEtableEnergy< Derived >::eval_dE_dR_over_r ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
EnergyMap const &  weights,
Vector f1,
Vector f2 
) const [inline]
template<class Derived >
Real core::scoring::etable::BaseEtableEnergy< Derived >::eval_dE_dR_over_r_ ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
EnergyMap const &  weights,
Vector f1,
Vector f2 
) const [inline, protected]
template<class Derived>
Real core::scoring::etable::BaseEtableEnergy< Derived >::eval_dE_dR_over_r_ ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
EnergyMap const &  weights,
Vector f1,
Vector f2 
) const [inline, protected]
template<class Derived>
Real core::scoring::etable::BaseEtableEnergy< Derived >::eval_dE_dR_over_r_ ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
EnergyMap const &  weights,
Vector f1,
Vector f2 
) const [inline, protected]
template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_derivatives ( conformation::Residue const &  rsd,
ResSingleMinimizationData const &  min_data,
pose::Pose const &  pose,
EnergyMap const &  weights,
utility::vector1< DerivVectorPair > &  atom_derivs 
) const [virtual]

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::conformation::Residue::atom(), core::pose::Pose::energies(), core::scoring::etab_single_nblist, core::scoring::ResSingleMinimizationData::get_data(), core::scoring::ResSingleMinimizationData::get_data_ref(), and core::scoring::Energies::use_nblist_auto_update().

template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_energy_ext ( conformation::Residue const &  rsd,
ResSingleMinimizationData const &  min_data,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]
template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::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 [virtual]
template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::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 [virtual]

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.

Reimplemented from core::scoring::methods::ShortRangeTwoBodyEnergy.

template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::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 [virtual]

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.

Reimplemented from core::scoring::methods::ShortRangeTwoBodyEnergy.

template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::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 [virtual]

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.

Reimplemented from core::scoring::methods::ShortRangeTwoBodyEnergy.

References core::scoring::Energies::data(), core::pose::Pose::energies(), core::scoring::methods::etable_method, core::scoring::EnergiesCacheableDataType::ETABLE_TRIE_COLLECTION, core::scoring::fa_rep, core::pose::Pose::residue(), and core::conformation::Residue::seqpos().

template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::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 [virtual]

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.

Reimplemented from core::scoring::methods::ShortRangeTwoBodyEnergy.

template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::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 [virtual]

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.

Reimplemented from core::scoring::methods::ShortRangeTwoBodyEnergy.

References core::scoring::methods::etable_method, core::scoring::fa_rep, core::conformation::RotamerSetBase::get_trie(), and core::conformation::RotamerSetBase::resid().

template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::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 [virtual]

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.

Reimplemented from core::scoring::methods::ShortRangeTwoBodyEnergy.

template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::fast_memb_env_energy ( conformation::Atom const &  atom1,
int const  attype1,
Real mbenvE 
) const [inline]

pba

template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::fast_memb_env_energy ( conformation::Atom const &  atom1,
int const  attype1,
Real mbenvE 
) const [inline]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::fast_memb_env_energy ( conformation::Atom const &  atom1,
int const  attype1,
Real mbenvE 
) const [inline, protected]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::fast_memb_env_energy ( conformation::Atom const &  atom1,
int const  attype1,
Real mbenvE 
) const [inline]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::fast_memb_env_energy ( conformation::Atom const &  atom1,
int const  attype1,
Real mbenvE 
) const [inline]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::fast_memb_env_energy ( conformation::Atom const &  atom1,
int const  attype1,
Real mbenvE 
) const [inline, protected]
template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::finalize_total_energy ( pose::Pose pose,
ScoreFunction const &  ,
EnergyMap totals 
) const [virtual]
template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::finalize_total_energy ( pose::Pose pose,
ScoreFunction const &  ,
EnergyMap totals 
) const [virtual]

called at the end of energy evaluation

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

template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::finalize_total_energy ( pose::Pose pose,
ScoreFunction const &  ,
EnergyMap totals 
) const [virtual]

called at the end of energy evaluation

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

template<class Derived>
count_pair::CountPairFunctionCOP core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function ( Size  res1,
Size  res2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn 
) const
template<class Derived>
count_pair::CountPairFunctionCOP core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function ( conformation::Residue const &  res1,
conformation::Residue const &  res2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn 
) const
template<class Derived>
count_pair::CountPairFunctionCOP core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function ( Size  res1,
Size  res2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn 
) const
template<class Derived>
count_pair::CountPairFunctionCOP core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function ( conformation::Residue const &  res1,
conformation::Residue const &  res2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn 
) const
template<class Derived >
count_pair::CountPairFunctionCOP core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function ( conformation::Residue const &  res1,
conformation::Residue const &  res2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn 
) const

and gets duplicated in a handful of other places within this class... this NEEDS to be reworked.

References core::scoring::methods::determine_crossover_behavior(), and core::conformation::Residue::is_DNA().

template<class Derived >
count_pair::CountPairFunctionCOP core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function ( Size  res1,
Size  res2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn 
) const
template<class Derived>
trie::TrieCountPairBaseOP core::scoring::etable::BaseEtableEnergy< Derived >::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 [protected]
template<class Derived>
trie::TrieCountPairBaseOP core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function_trie ( conformation::RotamerSetBase const &  set1,
conformation::RotamerSetBase const &  set2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn 
) const [protected]
template<class Derived>
trie::TrieCountPairBaseOP core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function_trie ( conformation::RotamerSetBase const &  set1,
conformation::RotamerSetBase const &  set2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn 
) const [protected]
template<class Derived>
trie::TrieCountPairBaseOP core::scoring::etable::BaseEtableEnergy< Derived >::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 [protected]
template<class Derived >
TrieCountPairBaseOP core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function_trie ( conformation::RotamerSetBase const &  set1,
conformation::RotamerSetBase const &  set2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn 
) const [protected]

figure out the trie count pair function to use Need to refactor this so that the decision "what kind of count pair behavior should I use" can be decoupled from class instantiation, and therefore shared between the creation of the trie count pair classes and the regular count pair classes

References core::scoring::methods::etable_method, core::conformation::RotamerSetBase::get_trie(), core::conformation::RotamerSetBase::resid(), and core::pose::Pose::residue().

template<class Derived >
TrieCountPairBaseOP core::scoring::etable::BaseEtableEnergy< Derived >::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 [protected]
template<class Derived>
count_pair::CountPairFunctionOP core::scoring::etable::BaseEtableEnergy< Derived >::get_intrares_countpair ( conformation::Residue const &  res,
pose::Pose const &  pose,
ScoreFunction const &  sfxn 
) const
template<class Derived>
count_pair::CountPairFunctionOP core::scoring::etable::BaseEtableEnergy< Derived >::get_intrares_countpair ( conformation::Residue const &  res,
pose::Pose const &  pose,
ScoreFunction const &  sfxn 
) const
template<class Derived >
count_pair::CountPairFunctionOP core::scoring::etable::BaseEtableEnergy< Derived >::get_intrares_countpair ( conformation::Residue const &  res,
pose::Pose const &  pose,
ScoreFunction const &  sfxn 
) const
template<class Derived>
Energy core::scoring::etable::BaseEtableEnergy< Derived >::heavyatom_heavyatom_energy ( etrie::EtableAtom const &  at1,
etrie::EtableAtom const &  at2,
DistanceSquared d2 
) const [inline]
template<class Derived>
Energy core::scoring::etable::BaseEtableEnergy< Derived >::heavyatom_heavyatom_energy ( etrie::EtableAtom const &  at1,
etrie::EtableAtom const &  at2,
DistanceSquared d2,
Size  
) const [inline]
template<class Derived>
Energy core::scoring::etable::BaseEtableEnergy< Derived >::heavyatom_heavyatom_energy ( etrie::EtableAtom const &  at1,
etrie::EtableAtom const &  at2,
DistanceSquared d2 
) const [inline]
template<class Derived>
Energy core::scoring::etable::BaseEtableEnergy< Derived >::heavyatom_hydrogenatom_energy ( etrie::EtableAtom const &  at1,
etrie::EtableAtom const &  at2 
) const [inline]
template<class Derived>
Energy core::scoring::etable::BaseEtableEnergy< Derived >::heavyatom_hydrogenatom_energy ( etrie::EtableAtom const &  at1,
etrie::EtableAtom const &  at2 
) const [inline]
template<class Derived>
Energy core::scoring::etable::BaseEtableEnergy< Derived >::heavyatom_hydrogenatom_energy ( etrie::EtableAtom const &  at1,
etrie::EtableAtom const &  at2,
Size  
) const [inline]
template<class Derived>
Real core::scoring::etable::BaseEtableEnergy< Derived >::hydrogen_interaction_cutoff2 ( ) const [inline]
template<class Derived>
Real core::scoring::etable::BaseEtableEnergy< Derived >::hydrogen_interaction_cutoff2 ( ) const [inline]
template<class Derived>
Real core::scoring::etable::BaseEtableEnergy< Derived >::hydrogen_interaction_cutoff2 ( ) const [inline]
template<class Derived>
Energy core::scoring::etable::BaseEtableEnergy< Derived >::hydrogenatom_heavyatom_energy ( etrie::EtableAtom const &  at1,
etrie::EtableAtom const &  at2 
) const [inline]
template<class Derived>
Energy core::scoring::etable::BaseEtableEnergy< Derived >::hydrogenatom_heavyatom_energy ( etrie::EtableAtom const &  at1,
etrie::EtableAtom const &  at2 
) const [inline]
template<class Derived>
Energy core::scoring::etable::BaseEtableEnergy< Derived >::hydrogenatom_heavyatom_energy ( etrie::EtableAtom const &  at1,
etrie::EtableAtom const &  at2,
Size  
) const [inline]
template<class Derived>
Energy core::scoring::etable::BaseEtableEnergy< Derived >::hydrogenatom_hydrogenatom_energy ( etrie::EtableAtom const &  at1,
etrie::EtableAtom const &  at2 
) const [inline]
template<class Derived>
Energy core::scoring::etable::BaseEtableEnergy< Derived >::hydrogenatom_hydrogenatom_energy ( etrie::EtableAtom const &  at1,
etrie::EtableAtom const &  at2 
) const [inline]
template<class Derived>
Energy core::scoring::etable::BaseEtableEnergy< Derived >::hydrogenatom_hydrogenatom_energy ( etrie::EtableAtom const &  at1,
etrie::EtableAtom const &  at2,
Size  
) const [inline]
template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::indicate_required_context_graphs ( utility::vector1< bool > &  context_graphs_required) const [virtual]

Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.

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

Reimplemented in core::scoring::etable::CoarseEtableEnergy.

template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::indicate_required_context_graphs ( utility::vector1< bool > &  context_graphs_required) const [virtual]

Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.

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

Reimplemented in core::scoring::etable::CoarseEtableEnergy.

template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::indicate_required_context_graphs ( utility::vector1< bool > &  context_graphs_required) const [virtual]

Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.

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

Reimplemented in core::scoring::etable::CoarseEtableEnergy.

template<class Derived >
bool core::scoring::etable::BaseEtableEnergy< Derived >::interpolate_bins ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
Real d2,
int disbin,
Real frac 
) const [inline, protected]
template<class Derived>
bool core::scoring::etable::BaseEtableEnergy< Derived >::interpolate_bins ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
Real d2,
int disbin,
Real frac 
) const [protected]
template<class Derived>
bool core::scoring::etable::BaseEtableEnergy< Derived >::interpolate_bins ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
Real d2,
int disbin,
Real frac 
) const [protected]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::memb_atom_pair_energy ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
Real const  weight,
EnergyMap emap,
Real dsq 
) const [inline]

pba

template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::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 [inline]

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.

pba

template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::memb_atom_pair_energy ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
Real const  weight,
EnergyMap emap,
Real dsq 
) const [inline]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::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 [inline]

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.

pba

template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::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 [inline, protected]
template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::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 [inline, protected]
template<class Derived>
Real core::scoring::etable::BaseEtableEnergy< Derived >::memb_eval_dE_dR_over_r ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
EnergyMap const &  weights,
Vector f1,
Vector f2 
) const [inline]

pba

template<class Derived>
Real core::scoring::etable::BaseEtableEnergy< Derived >::memb_eval_dE_dR_over_r ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
EnergyMap const &  weights,
Vector f1,
Vector f2 
) const [inline]

pba

template<class Derived>
Real core::scoring::etable::BaseEtableEnergy< Derived >::memb_eval_dE_dR_over_r_ ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
EnergyMap const &  weights,
Vector f1,
Vector f2 
) const [inline, protected]

pba

template<class Derived >
Real core::scoring::etable::BaseEtableEnergy< Derived >::memb_eval_dE_dR_over_r_ ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
EnergyMap const &  weights,
Vector f1,
Vector f2 
) const [inline, protected]
template<class Derived >
bool core::scoring::etable::BaseEtableEnergy< Derived >::minimize_in_whole_structure_context ( pose::Pose const &  pose) const [virtual]

The neighborlist-autoupdate algorithm requires that the EtableEnergy be able to control the definition and update for its atom-neighbors. This will bypass the standard neighborlist evaluation inside the ScoreFunction, avoiding the use the MinimizationGraph.

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

References core::pose::Pose::energies(), and core::scoring::Energies::use_nblist_auto_update().

template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::pair_energy_H ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
Real  weight,
Energy atr,
Energy rep,
Energy solv,
Energy bb 
) const [inline]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::pair_energy_H ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
Real  weight,
Energy atr,
Energy rep,
Energy solv,
Energy bb 
) const [inline]
template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::pair_energy_H ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
Real  weight,
EnergyMap emap 
) const [inline]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::pair_energy_H ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
Real  weight,
AtomPairEnergy ape 
) const [inline]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::pair_energy_H ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
Real  weight,
EnergyMap emap 
) const [inline]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::pair_energy_H ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
Real  weight,
EnergyMap emap 
) const [inline]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::pair_energy_H ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
Real  weight,
Energy atr,
Energy rep,
Energy solv,
Energy bb 
) const [inline]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::pair_energy_H_ ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
Real const  weight,
Real atr,
Real rep,
Real solv,
Real bb 
) const [inline, protected]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::pair_energy_H_ ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
Real const  weight,
Real atr,
Real rep,
Real solv,
Real bb 
) const [inline, protected]
template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::pair_energy_H_ ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
Real const  weight,
Real atr,
Real rep,
Real solv,
Real bb 
) const [inline, protected]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::prepare_for_residue_pair ( Size const  res1,
Size const  res2,
pose::Pose const &  pose 
) const [inline]

Should/Could these inlined" in a separate .inline.hh?

template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::prepare_for_residue_pair ( Size const  res1,
Size const  res2,
pose::Pose const &  pose 
) const [inline]

Should/Could these inlined" in a separate .inline.hh?

template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::prepare_for_residue_pair ( Size const  res1,
Size const  res2,
pose::Pose const &  pose 
) const [inline]

Should/Could these inlined" in a separate .inline.hh?

template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::prepare_rotamers_for_packing ( pose::Pose const &  ,
conformation::RotamerSetBase  
) const [virtual]

default implementation noop

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

template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::prepare_rotamers_for_packing ( pose::Pose const &  ,
conformation::RotamerSetBase  
) const [virtual]

default implementation noop

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

template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::prepare_rotamers_for_packing ( pose::Pose const &  ,
conformation::RotamerSetBase  
) const [virtual]

default implementation noop

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

References core::scoring::methods::etable_method.

template<class Derived >
ScoreType core::scoring::etable::BaseEtableEnergy< Derived >::rep_scoretype ( ) const [protected]
template<class Derived>
ScoreType core::scoring::etable::BaseEtableEnergy< Derived >::rep_scoretype ( ) const [protected]
template<class Derived>
ScoreType core::scoring::etable::BaseEtableEnergy< Derived >::rep_scoretype ( ) const [protected]
template<class Derived >
bool core::scoring::etable::BaseEtableEnergy< Derived >::requires_a_setup_for_derivatives_for_residue_opportunity ( pose::Pose const &  pose) const [virtual]

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.

template<class Derived >
bool core::scoring::etable::BaseEtableEnergy< Derived >::requires_a_setup_for_derivatives_for_residue_pair_opportunity ( pose::Pose const &  pose) const [virtual]

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.

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

template<class Derived >
bool core::scoring::etable::BaseEtableEnergy< Derived >::requires_a_setup_for_scoring_for_residue_opportunity ( pose::Pose const &  pose) const [virtual]

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.

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

template<class Derived >
bool core::scoring::etable::BaseEtableEnergy< Derived >::requires_a_setup_for_scoring_for_residue_pair_opportunity ( pose::Pose const &  pose) const [virtual]

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.

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

template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::residue_pair_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]

Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap.

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

template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::residue_pair_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]
template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::residue_pair_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]

Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap.

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

template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::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 [virtual]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::set_scoretypes ( ScoreType  atr_type,
ScoreType  rep_type,
ScoreType  sol_type 
) const [protected]
template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::set_scoretypes ( ScoreType  atr_type,
ScoreType  rep_type,
ScoreType  sol_type 
) const [protected]
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::set_scoretypes ( ScoreType  atr_type,
ScoreType  rep_type,
ScoreType  sol_type 
) const [protected]
template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_derivatives ( pose::Pose pose,
ScoreFunction const &  scfxn 
) const [virtual]
template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_derivatives ( pose::Pose pose,
ScoreFunction const &  sfxn 
) const [virtual]

Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls.

default implementation noop

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

template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_derivatives ( pose::Pose pose,
ScoreFunction const &  sfxn 
) const [virtual]

Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls.

default implementation noop

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

template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_derivatives_for_residue ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
ResSingleMinimizationData min_data 
) const [virtual]

Do any setup work necessary before evaluating the derivatives for this residue.

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

template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::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 [virtual]

Do any setup work necessary before evaluating the derivatives for this residue pair.

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

template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_minimizing ( pose::Pose pose,
ScoreFunction const &  sfxn,
kinematics::MinimizerMapBase const &  min_map 
) const [virtual]

stashes nblist if use_nblist is true

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

template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_minimizing ( pose::Pose pose,
ScoreFunction const &  sfxn,
kinematics::MinimizerMapBase const &  min_map 
) const [virtual]

stashes nblist if use_nblist is true

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

template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_minimizing ( pose::Pose pose,
ScoreFunction const &  sfxn,
kinematics::MinimizerMapBase const &  min_map 
) const [virtual]
template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_minimizing_for_residue ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
kinematics::MinimizerMapBase const &  minmap,
ResSingleMinimizationData min_data 
) const [virtual]
template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::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 [virtual]
template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_packing ( pose::Pose ,
utility::vector1< bool > const &  ,
utility::vector1< bool > const &   
) const [virtual]

default implementation noop

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

template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_packing ( pose::Pose ,
utility::vector1< bool > const &  ,
utility::vector1< bool > const &   
) const [virtual]
template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_packing ( pose::Pose ,
utility::vector1< bool > const &  ,
utility::vector1< bool > const &   
) const [virtual]

default implementation noop

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

template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_scoring ( pose::Pose pose,
ScoreFunction const &  scfxn 
) const [virtual]

check compatibility with atomtypeset

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

template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_scoring ( pose::Pose pose,
ScoreFunction const &  scfxn 
) const [virtual]
template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_scoring ( pose::Pose pose,
ScoreFunction const &  scfxn 
) const [virtual]

check compatibility with atomtypeset

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

template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_scoring_for_residue ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  ,
ResSingleMinimizationData min_data 
) const [virtual]

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.

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

template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::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 [virtual]

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.

template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::sidechain_sidechain_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]
template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::sidechain_sidechain_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]

Evaluates the interaction between the sidechain of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy.

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

template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::sidechain_sidechain_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]

Evaluates the interaction between the sidechain of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy.

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

template<class Derived>
Energy core::scoring::etable::BaseEtableEnergy< Derived >::sum_energies ( Real  atr,
Real  rep,
Real  solv,
Real  bb 
) const [inline]

Inline Methods For Trie-vs-Trie Algorithm.

template<class Derived>
Energy core::scoring::etable::BaseEtableEnergy< Derived >::sum_energies ( Real  atr,
Real  rep,
Real  solv,
Real  bb 
) const [inline]
template<class Derived>
Energy core::scoring::etable::BaseEtableEnergy< Derived >::sum_energies ( Real  atr,
Real  rep,
Real  solv,
Real  bb 
) const [inline]

Inline Methods For Trie-vs-Trie Algorithm.

template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::update_residue_for_packing ( pose::Pose pose,
Size  resid 
) const [virtual]
template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::update_residue_for_packing ( pose::Pose pose,
Size  resid 
) const [virtual]
template<class Derived>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::update_residue_for_packing ( pose::Pose pose,
Size  resid 
) const [virtual]
template<class Derived >
bool core::scoring::etable::BaseEtableEnergy< Derived >::use_extended_intrares_energy_interface ( ) const [virtual]

APL -- note, new.

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

template<class Derived >
bool core::scoring::etable::BaseEtableEnergy< Derived >::use_extended_residue_pair_energy_interface ( ) const [virtual]

APL -- note, new.

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

template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::virtual_atom_pair_energy ( EnergyMap emap) const [inline]

Friends And Related Function Documentation

template<class Derived>
friend class core::scoring::rna::RNA_FullAtomVDW_BasePhosphateCreator [friend]

Member Data Documentation

template<class Derived>
core::scoring::etable::BaseEtableEnergy< Derived >::__pad0__
template<class Derived>
core::scoring::etable::BaseEtableEnergy< Derived >::__pad1__
template<class Derived>
Etable const & core::scoring::etable::BaseEtableEnergy< Derived >::etable_ [protected]

The documentation for this class was generated from the following files:
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines