Rosetta Core  2014.35
Public Member Functions | Public Attributes | Protected Member Functions | Private Attributes | List of all members
core::scoring::etable::BaseEtableEnergy< Derived > Class Template Reference

#include <BaseMembEtableEnergy.hh>

Public Member Functions

 BaseEtableEnergy (methods::EnergyMethodCreatorOP creator, Etable const &etable_in, methods::EnergyMethodOptions const &options)
 construction with an etable More...
 
 BaseEtableEnergy (BaseEtableEnergy< Derived > const &)
 explicit copy constructor, since the BaseEtableEnergy now contains OP data More...
 
virtual bool minimize_in_whole_structure_context (pose::Pose const &) const
 NO! friend class core::scoring::rna::RNA_FullAtomVDW_BasePhosphateCreator;. More...
 
virtual void setup_for_minimizing (pose::Pose &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map) const
 stashes nblist if pose.energies().use_nblist_auto_update() is true This is only invoked, now, if the neighborlist-autoupdate flag is on. More...
 
virtual void setup_for_scoring (pose::Pose &pose, ScoreFunction const &scfxn) const
 check compatibility with atomtypeset More...
 
virtual void setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) const
 
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
 ensure this function gets called. The default behavior is to do nothing. More...
 
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. More...
 
count_pair::CountPairFunctionOP get_intrares_countpair (conformation::Residue const &res, pose::Pose const &pose, ScoreFunction const &sfxn) const
 
virtual void residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap. More...
 
virtual bool use_extended_residue_pair_energy_interface () const
 APL – note, new. More...
 
virtual void residue_pair_energy_ext (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResPairMinimizationData const &min_data, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 APL – note, new. More...
 
virtual void setup_for_minimizing_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, ResSingleMinimizationData const &res1_data_cache, ResSingleMinimizationData const &res2_data_cache, ResPairMinimizationData &min_data) const
 APL – note, new. More...
 
virtual bool requires_a_setup_for_scoring_for_residue_opportunity (pose::Pose const &pose) const
 Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. More...
 
virtual void setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &, ResSingleMinimizationData &min_data) const
 Do any setup work should the coordinates of this residue (who is still guaranteed to be of the same residue type as when setup_for_minimizing_for_residue was called) have changed so dramatically as to possibly require some amount of setup work before scoring should proceed. This function is used for both intra-residue setup and pre-inter-residue setup. More...
 
virtual bool requires_a_setup_for_derivatives_for_residue_opportunity (pose::Pose const &pose) const
 Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so. More...
 
virtual void setup_for_derivatives_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &, ResSingleMinimizationData &min_data) const
 Do any setup work necessary before evaluating the derivatives for this residue. More...
 
virtual bool requires_a_setup_for_scoring_for_residue_pair_opportunity (pose::Pose const &pose) const
 Does this EnergyMethod require the opportunity to examine each residue pair before scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so. More...
 
virtual void setup_for_scoring_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &minsingle_data1, ResSingleMinimizationData const &minsingle_data2, pose::Pose const &pose, ScoreFunction const &, ResPairMinimizationData &data_cache) const
 Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed. More...
 
virtual bool requires_a_setup_for_derivatives_for_residue_pair_opportunity (pose::Pose const &pose) const
 Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so. More...
 
virtual void setup_for_derivatives_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &minsingle_data1, ResSingleMinimizationData const &minsingle_data2, pose::Pose const &pose, ScoreFunction const &, ResPairMinimizationData &data_cache) const
 Do any setup work necessary before evaluating the derivatives for this residue pair. More...
 
virtual void eval_residue_pair_derivatives (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &, ResSingleMinimizationData const &, ResPairMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_at_derivs, utility::vector1< DerivVectorPair > &r2_at_derivs) const
 APL – note, new. More...
 
virtual void backbone_backbone_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluates the interaction between the backbone of rsd1 and the backbone of rsd2 and accumulates the unweighted energy. More...
 
virtual void backbone_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluates the interaction between the backbone of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy. More...
 
virtual void sidechain_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluates the interaction between the sidechain of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy. More...
 
virtual void evaluate_rotamer_pair_energies (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const
 Batch computation of rotamer pair energies. Need not be overriden in derived class – by default, iterates over all pairs of rotamers, and calls derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...
 
virtual void evaluate_rotamer_background_energies (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< core::PackerEnergy > &energy_vector) const
 Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...
 
virtual bool use_extended_intrares_energy_interface () const
 APL – note, new. More...
 
virtual void eval_intrares_energy_ext (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 APL – note, new. More...
 
virtual void setup_for_minimizing_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, ResSingleMinimizationData &min_data) const
 APL – note, new. More...
 
void eval_intrares_derivatives (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &atom_derivs) const
 Evaluate the derivative for the intra-residue component of this energy method for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd. More...
 
virtual void bump_energy_full (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 
virtual void bump_energy_backbone (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 
virtual void finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) const
 called at the end of energy evaluation More...
 
virtual void eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &, ScoreFunction const &sfxn, EnergyMap const &weights, Vector &F1, Vector &F2) const
 called during gradient-based minimization inside dfunc More...
 
void prepare_for_residue_pair (Size const res1, Size const res2, pose::Pose const &pose) const
 Should/Could these inlined" in a separate .inline.hh? More...
 
void atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, EnergyMap &emap, Real &dsq) const
 
void atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb, Real &dsq) const
 for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication. More...
 
void atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, AtomPairEnergy &ape) const
 APL – consider reinstating this function! More...
 
void pair_energy_H (conformation::Atom const &atom1, conformation::Atom const &atom2, Real weight, EnergyMap &emap) const
 APL – Consider reinstating this function! More...
 
Real hydrogen_interaction_cutoff2 () const
 
virtual Distance atomic_interaction_cutoff () const
 Etable atomic distance cutoff is 5.5 A. More...
 
virtual bool divides_backbone_and_sidechain_energetics () const
 A derived class should return true for this function if it implements its own versions of the backbone_backbone_energy, backbone_sidechain_energy and sidechain_sidechain_energy functions. The default sidechain_sidechain_energy implemented by the TwoBodyEnergy base class calls residue_pair_energy. If the derived class implements its own versions of these functions, then calling code may avoid calling it on pairs of residues that are "provably distant" based on a pair of bounding spheres for a sidechains and backbones and this method's atomic_interaction_cutoff energy method. More...
 
virtual void indicate_required_context_graphs (utility::vector1< bool > &) const
 Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed. More...
 
 BaseEtableEnergy (Etable const &etable_in, methods::EnergyMethodOptions const &options, ScoreType st_atr, ScoreType st_rep, ScoreType st_sol)
 construction with an etable More...
 
virtual void setup_for_minimizing (pose::Pose &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map) const
 stashes nblist if use_nblist is true More...
 
virtual void setup_for_scoring (pose::Pose &pose, ScoreFunction const &scfxn) const
 check compatibility with atomtypeset More...
 
virtual void setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) const
 Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. More...
 
virtual void setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const
 
virtual void prepare_rotamers_for_packing (pose::Pose const &pose, conformation::RotamerSetBase &set) const
 
virtual void update_residue_for_packing (pose::Pose &pose, Size resid) const
 ensure this function gets called. The default behavior is to do nothing. More...
 
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. More...
 
virtual void backbone_backbone_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluates the interaction between the backbone of rsd1 and the backbone of rsd2 and accumulates the unweighted energy. More...
 
virtual void backbone_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluates the interaction between the backbone of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy. More...
 
virtual void sidechain_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluates the interaction between the sidechain of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy. More...
 
virtual void evaluate_rotamer_pair_energies (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const
 Batch computation of rotamer pair energies. Need not be overriden in derived class – by default, iterates over all pairs of rotamers, and calls derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...
 
virtual void evaluate_rotamer_background_energies (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< core::PackerEnergy > &energy_vector) const
 Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...
 
virtual void 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 More...
 
virtual void eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &, ScoreFunction const &sfxn, EnergyMap const &weights, Vector &F1, Vector &F2) const
 called during gradient-based minimization inside dfunc More...
 
void prepare_for_residue_pair (Size const res1, Size const res2, pose::Pose const &pose) const
 Should/Could these inlined" in a separate .inline.hh? More...
 
void 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 More...
 
void fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const
 pba More...
 
void atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb, Real &dsq) const
 for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication. More...
 
void memb_atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb, Real &dsq) const
 for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication. More...
 
void fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const
 
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 More...
 
Real hydrogen_interaction_cutoff2 () const
 
virtual Distance atomic_interaction_cutoff () const
 Etable atomic distance cutoff is 5.5 A. More...
 
virtual bool divides_backbone_and_sidechain_energetics () const
 A derived class should return true for this function if it implements its own versions of the backbone_backbone_energy, backbone_sidechain_energy and sidechain_sidechain_energy functions. The default sidechain_sidechain_energy implemented by the TwoBodyEnergy base class calls residue_pair_energy. If the derived class implements its own versions of these functions, then calling code may avoid calling it on pairs of residues that are "provably distant" based on a pair of bounding spheres for a sidechains and backbones and this method's atomic_interaction_cutoff energy method. More...
 
virtual void indicate_required_context_graphs (utility::vector1< bool > &) const
 Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed. More...
 
Energy sum_energies (Real atr, Real rep, Real solv, Real bb) const
 Inline Methods For Trie-vs-Trie Algorithm. More...
 
Energy heavyatom_heavyatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2, DistanceSquared &d2) const
 
Energy heavyatom_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)
 Construct given an Etable. More...
 
virtual void setup_for_minimizing (pose::Pose &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map) const
 Setup TwoBody Energy for Minimization. More...
 
virtual void setup_for_scoring (pose::Pose &pose, ScoreFunction const &scfxn) const
 Setup for Scoring Two Body Term. More...
 
virtual void setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) const
 Setup two-body terms for derivatives. More...
 
virtual void setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const
 Setup Two body Term for Packing. More...
 
virtual void prepare_rotamers_for_packing (pose::Pose const &pose, conformation::RotamerSetBase &set) const
 Create Rotamer Trie for the input set of rotamers and scores the trie in the rotamer set. More...
 
virtual void update_residue_for_packing (pose::Pose &pose, Size resid) const
 Updates the cached rotamer trie for a residue if it has changed during the course of a repacking. More...
 
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
 Compute Two-Body residue Pair energy. More...
 
virtual void backbone_backbone_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluates the interaction between the backbone of rsd1 and the backbone of rsd2 and accumulates the unweighted energy. More...
 
virtual void backbone_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluates the interaction between the backbone of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy. More...
 
virtual void sidechain_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluates the interaction between the sidechain of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy. More...
 
virtual void evaluate_rotamer_pair_energies (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const
 Batch computation of rotamer pair energies. Need not be overriden in derived class – by default, iterates over all pairs of rotamers, and calls derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...
 
virtual void evaluate_rotamer_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
 Overrides default rotamer/background energy calculation and uses the trie-vs-trie algorithm instead. More...
 
virtual void bump_energy_full (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 
virtual void bump_energy_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 an energy evaluation. More...
 
virtual void eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &, ScoreFunction const &sfxn, EnergyMap const &weights, Vector &F1, Vector &F2) const
 Called during graident-based minimization inside dfunc. More...
 
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
 Standard Atom Pair Energy. More...
 
void memb_atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, EnergyMap &emap, Real &dsq) const
 Membrane Specific Atom Pair Energy. More...
 
void fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const
 Speed Optimized Membrane Environment Energy. More...
 
void atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb, Real &dsq) const
 for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication. More...
 
void memb_atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb, Real &dsq) const
 for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication. More...
 
void fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const
 Compute fast membrane environment energy. More...
 
void pair_energy_H (conformation::Atom const &atom1, conformation::Atom const &atom2, Real weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb) const
 
void pair_energy_H (conformation::Atom const &atom1, conformation::Atom const &atom2, Real weight, EnergyMap &emap) const
 
Real eval_dE_dR_over_r (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
 
Real memb_eval_dE_dR_over_r (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
 pba More...
 
Real hydrogen_interaction_cutoff2 () const
 
virtual Distance atomic_interaction_cutoff () const
 Etable atomic distance cutoff is 5.5 A. More...
 
virtual void indicate_required_context_graphs (utility::vector1< bool > &) const
 Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed. More...
 
Energy sum_energies (Real atr, Real rep, Real solv, Real bb) const
 Inline Methods For Trie-vs-Trie Algorithm. More...
 
Energy heavyatom_heavyatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2, DistanceSquared &d2) const
 
Energy heavyatom_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 Member Functions inherited from core::scoring::methods::ContextIndependentTwoBodyEnergy
 ContextIndependentTwoBodyEnergy (EnergyMethodCreatorOP)
 Constructor with an EnergyMethodCreator to inform the ancestor EnergyMethod class which ScoreTypes this EnergyMethod is responsible for computing. More...
 
virtual ~ContextIndependentTwoBodyEnergy ()
 
EnergyMethodType method_type () const
 Return one of the 7 kinds of energy methods that exist: e.g. context-dependent-one-body vs whole-structure. More...
 
- Public Member Functions inherited from core::scoring::methods::ShortRangeTwoBodyEnergy
 ShortRangeTwoBodyEnergy (EnergyMethodCreatorOP)
 Constructor with EnergyMethodCreator to provide to the EnergyMethod grandparent the list of the ScoreTypes this EnergyMethod is responsible for computing. More...
 
virtual ~ShortRangeTwoBodyEnergy ()
 
virtual void evaluate_rotamer_background_energy_maps (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< EnergyMap > &emaps) const
 Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...
 
- Public Member Functions inherited from core::scoring::methods::TwoBodyEnergy
 TwoBodyEnergy (EnergyMethodCreatorOP)
 Constructor, requiring an EnergyMethodCreator. No default constructor provided to force EnergyMethod writers to provide an energy-method-creator at construction time. More...
 
virtual ~TwoBodyEnergy ()
 
virtual bool defines_score_for_residue_pair (conformation::Residue const &res1, conformation::Residue const &res2, bool res_moving_wrt_eachother) const
 During minimization, energy methods are allowed to decide that they say nothing about a particular residue pair (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default implementation returns "true" for all residue pairs. Context-dependent two-body energies have the option of behaving as if they are context-independent by returning "false" for residue pairs that do no move wrt each other. More...
 
virtual bool defines_intrares_energy (EnergyMap const &weights) const =0
 Two body energies are able to define intra-residue energies, and to do so only in the presence of certain non-zero weights. The ScoreFunction will hand over its weight set as it asks whether the energy method defines an intraresidue energy or not. More...
 
virtual void eval_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const =0
 Evaluate the intra-residue energy for a given residue. More...
 
virtual bool defines_intrares_energy_for_residue (conformation::Residue const &res) const
 If a score function defines no intra-residue scores for a particular residue, then it may opt-out of being asked during minimization to evaluate the score for this residue. More...
 
virtual bool defines_intrares_dof_derivatives (pose::Pose const &p) const
 Use the dof_derivative interface for this energy method when calculating derivatives? It is possible to define both dof_derivatives and atom-derivatives; they are not mutually exclusive. More...
 
virtual Real eval_intraresidue_dof_derivative (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights) const
 Evaluate the DOF derivative for a particular residue. The Pose merely serves as context, and the input residue is not required to be a member of the Pose. More...
 
virtual void evaluate_rotamer_intrares_energies (conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< core::PackerEnergy > &energies) const
 Batch computation of rotamer intrares energies. Need not be overriden in derived class – by default, iterates over all rotamers, and calls derived class's intrares _energy method. More...
 
virtual void evaluate_rotamer_intrares_energy_maps (conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< EnergyMap > &emaps) const
 Batch computation of rotamer intrares energy map. Need not be overriden in derived class – by default, iterates over all rotamers, and calls derived class's intrares _energy method. More...
 
- Public Member Functions inherited from core::scoring::methods::EnergyMethod
 EnergyMethod (EnergyMethodCreatorOP creator)
 Constructor with EnergyMethodCreator, which lists the score types that this energy method is responsible for. More...
 
 EnergyMethod (EnergyMethod const &src)
 Copy constructor copies over the score types of the source. More...
 
virtual ~EnergyMethod ()
 
virtual EnergyMethodOP clone () const =0
 
virtual void finalize_after_derivatives (pose::Pose &, ScoreFunction const &) const
 called at the end of derivatives evaluation More...
 
virtual bool defines_high_order_terms (pose::Pose const &) const
 Should this EnergyMethod have score and derivative evaluation evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta's get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns "false". More...
 
virtual void eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &sfxn, EnergyMap const &emap, Vector &F1, Vector &F2) const
 Evaluate the XYZ derivative for an atom in the pose. Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom's XYZ derivative. More...
 
ScoreTypes const & score_types () const
 Returns the score types that this energy method computes. More...
 
virtual core::Size version () const =0
 Return the version of the energy method. More...
 

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
 Inline Methods For Trie-vs-Trie Algorithm. More...
 
trie::TrieCountPairBaseOP get_count_pair_function_trie (conformation::Residue const &res1, conformation::Residue const &res2, trie::RotamerTrieBaseCOP trie1, trie::RotamerTrieBaseCOP trie2, pose::Pose const &pose, ScoreFunction const &sfxn) const
 
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. More...
 
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
 
Real eval_dE_dR_over_r_ (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
 
void derived_prepare_for_residue_pair (Size const, Size const, pose::Pose const &) const
 
bool interpolate_bins (conformation::Atom const &atom1, conformation::Atom const &atom2, Real &d2, int &disbin, Real &frac) const
 
ScoreType rep_scoretype () const
 
Etable const & etable () 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 More...
 
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 More...
 
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 Member Functions inherited from core::scoring::methods::EnergyMethod
void set_score_types (EnergyMethodCreatorOP creator)
 Override the entirety of the score types list if they were initialized incorrectly in a parent's constructor. More...
 

Private Attributes

Etable const & etable_
 
Real safe_max_dis2
 
Real hydrogen_interaction_cutoff2_
 
bool exclude_DNA_DNA
 
ObjexxFCL::FArray3D< Real > const & ljatr_
 these guys are taken from the etable More...
 
ObjexxFCL::FArray3D< Real > const & ljrep_
 
ObjexxFCL::FArray3D< Real > const & solv1_
 
ObjexxFCL::FArray3D< Real > const & solv2_
 
ObjexxFCL::FArray3D< Real > const & dljatr_
 
ObjexxFCL::FArray3D< Real > const & dljrep_
 
ObjexxFCL::FArray3D< Real > const & dsolv_
 
ObjexxFCL::FArray3D< Real > const & memb_solv1_
 
ObjexxFCL::FArray3D< Real > const & memb_solv2_
 
ObjexxFCL::FArray3D< Real > const & memb_dsolv_
 
int etable_bins_per_A2
 
ScoreType st_rep_
 
ScoreType st_atr_
 
ScoreType st_sol_
 
EnergyMap weights_
 

Additional Inherited Members

- Public Types inherited from core::scoring::methods::ContextIndependentTwoBodyEnergy
typedef ShortRangeTwoBodyEnergy parent
 
- Public Types inherited from core::scoring::methods::ShortRangeTwoBodyEnergy
typedef TwoBodyEnergy parent
 
- Public Types inherited from core::scoring::methods::TwoBodyEnergy
typedef EnergyMethod parent
 
- Public Types inherited from core::scoring::methods::EnergyMethod
typedef
utility::pointer::ReferenceCount 
parent
 

Constructor & Destructor Documentation

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

construction with an etable

References fa_Hatr, option, and score.

template<class Derived>
core::scoring::etable::BaseEtableEnergy< Derived >::BaseEtableEnergy ( BaseEtableEnergy< Derived > const &  src)

explicit copy constructor, since the BaseEtableEnergy now contains OP data

an explicit copy constructor is required so that the etable_evaluator_ instance, which is held in an owning pointer, is not shared between multiple instances of this (or rather the derived) class.

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 
)

Construct given 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

Standard Atom Pair Energy.

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,
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

APL – consider reinstating this function!

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
inlineprotected
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
inlineprotected
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 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 score::fa_Hatr, core::chemical::MAX_CHEMICAL_BOND_TO_HYDROGEN_LENGTH, and option.

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

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

do not use this during minimization

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

References core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function_and_invoke(), core::scoring::methods::determine_crossover_behavior(), core::pose::Pose::energies(), core::conformation::Residue::is_DNA(), and core::scoring::Energies::use_nblist().

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

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

do not use this during minimization

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

References core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function_and_invoke(), core::scoring::methods::determine_crossover_behavior(), core::pose::Pose::energies(), core::conformation::Residue::is_DNA(), and core::scoring::Energies::use_nblist().

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_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_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 >
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::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>
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
inlineprotected
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::derived_prepare_for_residue_pair ( Size const  res1,
Size const  res2,
pose::Pose const &   
) const
inlineprotected
template<class Derived>
void core::scoring::etable::BaseEtableEnergy< Derived >::derived_prepare_for_residue_pair ( Size  const,
Size  const,
pose::Pose const &   
) const
inlineprotected
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
inlinevirtual

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
inlinevirtual

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>
Etable const& core::scoring::etable::BaseEtableEnergy< Derived >::etable ( ) const
inlineprotected
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 graident-based minimization inside dfunc.

F1 and F2 are not zeroed – contributions from this atom are just summed in.

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

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>
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
inlineprotected
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
inlineprotected
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
inlineprotected
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

Overrides default rotamer/background energy calculation and uses the trie-vs-trie algorithm instead.

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 cp, core::scoring::Energies::data(), core::pose::Pose::energies(), core::scoring::methods::etable_method, core::scoring::EnergiesCacheableDataType::ETABLE_TRIE_COLLECTION, basic::datacache::BasicDataCache::get(), core::conformation::RotamerSetBase::get_trie(), core::conformation::RotamerSetBase::num_rotamers(), core::conformation::RotamerSetBase::resid(), 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>
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 cp, core::scoring::methods::etable_method, core::conformation::RotamerSetBase::get_trie(), and core::conformation::RotamerSetBase::resid().

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

Speed Optimized Membrane Environment Energy.

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

Compute fast membrane environment energy.

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

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>
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>
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

Inline Methods For Trie-vs-Trie Algorithm.

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 
) 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>
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_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>
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>
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>
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 >
bool core::scoring::etable::BaseEtableEnergy< Derived >::interpolate_bins ( conformation::Atom const &  atom1,
conformation::Atom const &  atom2,
Real d2,
int disbin,
Real frac 
) const
inlineprotected
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

Membrane Specific Atom Pair Energy.

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.

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
inlineprotected
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
inlineprotected
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
inlineprotected

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
inlineprotected
template<class Derived >
bool core::scoring::etable::BaseEtableEnergy< Derived >::minimize_in_whole_structure_context ( pose::Pose const &  pose) const
virtual

NO! friend class core::scoring::rna::RNA_FullAtomVDW_BasePhosphateCreator;.

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,
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  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 const  weight,
Real atr,
Real rep,
Real solv,
Real bb 
) const
inlineprotected
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
inlineprotected
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
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 &  pose,
conformation::RotamerSetBase set 
) const
virtual

Create Rotamer Trie for the input set of rotamers and scores the trie in the rotamer set.

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
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

Compute Two-Body residue Pair energy.

Implements 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 >
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>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_derivatives ( pose::Pose pose,
ScoreFunction const &  scfxn 
) const
virtual

Setup two-body terms for derivatives.

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 ( pose::Pose pose,
ScoreFunction const &  scfxn 
) const
virtual
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

Setup TwoBody Energy for Minimization.

Stash 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

Setup Two body Term for Packing.

Etable Energy method scores a vector of rotamer trie objects in the energies object for use in rapid rotamer/background energy calculations. Overrides default do-nothing behavior.

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

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_scoring ( pose::Pose pose,
ScoreFunction const &  scfxn 
) const
virtual

Setup for Scoring Two Body Term.

Check compatibility with atom typeset

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 >
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>
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 >
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>
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>
virtual void core::scoring::etable::BaseEtableEnergy< Derived >::update_residue_for_packing ( pose::Pose pose,
Size  resid 
) const
virtual

Updates the cached rotamer trie for a residue if it has changed during the course of a repacking.

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

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

ensure this function gets called. The default behavior is to do nothing.

default implementation noop

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

template<class Derived >
void core::scoring::etable::BaseEtableEnergy< Derived >::update_residue_for_packing ( 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.

Member Data Documentation

template<class Derived>
core::scoring::etable::BaseEtableEnergy< Derived >::__pad0__
template<class Derived>
core::scoring::etable::BaseEtableEnergy< Derived >::__pad1__
template<class Derived>
ObjexxFCL::FArray3D< Real > const & core::scoring::etable::BaseEtableEnergy< Derived >::dljatr_
private
template<class Derived>
ObjexxFCL::FArray3D< Real > const & core::scoring::etable::BaseEtableEnergy< Derived >::dljrep_
private
template<class Derived>
ObjexxFCL::FArray3D< Real > const & core::scoring::etable::BaseEtableEnergy< Derived >::dsolv_
private
template<class Derived>
Etable const & core::scoring::etable::BaseEtableEnergy< Derived >::etable_
private
template<class Derived>
int core::scoring::etable::BaseEtableEnergy< Derived >::etable_bins_per_A2
private
template<class Derived>
bool core::scoring::etable::BaseEtableEnergy< Derived >::exclude_DNA_DNA
private
template<class Derived>
Real core::scoring::etable::BaseEtableEnergy< Derived >::hydrogen_interaction_cutoff2_
private
template<class Derived>
ObjexxFCL::FArray3D< Real > const & core::scoring::etable::BaseEtableEnergy< Derived >::ljatr_
private

these guys are taken from the etable

template<class Derived>
ObjexxFCL::FArray3D< Real > const & core::scoring::etable::BaseEtableEnergy< Derived >::ljrep_
private
template<class Derived>
ObjexxFCL::FArray3D< Real > const & core::scoring::etable::BaseEtableEnergy< Derived >::memb_dsolv_
private
template<class Derived>
ObjexxFCL::FArray3D< Real > const & core::scoring::etable::BaseEtableEnergy< Derived >::memb_solv1_
private
template<class Derived>
ObjexxFCL::FArray3D< Real > const & core::scoring::etable::BaseEtableEnergy< Derived >::memb_solv2_
private
template<class Derived>
Real core::scoring::etable::BaseEtableEnergy< Derived >::safe_max_dis2
private
template<class Derived>
ObjexxFCL::FArray3D< Real > const & core::scoring::etable::BaseEtableEnergy< Derived >::solv1_
private
template<class Derived>
ObjexxFCL::FArray3D< Real > const & core::scoring::etable::BaseEtableEnergy< Derived >::solv2_
private
template<class Derived>
ScoreType core::scoring::etable::BaseEtableEnergy< Derived >::st_atr_
mutableprivate
template<class Derived>
ScoreType core::scoring::etable::BaseEtableEnergy< Derived >::st_rep_
mutableprivate
template<class Derived>
ScoreType core::scoring::etable::BaseEtableEnergy< Derived >::st_sol_
mutableprivate
template<class Derived>
EnergyMap core::scoring::etable::BaseEtableEnergy< Derived >::weights_
mutableprivate

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