core::scoring::etable::BaseEtableEnergy< Derived > Class Template Reference

#include <BaseMembEtableEnergy.hh>

Inheritance diagram for core::scoring::etable::BaseEtableEnergy< Derived >:

Collaboration diagram for core::scoring::etable::BaseEtableEnergy< Derived >:

List of all members.

Public Member Functions
	BaseEtableEnergy (methods::EnergyMethodCreatorOP creator, Etable const &etable_in, methods::EnergyMethodOptions const &options, ScoreType st_atr, ScoreType st_rep, ScoreType st_sol)
	construction with an etable
virtual bool	minimize_in_whole_structure_context (pose::Pose const &) const
	The neighborlist-autoupdate algorithm requires that the EtableEnergy be able to control the definition and update for its atom-neighbors. This will bypass the standard neighborlist evaluation inside the ScoreFunction, avoiding the use the MinimizationGraph.
virtual void	setup_for_minimizing (pose::Pose &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map) const
	stashes nblist if pose.energies().use_nblist_auto_update() is true This is only invoked, now, if the neighborlist-autoupdate flag is on.
virtual void	setup_for_scoring (pose::Pose &pose, ScoreFunction const &scfxn) const
	check compatibility with atomtypeset
virtual void	setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) const
virtual void	setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const
virtual void	prepare_rotamers_for_packing (pose::Pose const &pose, conformation::RotamerSetBase &set) const
virtual void	update_residue_for_packing (pose::Pose &pose, Size resid) const
count_pair::CountPairFunctionCOP	get_count_pair_function (Size res1, Size res2, pose::Pose const &pose, ScoreFunction const &sfxn) const
count_pair::CountPairFunctionCOP	get_count_pair_function (conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &pose, ScoreFunction const &sfxn) const
	and gets duplicated in a handful of other places within this class... this NEEDS to be reworked.
count_pair::CountPairFunctionOP	get_intrares_countpair (conformation::Residue const &res, pose::Pose const &pose, ScoreFunction const &sfxn) const
virtual void	residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap.
virtual bool	use_extended_residue_pair_energy_interface () const
	APL -- note, new.
virtual void	residue_pair_energy_ext (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResPairMinimizationData const &min_data, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	APL -- note, new.
virtual void	setup_for_minimizing_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, ResSingleMinimizationData const &res1_data_cache, ResSingleMinimizationData const &res2_data_cache, ResPairMinimizationData &min_data) const
	APL -- note, new.
virtual bool	requires_a_setup_for_scoring_for_residue_opportunity (pose::Pose const &pose) const
	Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.
virtual void	setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &, ResSingleMinimizationData &min_data) const
	Do any setup work should the coordinates of this residue (who is still guaranteed to be of the same residue type as when setup_for_minimizing_for_residue was called) have changed so dramatically as to possibly require some amount of setup work before scoring should proceed. This function is used for both intra-residue setup and pre-inter-residue setup.
virtual bool	requires_a_setup_for_derivatives_for_residue_opportunity (pose::Pose const &pose) const
	Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.
virtual void	setup_for_derivatives_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &, ResSingleMinimizationData &min_data) const
	Do any setup work necessary before evaluating the derivatives for this residue.
virtual bool	requires_a_setup_for_scoring_for_residue_pair_opportunity (pose::Pose const &pose) const
	Does this EnergyMethod require the opportunity to examine each residue pair before scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.
virtual void	setup_for_scoring_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &minsingle_data1, ResSingleMinimizationData const &minsingle_data2, pose::Pose const &pose, ScoreFunction const &, ResPairMinimizationData &data_cache) const
	Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed.
virtual bool	requires_a_setup_for_derivatives_for_residue_pair_opportunity (pose::Pose const &pose) const
	Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.
virtual void	setup_for_derivatives_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &minsingle_data1, ResSingleMinimizationData const &minsingle_data2, pose::Pose const &pose, ScoreFunction const &, ResPairMinimizationData &data_cache) const
	Do any setup work necessary before evaluating the derivatives for this residue pair.
virtual void	eval_residue_pair_derivatives (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &, ResSingleMinimizationData const &, ResPairMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_at_derivs, utility::vector1< DerivVectorPair > &r2_at_derivs) const
	APL -- note, new.
virtual void	backbone_backbone_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluates the interaction between the backbone of rsd1 and the backbone of rsd2 and accumulates the unweighted energy.
virtual void	backbone_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluates the interaction between the backbone of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy.
virtual void	sidechain_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluates the interaction between the sidechain of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy.
virtual void	evaluate_rotamer_pair_energies (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const
	Batch computation of rotamer pair energies. Need not be overriden in derived class -- by default, iterates over all pairs of rotamers, and calls derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.
virtual void	evaluate_rotamer_background_energies (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< core::PackerEnergy > &energy_vector) const
	Batch computation of rotamer/background energies. Need not be overriden in derived class -- by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.
virtual bool	use_extended_intrares_energy_interface () const
	APL -- note, new.
virtual void	eval_intrares_energy_ext (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	APL -- note, new.
virtual void	setup_for_minimizing_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, ResSingleMinimizationData &min_data) const
	APL -- note, new.
void	eval_intrares_derivatives (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &atom_derivs) const
	Evaluate the derivative for the intra-residue component of this energy method for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd.
virtual void	bump_energy_full (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
virtual void	bump_energy_backbone (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
virtual void	finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) const
	called at the end of energy evaluation
virtual void	eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &, ScoreFunction const &sfxn, EnergyMap const &weights, Vector &F1, Vector &F2) const
	called during gradient-based minimization inside dfunc
void	prepare_for_residue_pair (Size const res1, Size const res2, pose::Pose const &pose) const
void	virtual_atom_pair_energy (EnergyMap &emap) const
void	atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, EnergyMap &emap, Real &dsq) const
void	atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb, Real &dsq) const
	for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication.
void	atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, AtomPairEnergy &ape) const
void	pair_energy_H (conformation::Atom const &atom1, conformation::Atom const &atom2, Real weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb) const
void	pair_energy_H (conformation::Atom const &atom1, conformation::Atom const &atom2, Real weight, AtomPairEnergy &ape) const
void	pair_energy_H (conformation::Atom const &atom1, conformation::Atom const &atom2, Real weight, EnergyMap &emap) const
Real	eval_dE_dR_over_r (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
Real	hydrogen_interaction_cutoff2 () const
virtual Distance	atomic_interaction_cutoff () const
	Etable atomic distance cutoff is 5.5 A.
virtual bool	divides_backbone_and_sidechain_energetics () const
	A derived class should return true for this function if it implements its own versions of the backbone_backbone_energy, backbone_sidechain_energy and sidechain_sidechain_energy functions. The default sidechain_sidechain_energy implemented by the TwoBodyEnergy base class calls residue_pair_energy. If the derived class implements its own versions of these functions, then calling code may avoid calling it on pairs of residues that are "provably distant" based on a pair of bounding spheres for a sidechains and backbones and this method's atomic_interaction_cutoff energy method.
virtual void	indicate_required_context_graphs (utility::vector1< bool > &) const
	Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.
Energy	sum_energies (Real atr, Real rep, Real solv, Real bb) const
	Inline Methods For Trie-vs-Trie Algorithm.
Energy	heavyatom_heavyatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2, DistanceSquared &d2, Size &) const
Energy	heavyatom_hydrogenatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2, Size &) const
Energy	hydrogenatom_heavyatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2, Size &) const
Energy	hydrogenatom_hydrogenatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2, Size &) const
	BaseEtableEnergy (Etable const &etable_in, methods::EnergyMethodOptions const &options, ScoreType st_atr, ScoreType st_rep, ScoreType st_sol)
	construction with an etable
virtual void	setup_for_minimizing (pose::Pose &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map) const
	stashes nblist if use_nblist is true
virtual void	setup_for_scoring (pose::Pose &pose, ScoreFunction const &scfxn) const
	check compatibility with atomtypeset
virtual void	setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) const
	Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls.
virtual void	setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const
virtual void	prepare_rotamers_for_packing (pose::Pose const &pose, conformation::RotamerSetBase &set) const
virtual void	update_residue_for_packing (pose::Pose &pose, Size resid) const
count_pair::CountPairFunctionCOP	get_count_pair_function (Size res1, Size res2, pose::Pose const &pose, ScoreFunction const &sfxn) const
count_pair::CountPairFunctionCOP	get_count_pair_function (conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &pose, ScoreFunction const &sfxn) const
count_pair::CountPairFunctionOP	get_intrares_countpair (conformation::Residue const &res, pose::Pose const &pose, ScoreFunction const &sfxn) const
virtual void	residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap.
virtual void	backbone_backbone_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluates the interaction between the backbone of rsd1 and the backbone of rsd2 and accumulates the unweighted energy.
virtual void	backbone_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluates the interaction between the backbone of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy.
virtual void	sidechain_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluates the interaction between the sidechain of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy.
virtual void	evaluate_rotamer_pair_energies (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const
	Batch computation of rotamer pair energies. Need not be overriden in derived class -- by default, iterates over all pairs of rotamers, and calls derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.
virtual void	evaluate_rotamer_background_energies (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< core::PackerEnergy > &energy_vector) const
	Batch computation of rotamer/background energies. Need not be overriden in derived class -- by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.
virtual void	bump_energy_full (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
virtual void	bump_energy_backbone (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
virtual void	finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) const
	called at the end of energy evaluation
virtual void	eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &, ScoreFunction const &sfxn, EnergyMap const &weights, Vector &F1, Vector &F2) const
	called during gradient-based minimization inside dfunc
void	prepare_for_residue_pair (Size const res1, Size const res2, pose::Pose const &pose) const
void	atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, EnergyMap &emap, Real &dsq) const
void	memb_atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, EnergyMap &emap, Real &dsq) const
	pba
void	fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const
	pba
void	atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb, Real &dsq) const
	for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication.
void	memb_atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb, Real &dsq) const
	for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication.
void	fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const
void	pair_energy_H (conformation::Atom const &atom1, conformation::Atom const &atom2, Real weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb) const
void	pair_energy_H (conformation::Atom const &atom1, conformation::Atom const &atom2, Real weight, EnergyMap &emap) const
Real	eval_dE_dR_over_r (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
Real	memb_eval_dE_dR_over_r (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
	pba
Real	hydrogen_interaction_cutoff2 () const
virtual Distance	atomic_interaction_cutoff () const
	Etable atomic distance cutoff is 5.5 A.
virtual bool	divides_backbone_and_sidechain_energetics () const
	A derived class should return true for this function if it implements its own versions of the backbone_backbone_energy, backbone_sidechain_energy and sidechain_sidechain_energy functions. The default sidechain_sidechain_energy implemented by the TwoBodyEnergy base class calls residue_pair_energy. If the derived class implements its own versions of these functions, then calling code may avoid calling it on pairs of residues that are "provably distant" based on a pair of bounding spheres for a sidechains and backbones and this method's atomic_interaction_cutoff energy method.
virtual void	indicate_required_context_graphs (utility::vector1< bool > &) const
	Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.
Energy	sum_energies (Real atr, Real rep, Real solv, Real bb) const
	Inline Methods For Trie-vs-Trie Algorithm.
Energy	heavyatom_heavyatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2, DistanceSquared &d2) const
Energy	heavyatom_hydrogenatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2) const
Energy	hydrogenatom_heavyatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2) const
Energy	hydrogenatom_hydrogenatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2) const
	BaseEtableEnergy (Etable const &etable_in, methods::EnergyMethodOptions const &options, ScoreType st_atr, ScoreType st_rep, ScoreType st_sol)
	construction with an etable
virtual void	setup_for_minimizing (pose::Pose &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map) const
	stashes nblist if use_nblist is true
virtual void	setup_for_scoring (pose::Pose &pose, ScoreFunction const &scfxn) const
	check compatibility with atomtypeset
virtual void	setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) const
	Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls.
virtual void	setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const
virtual void	prepare_rotamers_for_packing (pose::Pose const &pose, conformation::RotamerSetBase &set) const
virtual void	update_residue_for_packing (pose::Pose &pose, Size resid) const
count_pair::CountPairFunctionCOP	get_count_pair_function (Size res1, Size res2, pose::Pose const &pose, ScoreFunction const &sfxn) const
count_pair::CountPairFunctionCOP	get_count_pair_function (conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &pose, ScoreFunction const &sfxn) const
count_pair::CountPairFunctionOP	get_intrares_countpair (conformation::Residue const &res, pose::Pose const &pose, ScoreFunction const &sfxn) const
virtual void	residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap.
virtual void	backbone_backbone_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluates the interaction between the backbone of rsd1 and the backbone of rsd2 and accumulates the unweighted energy.
virtual void	backbone_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluates the interaction between the backbone of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy.
virtual void	sidechain_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluates the interaction between the sidechain of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy.
virtual void	evaluate_rotamer_pair_energies (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const
	Batch computation of rotamer pair energies. Need not be overriden in derived class -- by default, iterates over all pairs of rotamers, and calls derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.
virtual void	evaluate_rotamer_background_energies (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< core::PackerEnergy > &energy_vector) const
	Batch computation of rotamer/background energies. Need not be overriden in derived class -- by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.
virtual void	bump_energy_full (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
virtual void	bump_energy_backbone (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
virtual void	finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) const
	called at the end of energy evaluation
virtual void	eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &, ScoreFunction const &sfxn, EnergyMap const &weights, Vector &F1, Vector &F2) const
	called during gradient-based minimization inside dfunc
void	prepare_for_residue_pair (Size const res1, Size const res2, pose::Pose const &pose) const
void	atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, EnergyMap &emap, Real &dsq) const
void	memb_atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, EnergyMap &emap, Real &dsq) const
	pba
void	fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const
	pba
void	atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb, Real &dsq) const
	for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication.
void	memb_atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb, Real &dsq) const
	for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication.
void	fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const
void	pair_energy_H (conformation::Atom const &atom1, conformation::Atom const &atom2, Real weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb) const
void	pair_energy_H (conformation::Atom const &atom1, conformation::Atom const &atom2, Real weight, EnergyMap &emap) const
Real	eval_dE_dR_over_r (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
Real	memb_eval_dE_dR_over_r (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
	pba
Real	hydrogen_interaction_cutoff2 () const
virtual Distance	atomic_interaction_cutoff () const
	Etable atomic distance cutoff is 5.5 A.
virtual void	indicate_required_context_graphs (utility::vector1< bool > &) const
	Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.
Energy	sum_energies (Real atr, Real rep, Real solv, Real bb) const
	Inline Methods For Trie-vs-Trie Algorithm.
Energy	heavyatom_heavyatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2, DistanceSquared &d2) const
Energy	heavyatom_hydrogenatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2) const
Energy	hydrogenatom_heavyatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2) const
Energy	hydrogenatom_hydrogenatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2) const
Public Attributes
	__pad0__:ContextIndependentTwoBodyEnergy parent
	__pad1__:EnergyMethodOP EnergyMethodOP
Protected Member Functions
trie::TrieCountPairBaseOP	get_count_pair_function_trie (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn) const
	figure out the trie count pair function to use Need to refactor this so that the decision "what kind of count pair behavior should I use" can be decoupled from class instantiation, and therefore shared between the creation of the trie count pair classes and the regular count pair classes
trie::TrieCountPairBaseOP	get_count_pair_function_trie (conformation::Residue const &res1, conformation::Residue const &res2, trie::RotamerTrieBaseCOP trie1, trie::RotamerTrieBaseCOP trie2, pose::Pose const &pose, ScoreFunction const &sfxn) const
count_pair::CPCrossoverBehavior	determine_crossover_behavior (conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &, ScoreFunction const &sfxn) const
etrie::EtableRotamerTrieOP	create_rotamer_trie (conformation::RotamerSetBase const &rotset, pose::Pose const &pose) const
	create a rotamer trie for a particular set, deciding upon the kind of count pair data that needs to be contained by the trie.
etrie::EtableRotamerTrieOP	create_rotamer_trie (conformation::Residue const &residue, pose::Pose const &) const
etrie::EtableRotamerTrieOP	create_rotamer_trie_2 (conformation::RotamerSetBase const &rotset) const
etrie::EtableRotamerTrieOP	create_rotamer_trie_1 (conformation::RotamerSetBase const &rotset, Size connection_type) const
void	atom_pair_energy_ (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Real &atr, Real &rep, Real &solv, Real &bb, Real &dsq) const
void	pair_energy_H_ (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Real &atr, Real &rep, Real &solv, Real &bb) const
Real	eval_dE_dR_over_r_ (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
void	derived_prepare_for_residue_pair (Size const res1, Size const res2, pose::Pose const &) const
bool	interpolate_bins (conformation::Atom const &atom1, conformation::Atom const &atom2, Real &d2, int &disbin, Real &frac) const
void	set_scoretypes (ScoreType atr_type, ScoreType rep_type, ScoreType sol_type) const
ScoreType	rep_scoretype () const
trie::TrieCountPairBaseOP	get_count_pair_function_trie (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn) const
trie::TrieCountPairBaseOP	get_count_pair_function_trie (conformation::Residue const &res1, conformation::Residue const &res2, trie::RotamerTrieBaseCOP trie1, trie::RotamerTrieBaseCOP trie2, pose::Pose const &pose, ScoreFunction const &sfxn) const
count_pair::CPCrossoverBehavior	determine_crossover_behavior (conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &, ScoreFunction const &sfxn) const
etrie::EtableRotamerTrieOP	create_rotamer_trie (conformation::RotamerSetBase const &rotset, pose::Pose const &pose) const
etrie::EtableRotamerTrieOP	create_rotamer_trie_2 (conformation::RotamerSetBase const &rotset) const
etrie::EtableRotamerTrieOP	create_rotamer_trie_1 (conformation::RotamerSetBase const &rotset, Size connection_type) const
void	atom_pair_energy_ (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Real &atr, Real &rep, Real &solv, Real &bb, Real &dsq) const
void	memb_atom_pair_energy_ (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Real &atr, Real &rep, Real &solv, Real &bb, Real &dsq) const
void	fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const
void	pair_energy_H_ (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Real &atr, Real &rep, Real &solv, Real &bb) const
Real	eval_dE_dR_over_r_ (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
Real	memb_eval_dE_dR_over_r_ (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
	pba
void	derived_prepare_for_residue_pair (Size const res1, Size const res2, pose::Pose const &) const
bool	interpolate_bins (conformation::Atom const &atom1, conformation::Atom const &atom2, Real &d2, int &disbin, Real &frac) const
void	set_scoretypes (ScoreType atr_type, ScoreType rep_type, ScoreType sol_type) const
ScoreType	rep_scoretype () const
trie::TrieCountPairBaseOP	get_count_pair_function_trie (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn) const
trie::TrieCountPairBaseOP	get_count_pair_function_trie (conformation::Residue const &res1, conformation::Residue const &res2, trie::RotamerTrieBaseCOP trie1, trie::RotamerTrieBaseCOP trie2, pose::Pose const &pose, ScoreFunction const &sfxn) const
count_pair::CPCrossoverBehavior	determine_crossover_behavior (conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &, ScoreFunction const &sfxn) const
etrie::EtableRotamerTrieOP	create_rotamer_trie (conformation::RotamerSetBase const &rotset, pose::Pose const &pose) const
etrie::EtableRotamerTrieOP	create_rotamer_trie_2 (conformation::RotamerSetBase const &rotset) const
etrie::EtableRotamerTrieOP	create_rotamer_trie_1 (conformation::RotamerSetBase const &rotset, Size connection_type) const
void	atom_pair_energy_ (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Real &atr, Real &rep, Real &solv, Real &bb, Real &dsq) const
void	memb_atom_pair_energy_ (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Real &atr, Real &rep, Real &solv, Real &bb, Real &dsq) const
void	fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const
void	pair_energy_H_ (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Real &atr, Real &rep, Real &solv, Real &bb) const
Real	eval_dE_dR_over_r_ (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
Real	memb_eval_dE_dR_over_r_ (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
	pba
void	derived_prepare_for_residue_pair (Size const res1, Size const res2, pose::Pose const &) const
bool	interpolate_bins (conformation::Atom const &atom1, conformation::Atom const &atom2, Real &d2, int &disbin, Real &frac) const
void	set_scoretypes (ScoreType atr_type, ScoreType rep_type, ScoreType sol_type) const
ScoreType	rep_scoretype () const
Protected Attributes
Etable const &	etable_
Friends
class	core::scoring::rna::RNA_FullAtomVDW_BasePhosphateCreator

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

---

Constructor & Destructor Documentation

template<class Derived >

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

construction with an etable

template<class Derived>

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

construction with an etable

template<class Derived>

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

construction with an etable

---

Member Function Documentation

template<class Derived>

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

Referenced by core::scoring::etable::BaseEtableEnergy< EtableEnergy >::atom_pair_energy(), core::scoring::etable::BaseEtableEnergy< EtableEnergy >::heavyatom_heavyatom_energy(), and core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy().

template<class Derived>

void core::scoring::etable::BaseEtableEnergy< Derived >::atom_pair_energy	(	conformation::Atom const &	atom1,
		conformation::Atom const &	atom2,
		Real const	weight,
		Energy &	atr,
		Energy &	rep,
		Energy &	solv,
		Energy &	bb,
		Real &	dsq
	)		const [inline]

for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication.

template<class Derived>

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

template<class Derived>

void core::scoring::etable::BaseEtableEnergy< Derived >::atom_pair_energy	(	conformation::Atom const &	atom1,
		conformation::Atom const &	atom2,
		Real const	weight,
		Energy &	atr,
		Energy &	rep,
		Energy &	solv,
		Energy &	bb,
		Real &	dsq
	)		const [inline]

for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication.

template<class Derived>

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

template<class Derived>

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

template<class Derived>

void core::scoring::etable::BaseEtableEnergy< Derived >::atom_pair_energy	(	conformation::Atom const &	atom1,
		conformation::Atom const &	atom2,
		Real const	weight,
		Energy &	atr,
		Energy &	rep,
		Energy &	solv,
		Energy &	bb,
		Real &	dsq
	)		const [inline]

for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication.

template<class Derived>

void core::scoring::etable::BaseEtableEnergy< Derived >::atom_pair_energy_	(	conformation::Atom const &	atom1,
		conformation::Atom const &	atom2,
		Real const	weight,
		Real &	atr,
		Real &	rep,
		Real &	solv,
		Real &	bb,
		Real &	dsq
	)		const [inline, protected]

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

template<class Derived >

void core::scoring::etable::BaseEtableEnergy< Derived >::atom_pair_energy_	(	conformation::Atom const &	atom1,
		conformation::Atom const &	atom2,
		Real const	weight,
		Real &	atr,
		Real &	rep,
		Real &	solv,
		Real &	bb,
		Real &	dsq
	)		const [inline, protected]

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

References core::conformation::Atom::type().

Referenced by core::scoring::etable::BaseEtableEnergy< EtableEnergy >::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,
		Real &	atr,
		Real &	rep,
		Real &	solv,
		Real &	bb,
		Real &	dsq
	)		const [inline, protected]

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

template<class Derived>

virtual Distance core::scoring::etable::BaseEtableEnergy< Derived >::atomic_interaction_cutoff

(

)

const [virtual]

Etable atomic distance cutoff is 5.5 A.

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

template<class Derived >

Distance core::scoring::etable::BaseEtableEnergy< Derived >::atomic_interaction_cutoff

(

)

const [virtual]

Etable atomic distance cutoff is 5.5 A.

return the Etables atomic distance cutoff

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

References core::chemical::MAX_CHEMICAL_BOND_TO_HYDROGEN_LENGTH.

template<class Derived>

virtual Distance core::scoring::etable::BaseEtableEnergy< Derived >::atomic_interaction_cutoff

(

)

const [virtual]

Etable atomic distance cutoff is 5.5 A.

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

template<class Derived>

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

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

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

template<class Derived>

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

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

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

template<class Derived >

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

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(), core::conformation::Residue::seqpos(), 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(), core::conformation::Residue::seqpos(), 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]

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

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]

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::conformation::Residue::is_DNA(), and core::conformation::Residue::seqpos().

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]

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

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]

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

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]

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::conformation::Residue::is_DNA(), and core::conformation::Residue::seqpos().

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]

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

template<class Derived>

etrie::EtableRotamerTrieOP core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie	(	conformation::RotamerSetBase const &	rotset,
		pose::Pose const &	pose
	)		const [protected]

template<class Derived>

etrie::EtableRotamerTrieOP core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie	(	conformation::RotamerSetBase const &	rotset,
		pose::Pose const &	pose
	)		const [protected]

template<class Derived >

EtableRotamerTrieOP core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie	(	conformation::Residue const &	residue,
		pose::Pose const &
	)		const [protected]

Create a one-residue trie.

References core::scoring::trie::create_cpdata_correspondence_for_rotamer(), core::scoring::trie::create_trie(), core::scoring::trie::CPDataCorrespondence::has_pseudobonds(), core::scoring::trie::CPDataCorrespondence::max_connpoints_for_residue(), and core::scoring::trie::CPDataCorrespondence::n_entries().

template<class Derived >

EtableRotamerTrieOP core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie	(	conformation::RotamerSetBase const &	rotset,
		pose::Pose const &	pose
	)		const [protected]

create a rotamer trie for a particular set, deciding upon the kind of count pair data that needs to be contained by the trie.

References core::scoring::trie::create_cpdata_correspondence_for_rotamerset(), core::scoring::trie::create_trie(), core::scoring::trie::CPDataCorrespondence::has_pseudobonds(), core::scoring::trie::CPDataCorrespondence::max_connpoints_for_residue(), and core::scoring::trie::CPDataCorrespondence::n_entries().

template<class Derived>

etrie::EtableRotamerTrieOP core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie_1	(	conformation::RotamerSetBase const &	rotset,
		Size	connection_type
	)		const [protected]

template<class Derived>

etrie::EtableRotamerTrieOP core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie_1	(	conformation::RotamerSetBase const &	rotset,
		Size	connection_type
	)		const [protected]

template<class Derived>

etrie::EtableRotamerTrieOP core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie_1	(	conformation::RotamerSetBase const &	rotset,
		Size	connection_type
	)		const [protected]

template<class Derived>

etrie::EtableRotamerTrieOP core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie_2

(

conformation::RotamerSetBase const &

rotset

)

const [protected]

template<class Derived>

etrie::EtableRotamerTrieOP core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie_2

(

conformation::RotamerSetBase const &

rotset

)

const [protected]

template<class Derived>

etrie::EtableRotamerTrieOP core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie_2

(

conformation::RotamerSetBase const &

rotset

)

const [protected]

template<class Derived>

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

Reimplemented in core::scoring::etable::CoarseEtableEnergy, and core::scoring::etable::EtableEnergy.

Referenced by core::scoring::etable::BaseEtableEnergy< EtableEnergy >::prepare_for_residue_pair().

template<class Derived>

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

Reimplemented in core::scoring::etable::CoarseEtableEnergy, and core::scoring::etable::EtableEnergy.

template<class Derived>

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

Reimplemented in core::scoring::etable::CoarseEtableEnergy, and core::scoring::etable::EtableEnergy.

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]

References core::scoring::etable::count_pair::CP_CROSSOVER_3, core::scoring::etable::count_pair::CP_CROSSOVER_4, core::scoring::ScoreFunction::has_zero_weight(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), core::scoring::mm_twist, core::conformation::Residue::polymeric_sequence_distance(), core::scoring::rama, and core::conformation::Residue::seqpos().

template<class Derived>

virtual bool core::scoring::etable::BaseEtableEnergy< Derived >::divides_backbone_and_sidechain_energetics

(

)

const [inline, virtual]

A derived class should return true for this function if it implements its own versions of the backbone_backbone_energy, backbone_sidechain_energy and sidechain_sidechain_energy functions. The default sidechain_sidechain_energy implemented by the TwoBodyEnergy base class calls residue_pair_energy. If the derived class implements its own versions of these functions, then calling code may avoid calling it on pairs of residues that are "provably distant" based on a pair of bounding spheres for a sidechains and backbones and this method's atomic_interaction_cutoff energy method.

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

template<class Derived>

virtual bool core::scoring::etable::BaseEtableEnergy< Derived >::divides_backbone_and_sidechain_energetics

(

)

const [inline, virtual]

A derived class should return true for this function if it implements its own versions of the backbone_backbone_energy, backbone_sidechain_energy and sidechain_sidechain_energy functions. The default sidechain_sidechain_energy implemented by the TwoBodyEnergy base class calls residue_pair_energy. If the derived class implements its own versions of these functions, then calling code may avoid calling it on pairs of residues that are "provably distant" based on a pair of bounding spheres for a sidechains and backbones and this method's atomic_interaction_cutoff energy method.

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

template<class Derived>

virtual void core::scoring::etable::BaseEtableEnergy< Derived >::eval_atom_derivative	(	id::AtomID const &	id,
		pose::Pose const &	pose,
		kinematics::DomainMap const &	,
		ScoreFunction const &	sfxn,
		EnergyMap const &	weights,
		Vector &	F1,
		Vector &	F2
	)		const [virtual]

called during gradient-based minimization inside dfunc

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

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

template<class Derived >

void core::scoring::etable::BaseEtableEnergy< Derived >::eval_atom_derivative	(	id::AtomID const &	id,
		pose::Pose const &	pose,
		kinematics::DomainMap const &	,
		ScoreFunction const &	sfxn,
		EnergyMap const &	weights,
		Vector &	F1,
		Vector &	F2
	)		const [virtual]

called during gradient-based minimization inside dfunc

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

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

References core::conformation::Residue::atom(), core::scoring::NeighborList::atom_neighbors(), core::scoring::AtomNeighbor::atomno(), core::pose::Pose::energies(), core::scoring::EnergiesCacheableDataType::ETABLE_NBLIST, core::scoring::Energies::nblist(), core::pose::Pose::residue(), core::scoring::AtomNeighbor::rsd(), core::scoring::Energies::use_nblist(), and core::scoring::AtomNeighbor::weight().

template<class Derived>

virtual void core::scoring::etable::BaseEtableEnergy< Derived >::eval_atom_derivative	(	id::AtomID const &	id,
		pose::Pose const &	pose,
		kinematics::DomainMap const &	,
		ScoreFunction const &	sfxn,
		EnergyMap const &	weights,
		Vector &	F1,
		Vector &	F2
	)		const [virtual]

called during gradient-based minimization inside dfunc

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

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

template<class Derived>

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

template<class Derived>

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

Referenced by core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative().

template<class Derived>

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

template<class Derived >

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

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

References core::conformation::Atom::type(), and core::conformation::Atom::xyz().

Referenced by core::scoring::etable::BaseEtableEnergy< EtableEnergy >::eval_dE_dR_over_r().

template<class Derived>

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

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

template<class Derived>

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

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

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]

APL -- note, new.

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_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]

APL -- note, new.

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

References core::conformation::Residue::atom(), core::pose::Pose::energies(), core::scoring::etab_pair_nblist, core::scoring::ResPairMinimizationData::get_data(), core::scoring::ResPairMinimizationData::get_data_ref(), core::conformation::Residue::natoms(), and core::scoring::Energies::use_nblist_auto_update().

template<class Derived>

virtual void core::scoring::etable::BaseEtableEnergy< Derived >::evaluate_rotamer_background_energies	(	conformation::RotamerSetBase const &	set,
		conformation::Residue const &	residue,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap const &	weights,
		utility::vector1< core::PackerEnergy > &	energy_vector
	)		const [virtual]

Batch computation of rotamer/background energies. Need not be overriden in derived class -- by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.

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

template<class Derived>

virtual void core::scoring::etable::BaseEtableEnergy< Derived >::evaluate_rotamer_background_energies	(	conformation::RotamerSetBase const &	set,
		conformation::Residue const &	residue,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap const &	weights,
		utility::vector1< core::PackerEnergy > &	energy_vector
	)		const [virtual]

Batch computation of rotamer/background energies. Need not be overriden in derived class -- by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.

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

template<class Derived >

void core::scoring::etable::BaseEtableEnergy< Derived >::evaluate_rotamer_background_energies	(	conformation::RotamerSetBase const &	set,
		conformation::Residue const &	residue,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap const &	weights,
		utility::vector1< core::PackerEnergy > &	energy_vector
	)		const [virtual]

Batch computation of rotamer/background energies. Need not be overriden in derived class -- by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.

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

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

template<class Derived>

virtual void core::scoring::etable::BaseEtableEnergy< Derived >::evaluate_rotamer_pair_energies	(	conformation::RotamerSetBase const &	set1,
		conformation::RotamerSetBase const &	set2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap const &	weights,
		ObjexxFCL::FArray2D< core::PackerEnergy > &	energy_table
	)		const [virtual]

Batch computation of rotamer pair energies. Need not be overriden in derived class -- by default, iterates over all pairs of rotamers, and calls derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.

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

template<class Derived >

void core::scoring::etable::BaseEtableEnergy< Derived >::evaluate_rotamer_pair_energies	(	conformation::RotamerSetBase const &	set1,
		conformation::RotamerSetBase const &	set2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap const &	weights,
		ObjexxFCL::FArray2D< core::PackerEnergy > &	energy_table
	)		const [virtual]

Batch computation of rotamer pair energies. Need not be overriden in derived class -- by default, iterates over all pairs of rotamers, and calls derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.

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

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

template<class Derived>

virtual void core::scoring::etable::BaseEtableEnergy< Derived >::evaluate_rotamer_pair_energies	(	conformation::RotamerSetBase const &	set1,
		conformation::RotamerSetBase const &	set2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap const &	weights,
		ObjexxFCL::FArray2D< core::PackerEnergy > &	energy_table
	)		const [virtual]

Batch computation of rotamer pair energies. Need not be overriden in derived class -- by default, iterates over all pairs of rotamers, and calls derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.

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

template<class Derived>

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

pba

template<class Derived>

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

template<class Derived>

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

template<class Derived>

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

pba

Referenced by core::scoring::etable::BaseEtableEnergy< EtableEnergy >::fast_memb_env_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, protected]

template<class Derived >

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.

References core::conformation::Residue::atom(), core::scoring::NeighborList::check_domain_map(), core::scoring::Energies::domain_map(), core::pose::Pose::energies(), core::scoring::EnergiesCacheableDataType::ETABLE_NBLIST, core::conformation::Residue::natoms(), core::scoring::Energies::nblist(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::scoring::Energies::use_nblist(), and core::scoring::Energies::use_nblist_auto_update().

template<class Derived>

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

called at the end of energy evaluation

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

template<class Derived>

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

called at the end of energy evaluation

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

template<class Derived>

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

template<class Derived>

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

template<class Derived>

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

template<class Derived>

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

template<class Derived >

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

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

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

template<class Derived >

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

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

template<class Derived>

trie::TrieCountPairBaseOP core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function_trie	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		trie::RotamerTrieBaseCOP	trie1,
		trie::RotamerTrieBaseCOP	trie2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn
	)		const [protected]

template<class Derived>

trie::TrieCountPairBaseOP core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function_trie	(	conformation::RotamerSetBase const &	set1,
		conformation::RotamerSetBase const &	set2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn
	)		const [protected]

template<class Derived>

trie::TrieCountPairBaseOP core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function_trie	(	conformation::RotamerSetBase const &	set1,
		conformation::RotamerSetBase const &	set2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn
	)		const [protected]

template<class Derived>

trie::TrieCountPairBaseOP core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function_trie	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		trie::RotamerTrieBaseCOP	trie1,
		trie::RotamerTrieBaseCOP	trie2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn
	)		const [protected]

template<class Derived >

TrieCountPairBaseOP core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function_trie	(	conformation::RotamerSetBase const &	set1,
		conformation::RotamerSetBase const &	set2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn
	)		const [protected]

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

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

template<class Derived >

TrieCountPairBaseOP core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function_trie	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		trie::RotamerTrieBaseCOP	trie1,
		trie::RotamerTrieBaseCOP	trie2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn
	)		const [protected]

References core::scoring::etable::count_pair::CP_CROSSOVER_3, core::scoring::etable::count_pair::CP_CROSSOVER_4, core::scoring::etable::count_pair::CP_MULTIPLE_BONDS_OR_PSEUDOBONDS, core::scoring::etable::count_pair::CP_ONE_BOND, core::scoring::methods::determine_crossover_behavior(), core::scoring::etable::count_pair::CountPairFactory::determine_residue_connection(), core::conformation::Residue::is_DNA(), and core::conformation::Residue::seqpos().

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

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

template<class Derived>

Energy core::scoring::etable::BaseEtableEnergy< Derived >::heavyatom_heavyatom_energy	(	etrie::EtableAtom const &	at1,
		etrie::EtableAtom const &	at2,
		DistanceSquared &	d2
	)		const [inline]

template<class Derived>

Energy core::scoring::etable::BaseEtableEnergy< Derived >::heavyatom_heavyatom_energy	(	etrie::EtableAtom const &	at1,
		etrie::EtableAtom const &	at2,
		DistanceSquared &	d2,
		Size &
	)		const [inline]

template<class Derived>

Energy core::scoring::etable::BaseEtableEnergy< Derived >::heavyatom_heavyatom_energy	(	etrie::EtableAtom const &	at1,
		etrie::EtableAtom const &	at2,
		DistanceSquared &	d2
	)		const [inline]

template<class Derived>

Energy core::scoring::etable::BaseEtableEnergy< Derived >::heavyatom_hydrogenatom_energy	(	etrie::EtableAtom const &	at1,
		etrie::EtableAtom const &	at2
	)		const [inline]

template<class Derived>

Energy core::scoring::etable::BaseEtableEnergy< Derived >::heavyatom_hydrogenatom_energy	(	etrie::EtableAtom const &	at1,
		etrie::EtableAtom const &	at2
	)		const [inline]

template<class Derived>

Energy core::scoring::etable::BaseEtableEnergy< Derived >::heavyatom_hydrogenatom_energy	(	etrie::EtableAtom const &	at1,
		etrie::EtableAtom const &	at2,
		Size &
	)		const [inline]

template<class Derived>

Real core::scoring::etable::BaseEtableEnergy< Derived >::hydrogen_interaction_cutoff2

(

)

const [inline]

template<class Derived>

Real core::scoring::etable::BaseEtableEnergy< Derived >::hydrogen_interaction_cutoff2

(

)

const [inline]

Referenced by core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy().

template<class Derived>

Real core::scoring::etable::BaseEtableEnergy< Derived >::hydrogen_interaction_cutoff2

(

)

const [inline]

template<class Derived>

Energy core::scoring::etable::BaseEtableEnergy< Derived >::hydrogenatom_heavyatom_energy	(	etrie::EtableAtom const &	at1,
		etrie::EtableAtom const &	at2
	)		const [inline]

template<class Derived>

Energy core::scoring::etable::BaseEtableEnergy< Derived >::hydrogenatom_heavyatom_energy	(	etrie::EtableAtom const &	at1,
		etrie::EtableAtom const &	at2
	)		const [inline]

template<class Derived>

Energy core::scoring::etable::BaseEtableEnergy< Derived >::hydrogenatom_heavyatom_energy	(	etrie::EtableAtom const &	at1,
		etrie::EtableAtom const &	at2,
		Size &
	)		const [inline]

template<class Derived>

Energy core::scoring::etable::BaseEtableEnergy< Derived >::hydrogenatom_hydrogenatom_energy	(	etrie::EtableAtom const &	at1,
		etrie::EtableAtom const &	at2
	)		const [inline]

template<class Derived>

Energy core::scoring::etable::BaseEtableEnergy< Derived >::hydrogenatom_hydrogenatom_energy	(	etrie::EtableAtom const &	at1,
		etrie::EtableAtom const &	at2
	)		const [inline]

template<class Derived>

Energy core::scoring::etable::BaseEtableEnergy< Derived >::hydrogenatom_hydrogenatom_energy	(	etrie::EtableAtom const &	at1,
		etrie::EtableAtom const &	at2,
		Size &
	)		const [inline]

template<class Derived>

virtual void core::scoring::etable::BaseEtableEnergy< Derived >::indicate_required_context_graphs

(

utility::vector1< bool > &

context_graphs_required

)

const [virtual]

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

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

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

template<class Derived >

void core::scoring::etable::BaseEtableEnergy< Derived >::indicate_required_context_graphs

(

utility::vector1< bool > &

context_graphs_required

)

const [virtual]

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

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

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

template<class Derived>

virtual void core::scoring::etable::BaseEtableEnergy< Derived >::indicate_required_context_graphs

(

utility::vector1< bool > &

context_graphs_required

)

const [virtual]

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

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

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

template<class Derived >

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

References core::conformation::Atom::xyz().

template<class Derived>

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

template<class Derived>

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

template<class Derived>

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

pba

template<class Derived>

void core::scoring::etable::BaseEtableEnergy< Derived >::memb_atom_pair_energy	(	conformation::Atom const &	atom1,
		conformation::Atom const &	atom2,
		Real const	weight,
		Energy &	atr,
		Energy &	rep,
		Energy &	solv,
		Energy &	bb,
		Real &	dsq
	)		const [inline]

for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication.

pba

template<class Derived>

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

pba

Referenced by core::scoring::etable::BaseEtableEnergy< EtableEnergy >::memb_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,
		Energy &	atr,
		Energy &	rep,
		Energy &	solv,
		Energy &	bb,
		Real &	dsq
	)		const [inline]

for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication.

pba

template<class Derived>

void core::scoring::etable::BaseEtableEnergy< Derived >::memb_atom_pair_energy_	(	conformation::Atom const &	atom1,
		conformation::Atom const &	atom2,
		Real const	weight,
		Real &	atr,
		Real &	rep,
		Real &	solv,
		Real &	bb,
		Real &	dsq
	)		const [inline, protected]

template<class Derived >

void core::scoring::etable::BaseEtableEnergy< Derived >::memb_atom_pair_energy_	(	conformation::Atom const &	atom1,
		conformation::Atom const &	atom2,
		Real const	weight,
		Real &	atr,
		Real &	rep,
		Real &	solv,
		Real &	bb,
		Real &	dsq
	)		const [inline, protected]

References make_table_of_pilot_apps::f, core::scoring::MembraneEmbed_from_pose(), core::conformation::Atom::type(), and core::conformation::Atom::xyz().

Referenced by core::scoring::etable::BaseEtableEnergy< EtableEnergy >::memb_atom_pair_energy().

template<class Derived>

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

pba

template<class Derived>

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

pba

template<class Derived>

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

pba

template<class Derived >

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

pba

References make_table_of_pilot_apps::f, core::scoring::MembraneEmbed_from_pose(), core::conformation::Atom::type(), and core::conformation::Atom::xyz().

Referenced by core::scoring::etable::BaseEtableEnergy< EtableEnergy >::memb_eval_dE_dR_over_r().

template<class Derived >

bool core::scoring::etable::BaseEtableEnergy< Derived >::minimize_in_whole_structure_context

(

pose::Pose const &

pose

)

const [virtual]

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

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

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

template<class Derived>

void core::scoring::etable::BaseEtableEnergy< Derived >::pair_energy_H	(	conformation::Atom const &	atom1,
		conformation::Atom const &	atom2,
		Real	weight,
		Energy &	atr,
		Energy &	rep,
		Energy &	solv,
		Energy &	bb
	)		const [inline]

template<class Derived>

void core::scoring::etable::BaseEtableEnergy< Derived >::pair_energy_H	(	conformation::Atom const &	atom1,
		conformation::Atom const &	atom2,
		Real	weight,
		Energy &	atr,
		Energy &	rep,
		Energy &	solv,
		Energy &	bb
	)		const [inline]

template<class Derived >

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

References core::scoring::coarse_beadlj.

template<class Derived>

void core::scoring::etable::BaseEtableEnergy< Derived >::pair_energy_H	(	conformation::Atom const &	atom1,
		conformation::Atom const &	atom2,
		Real	weight,
		AtomPairEnergy &	ape
	)		const [inline]

template<class Derived>

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

template<class Derived>

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

template<class Derived>

void core::scoring::etable::BaseEtableEnergy< Derived >::pair_energy_H	(	conformation::Atom const &	atom1,
		conformation::Atom const &	atom2,
		Real	weight,
		Energy &	atr,
		Energy &	rep,
		Energy &	solv,
		Energy &	bb
	)		const [inline]

Referenced by core::scoring::etable::BaseEtableEnergy< EtableEnergy >::heavyatom_hydrogenatom_energy(), core::scoring::etable::BaseEtableEnergy< EtableEnergy >::hydrogenatom_heavyatom_energy(), core::scoring::etable::BaseEtableEnergy< EtableEnergy >::hydrogenatom_hydrogenatom_energy(), core::scoring::etable::BaseEtableEnergy< EtableEnergy >::pair_energy_H(), and core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_fast_pair_energy_attached_H().

template<class Derived>

void core::scoring::etable::BaseEtableEnergy< Derived >::pair_energy_H_	(	conformation::Atom const &	atom1,
		conformation::Atom const &	atom2,
		Real const	weight,
		Real &	atr,
		Real &	rep,
		Real &	solv,
		Real &	bb
	)		const [inline, protected]

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

template<class Derived>

void core::scoring::etable::BaseEtableEnergy< Derived >::pair_energy_H_	(	conformation::Atom const &	atom1,
		conformation::Atom const &	atom2,
		Real const	weight,
		Real &	atr,
		Real &	rep,
		Real &	solv,
		Real &	bb
	)		const [inline, protected]

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

template<class Derived >

void core::scoring::etable::BaseEtableEnergy< Derived >::pair_energy_H_	(	conformation::Atom const &	atom1,
		conformation::Atom const &	atom2,
		Real const	weight,
		Real &	atr,
		Real &	rep,
		Real &	solv,
		Real &	bb
	)		const [inline, protected]

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

References core::conformation::Atom::type().

Referenced by core::scoring::etable::BaseEtableEnergy< EtableEnergy >::pair_energy_H().

template<class Derived>

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

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

template<class Derived>

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

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

template<class Derived>

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

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

template<class Derived>

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

default implementation noop

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

template<class Derived>

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

default implementation noop

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

template<class Derived >

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

default implementation noop

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

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

template<class Derived >

ScoreType core::scoring::etable::BaseEtableEnergy< Derived >::rep_scoretype

(

)

const [protected]

template<class Derived>

ScoreType core::scoring::etable::BaseEtableEnergy< Derived >::rep_scoretype

(

)

const [protected]

template<class Derived>

ScoreType core::scoring::etable::BaseEtableEnergy< Derived >::rep_scoretype

(

)

const [protected]

template<class Derived >

bool core::scoring::etable::BaseEtableEnergy< Derived >::requires_a_setup_for_derivatives_for_residue_opportunity

(

pose::Pose const &

pose

)

const [virtual]

Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

template<class Derived >

bool core::scoring::etable::BaseEtableEnergy< Derived >::requires_a_setup_for_derivatives_for_residue_pair_opportunity

(

pose::Pose const &

pose

)

const [virtual]

Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

template<class Derived >

bool core::scoring::etable::BaseEtableEnergy< Derived >::requires_a_setup_for_scoring_for_residue_opportunity

(

pose::Pose const &

pose

)

const [virtual]

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

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

template<class Derived >

bool core::scoring::etable::BaseEtableEnergy< Derived >::requires_a_setup_for_scoring_for_residue_pair_opportunity

(

pose::Pose const &

pose

)

const [virtual]

Does this EnergyMethod require the opportunity to examine each residue pair before scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

template<class Derived>

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

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

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

template<class Derived >

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

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

Implements 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(), core::conformation::Residue::seqpos(), and core::scoring::Energies::use_nblist().

template<class Derived>

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

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

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

template<class Derived >

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

APL -- note, new.

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

References core::conformation::Residue::atom(), core::pose::Pose::energies(), core::scoring::etab_pair_nblist, core::scoring::ResPairMinimizationData::get_data(), core::scoring::ResPairMinimizationData::get_data_ref(), and core::scoring::Energies::use_nblist_auto_update().

template<class Derived>

void core::scoring::etable::BaseEtableEnergy< Derived >::set_scoretypes	(	ScoreType	atr_type,
		ScoreType	rep_type,
		ScoreType	sol_type
	)		const [protected]

template<class Derived >

void core::scoring::etable::BaseEtableEnergy< Derived >::set_scoretypes	(	ScoreType	atr_type,
		ScoreType	rep_type,
		ScoreType	sol_type
	)		const [protected]

template<class Derived>

void core::scoring::etable::BaseEtableEnergy< Derived >::set_scoretypes	(	ScoreType	atr_type,
		ScoreType	rep_type,
		ScoreType	sol_type
	)		const [protected]

template<class Derived >

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

Make sure that the neighborlist is up-to-date bfore evaluating derivatives

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

References core::pose::Pose::energies(), core::scoring::EnergiesCacheableDataType::ETABLE_NBLIST, core::scoring::Energies::nblist(), core::scoring::NeighborList::prepare_for_scoring(), and core::scoring::Energies::use_nblist().

template<class Derived>

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

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

default implementation noop

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

template<class Derived>

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

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

default implementation noop

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

template<class Derived >

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

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

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

template<class Derived >

void core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_derivatives_for_residue_pair	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		ResSingleMinimizationData const &	minsingle_data1,
		ResSingleMinimizationData const &	minsingle_data2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		ResPairMinimizationData &	data_cache
	)		const [virtual]

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

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

template<class Derived>

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

stashes nblist if use_nblist is true

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

template<class Derived>

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

stashes nblist if use_nblist is true

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

template<class Derived >

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

stashes nblist if pose.energies().use_nblist_auto_update() is true This is only invoked, now, if the neighborlist-autoupdate flag is on.

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

References core::kinematics::MinimizerMapBase::domain_map(), core::pose::Pose::energies(), core::scoring::EnergiesCacheableDataType::ETABLE_NBLIST, core::scoring::NeighborList::set_auto_update(), core::scoring::NeighborList::setup(), core::scoring::Energies::use_nblist(), core::scoring::Energies::use_nblist_auto_update(), and XX.

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]

APL -- note, new.

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

References core::pose::Pose::energies(), core::scoring::etab_single_nblist, core::scoring::ResSingleMinimizationData::get_data(), core::scoring::ResSingleMinimizationData::set_data(), core::scoring::Energies::use_nblist_auto_update(), core::scoring::ScoreFunction::weights(), and XX.

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]

APL -- note, new.

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

References core::pose::Pose::energies(), core::scoring::etab_pair_nblist, core::scoring::ResPairMinimizationData::get_data(), core::scoring::ResPairMinimizationData::set_data(), core::scoring::Energies::use_nblist_auto_update(), and XX.

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]

default implementation noop

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

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::scoring::Energies::data(), core::pose::Pose::energies(), core::scoring::EnergiesCacheableDataType::ETABLE_TRIE_COLLECTION, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

template<class Derived>

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

default implementation noop

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

template<class Derived>

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

check compatibility with atomtypeset

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

template<class Derived >

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

check compatibility with atomtypeset

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

References core::pose::Pose::energies(), core::scoring::EnergiesCacheableDataType::ETABLE_NBLIST, core::scoring::Energies::nblist(), core::scoring::NeighborList::prepare_for_scoring(), and core::scoring::Energies::use_nblist().

template<class Derived>

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

check compatibility with atomtypeset

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

template<class Derived >

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

Do any setup work should the coordinates of this residue (who is still guaranteed to be of the same residue type as when setup_for_minimizing_for_residue was called) have changed so dramatically as to possibly require some amount of setup work before scoring should proceed. This function is used for both intra-residue setup and pre-inter-residue setup.

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

template<class Derived >

void core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_scoring_for_residue_pair	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		ResSingleMinimizationData const &	minsingle_data1,
		ResSingleMinimizationData const &	minsingle_data2,
		pose::Pose const &	pose,
		ScoreFunction const &	,
		ResPairMinimizationData &	data_cache
	)		const [virtual]

Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed.

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

template<class Derived >

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

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

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(), core::conformation::Residue::seqpos(), and core::scoring::Energies::use_nblist().

template<class Derived>

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

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

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

template<class Derived>

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

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

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

template<class Derived>

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

Inline Methods For Trie-vs-Trie Algorithm.

template<class Derived>

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

Inline Methods For Trie-vs-Trie Algorithm.

Referenced by core::scoring::etable::BaseEtableEnergy< EtableEnergy >::heavyatom_heavyatom_energy(), core::scoring::etable::BaseEtableEnergy< EtableEnergy >::heavyatom_hydrogenatom_energy(), core::scoring::etable::BaseEtableEnergy< EtableEnergy >::hydrogenatom_heavyatom_energy(), and core::scoring::etable::BaseEtableEnergy< EtableEnergy >::hydrogenatom_hydrogenatom_energy().

template<class Derived>

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

Inline Methods For Trie-vs-Trie Algorithm.

template<class Derived >

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

References core::scoring::Energies::data(), core::pose::Pose::energies(), core::scoring::EnergiesCacheableDataType::ETABLE_TRIE_COLLECTION, and core::pose::Pose::residue().

template<class Derived>

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

template<class Derived>

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

template<class Derived >

bool core::scoring::etable::BaseEtableEnergy< Derived >::use_extended_intrares_energy_interface

(

)

const [virtual]

APL -- note, new.

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

template<class Derived >

bool core::scoring::etable::BaseEtableEnergy< Derived >::use_extended_residue_pair_energy_interface

(

)

const [virtual]

APL -- note, new.

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

template<class Derived>

void core::scoring::etable::BaseEtableEnergy< Derived >::virtual_atom_pair_energy

(

EnergyMap &

emap

)

const [inline]

---

Friends And Related Function Documentation

template<class Derived>

friend class core::scoring::rna::RNA_FullAtomVDW_BasePhosphateCreator [friend]

---

Member Data Documentation

template<class Derived>

core::scoring::etable::BaseEtableEnergy< Derived >::__pad0__

template<class Derived>

core::scoring::etable::BaseEtableEnergy< Derived >::__pad1__

template<class Derived>

Etable const & core::scoring::etable::BaseEtableEnergy< Derived >::etable_ [protected]

---

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

• src/core/scoring/etable/BaseEtableEnergy.hh
• src/core/scoring/etable/BaseMembEtableEnergy.hh
• src/core/scoring/memb_etable/BaseMembEtableEnergy.hh
• src/core/scoring/etable/BaseEtableEnergy.tmpl.hh