#include <BaseEtableEnergy.hh>

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

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

Public Member Functions
	BaseEtableEnergy (methods::EnergyMethodCreatorOP creator, Etable const &etable_in, methods::EnergyMethodOptions const &options)
	construction with an etable More...

	BaseEtableEnergy (BaseEtableEnergy< Derived > const &)
	explicit copy constructor, since the BaseEtableEnergy now contains OP data More...

virtual bool	minimize_in_whole_structure_context (pose::Pose const &) const
	NO! friend class core::scoring::rna::RNA_FullAtomVDW_BasePhosphateCreator;. More...

virtual void	setup_for_minimizing (pose::Pose &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map) const
	stashes nblist if pose.energies().use_nblist_auto_update() is true This is only invoked, now, if the neighborlist-autoupdate flag is on. More...

virtual void	setup_for_scoring (pose::Pose &pose, ScoreFunction const &scfxn) const
	check compatibility with atomtypeset More...

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

virtual void	setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const

virtual void	prepare_rotamers_for_packing (pose::Pose const &pose, conformation::RotamerSetBase &set) const

virtual void	update_residue_for_packing (pose::Pose &pose, Size resid) const

count_pair::CountPairFunctionCOP	get_count_pair_function (Size res1, Size res2, pose::Pose const &pose, ScoreFunction const &sfxn) const

count_pair::CountPairFunctionCOP	get_count_pair_function (conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &pose, ScoreFunction const &sfxn) const
	and gets duplicated in a handful of other places within this class... this NEEDS to be reworked. More...

count_pair::CountPairFunctionOP	get_intrares_countpair (conformation::Residue const &res, pose::Pose const &pose, ScoreFunction const &sfxn) const

virtual void	residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap. More...

virtual bool	use_extended_residue_pair_energy_interface () const
	APL – note, new. More...

virtual void	residue_pair_energy_ext (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResPairMinimizationData const &min_data, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	APL – note, new. More...

virtual void	setup_for_minimizing_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, ResSingleMinimizationData const &res1_data_cache, ResSingleMinimizationData const &res2_data_cache, ResPairMinimizationData &min_data) const
	APL – note, new. More...

virtual bool	requires_a_setup_for_scoring_for_residue_opportunity (pose::Pose const &pose) const
	Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. More...

virtual void	setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &, ResSingleMinimizationData &min_data) const
	Do any setup work should the coordinates of this residue (who is still guaranteed to be of the same residue type as when setup_for_minimizing_for_residue was called) have changed so dramatically as to possibly require some amount of setup work before scoring should proceed. This function is used for both intra-residue setup and pre-inter-residue setup. More...

virtual bool	requires_a_setup_for_derivatives_for_residue_opportunity (pose::Pose const &pose) const
	Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so. More...

virtual void	setup_for_derivatives_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &, ResSingleMinimizationData &min_data) const
	Do any setup work necessary before evaluating the derivatives for this residue. More...

virtual bool	requires_a_setup_for_scoring_for_residue_pair_opportunity (pose::Pose const &pose) const
	Does this EnergyMethod require the opportunity to examine each residue pair before scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so. More...

virtual void	setup_for_scoring_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &minsingle_data1, ResSingleMinimizationData const &minsingle_data2, pose::Pose const &pose, ScoreFunction const &, ResPairMinimizationData &data_cache) const
	Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed. More...

virtual bool	requires_a_setup_for_derivatives_for_residue_pair_opportunity (pose::Pose const &pose) const
	Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so. More...

virtual void	setup_for_derivatives_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &minsingle_data1, ResSingleMinimizationData const &minsingle_data2, pose::Pose const &pose, ScoreFunction const &, ResPairMinimizationData &data_cache) const
	Do any setup work necessary before evaluating the derivatives for this residue pair. More...

virtual void	eval_residue_pair_derivatives (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &, ResSingleMinimizationData const &, ResPairMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_at_derivs, utility::vector1< DerivVectorPair > &r2_at_derivs) const
	APL – note, new. More...

virtual void	backbone_backbone_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluates the interaction between the backbone of rsd1 and the backbone of rsd2 and accumulates the unweighted energy. More...

virtual void	backbone_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluates the interaction between the backbone of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy. More...

virtual void	sidechain_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluates the interaction between the sidechain of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy. More...

virtual void	evaluate_rotamer_pair_energies (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const
	Batch computation of rotamer pair energies. Need not be overriden in derived class – by default, iterates over all pairs of rotamers, and calls derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...

virtual void	evaluate_rotamer_background_energies (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< core::PackerEnergy > &energy_vector) const
	Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...

virtual bool	use_extended_intrares_energy_interface () const
	APL – note, new. More...

virtual void	eval_intrares_energy_ext (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	APL – note, new. More...

virtual void	setup_for_minimizing_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, ResSingleMinimizationData &min_data) const
	APL – note, new. More...

void	eval_intrares_derivatives (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &atom_derivs) const
	Evaluate the derivative for the intra-residue component of this energy method for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd. More...

virtual void	bump_energy_full (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const

virtual void	bump_energy_backbone (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const

virtual void	finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) const
	called at the end of energy evaluation More...

virtual void	eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &, ScoreFunction const &sfxn, EnergyMap const &weights, Vector &F1, Vector &F2) const
	called during gradient-based minimization inside dfunc More...

void	prepare_for_residue_pair (Size const res1, Size const res2, pose::Pose const &pose) const
	Should/Could these inlined" in a separate .inline.hh? More...

void	atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, EnergyMap &emap, Real &dsq) const

void	atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb, Real &dsq) const
	for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication. More...

void	atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, AtomPairEnergy &ape) const
	APL – consider reinstating this function! More...

void	pair_energy_H (conformation::Atom const &atom1, conformation::Atom const &atom2, Real weight, EnergyMap &emap) const
	APL – Consider reinstating this function! More...

Real	hydrogen_interaction_cutoff2 () const

virtual Distance	atomic_interaction_cutoff () const
	Etable atomic distance cutoff is 5.5 A. More...

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

virtual void	indicate_required_context_graphs (utility::vector1< bool > &) const
	Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed. More...

	BaseEtableEnergy (Etable const &etable_in, methods::EnergyMethodOptions const &options, ScoreType st_atr, ScoreType st_rep, ScoreType st_sol)
	construction with an etable More...

virtual void	setup_for_minimizing (pose::Pose &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map) const
	stashes nblist if use_nblist is true More...

virtual void	setup_for_scoring (pose::Pose &pose, ScoreFunction const &scfxn) const
	check compatibility with atomtypeset More...

virtual void	setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) const
	Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. More...

virtual void	setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const

virtual void	prepare_rotamers_for_packing (pose::Pose const &pose, conformation::RotamerSetBase &set) const

virtual void	update_residue_for_packing (pose::Pose &pose, Size resid) const

count_pair::CountPairFunctionCOP	get_count_pair_function (Size res1, Size res2, pose::Pose const &pose, ScoreFunction const &sfxn) const

count_pair::CountPairFunctionCOP	get_count_pair_function (conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &pose, ScoreFunction const &sfxn) const

count_pair::CountPairFunctionOP	get_intrares_countpair (conformation::Residue const &res, pose::Pose const &pose, ScoreFunction const &sfxn) const

virtual void	residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap. More...

virtual void	backbone_backbone_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluates the interaction between the backbone of rsd1 and the backbone of rsd2 and accumulates the unweighted energy. More...

virtual void	backbone_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluates the interaction between the backbone of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy. More...

virtual void	sidechain_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluates the interaction between the sidechain of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy. More...

virtual void	evaluate_rotamer_pair_energies (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const
	Batch computation of rotamer pair energies. Need not be overriden in derived class – by default, iterates over all pairs of rotamers, and calls derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...

virtual void	evaluate_rotamer_background_energies (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< core::PackerEnergy > &energy_vector) const
	Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...

virtual void	bump_energy_full (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const

virtual void	bump_energy_backbone (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const

virtual void	finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) const
	called at the end of energy evaluation More...

virtual void	eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &, ScoreFunction const &sfxn, EnergyMap const &weights, Vector &F1, Vector &F2) const
	called during gradient-based minimization inside dfunc More...

void	prepare_for_residue_pair (Size const res1, Size const res2, pose::Pose const &pose) const
	Should/Could these inlined" in a separate .inline.hh? More...

void	atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, EnergyMap &emap, Real &dsq) const

void	memb_atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, EnergyMap &emap, Real &dsq) const
	pba More...

void	fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const
	pba More...

void	atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb, Real &dsq) const
	for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication. More...

void	memb_atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb, Real &dsq) const
	for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication. More...

void	fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const

void	pair_energy_H (conformation::Atom const &atom1, conformation::Atom const &atom2, Real weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb) const

void	pair_energy_H (conformation::Atom const &atom1, conformation::Atom const &atom2, Real weight, EnergyMap &emap) const

Real	eval_dE_dR_over_r (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const

Real	memb_eval_dE_dR_over_r (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
	pba More...

Real	hydrogen_interaction_cutoff2 () const

virtual Distance	atomic_interaction_cutoff () const
	Etable atomic distance cutoff is 5.5 A. More...

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

virtual void	indicate_required_context_graphs (utility::vector1< bool > &) const
	Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed. More...

Energy	sum_energies (Real atr, Real rep, Real solv, Real bb) const
	Inline Methods For Trie-vs-Trie Algorithm. More...

Energy	heavyatom_heavyatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2, DistanceSquared &d2) const

Energy	heavyatom_hydrogenatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2) const

Energy	hydrogenatom_heavyatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2) const

Energy	hydrogenatom_hydrogenatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2) const

	BaseEtableEnergy (Etable const &etable_in, methods::EnergyMethodOptions const &options, ScoreType st_atr, ScoreType st_rep, ScoreType st_sol)
	construction with an etable More...

virtual void	setup_for_minimizing (pose::Pose &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map) const
	stashes nblist if use_nblist is true More...

virtual void	setup_for_scoring (pose::Pose &pose, ScoreFunction const &scfxn) const
	check compatibility with atomtypeset More...

virtual void	setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) const
	Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. More...

virtual void	setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const

virtual void	prepare_rotamers_for_packing (pose::Pose const &pose, conformation::RotamerSetBase &set) const

virtual void	update_residue_for_packing (pose::Pose &pose, Size resid) const

count_pair::CountPairFunctionCOP	get_count_pair_function (Size res1, Size res2, pose::Pose const &pose, ScoreFunction const &sfxn) const

count_pair::CountPairFunctionCOP	get_count_pair_function (conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &pose, ScoreFunction const &sfxn) const

count_pair::CountPairFunctionOP	get_intrares_countpair (conformation::Residue const &res, pose::Pose const &pose, ScoreFunction const &sfxn) const

virtual void	residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap. More...

virtual void	backbone_backbone_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluates the interaction between the backbone of rsd1 and the backbone of rsd2 and accumulates the unweighted energy. More...

virtual void	backbone_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluates the interaction between the backbone of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy. More...

virtual void	sidechain_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluates the interaction between the sidechain of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy. More...

virtual void	evaluate_rotamer_pair_energies (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const
	Batch computation of rotamer pair energies. Need not be overriden in derived class – by default, iterates over all pairs of rotamers, and calls derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...

virtual void	evaluate_rotamer_background_energies (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< core::PackerEnergy > &energy_vector) const
	Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...

virtual void	bump_energy_full (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const

virtual void	bump_energy_backbone (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const

virtual void	finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) const
	called at the end of energy evaluation More...

virtual void	eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &, ScoreFunction const &sfxn, EnergyMap const &weights, Vector &F1, Vector &F2) const
	called during gradient-based minimization inside dfunc More...

void	prepare_for_residue_pair (Size const res1, Size const res2, pose::Pose const &pose) const
	Should/Could these inlined" in a separate .inline.hh? More...

void	atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, EnergyMap &emap, Real &dsq) const

void	memb_atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, EnergyMap &emap, Real &dsq) const
	pba More...

void	fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const
	pba More...

void	atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb, Real &dsq) const
	for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication. More...

void	memb_atom_pair_energy (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb, Real &dsq) const
	for the trie-vs-trie algorithm; could test if the other atom pair energy function could inline this function to avoid the table reading code duplication. More...

void	fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const

void	pair_energy_H (conformation::Atom const &atom1, conformation::Atom const &atom2, Real weight, Energy &atr, Energy &rep, Energy &solv, Energy &bb) const

void	pair_energy_H (conformation::Atom const &atom1, conformation::Atom const &atom2, Real weight, EnergyMap &emap) const

Real	eval_dE_dR_over_r (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const

Real	memb_eval_dE_dR_over_r (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
	pba More...

Real	hydrogen_interaction_cutoff2 () const

virtual Distance	atomic_interaction_cutoff () const
	Etable atomic distance cutoff is 5.5 A. More...

virtual void	indicate_required_context_graphs (utility::vector1< bool > &) const
	Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed. More...

Energy	sum_energies (Real atr, Real rep, Real solv, Real bb) const
	Inline Methods For Trie-vs-Trie Algorithm. More...

Energy	heavyatom_heavyatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2, DistanceSquared &d2) const

Energy	heavyatom_hydrogenatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2) const

Energy	hydrogenatom_heavyatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2) const

Energy	hydrogenatom_hydrogenatom_energy (etrie::EtableAtom const &at1, etrie::EtableAtom const &at2) const

Public Member Functions inherited from core::scoring::methods::ContextIndependentTwoBodyEnergy
	ContextIndependentTwoBodyEnergy (EnergyMethodCreatorOP)
	Constructor with an EnergyMethodCreator to inform the ancestor EnergyMethod class which ScoreTypes this EnergyMethod is responsible for computing. More...

virtual	~ContextIndependentTwoBodyEnergy ()

EnergyMethodType	method_type () const
	Return one of the 7 kinds of energy methods that exist: e.g. context-dependent-one-body vs whole-structure. More...

Public Member Functions inherited from core::scoring::methods::ShortRangeTwoBodyEnergy
	ShortRangeTwoBodyEnergy (EnergyMethodCreatorOP)
	Constructor with EnergyMethodCreator to provide to the EnergyMethod grandparent the list of the ScoreTypes this EnergyMethod is responsible for computing. More...

virtual	~ShortRangeTwoBodyEnergy ()

virtual void	evaluate_rotamer_background_energy_maps (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< EnergyMap > &emaps) const
	Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...

Public Member Functions inherited from core::scoring::methods::TwoBodyEnergy
	TwoBodyEnergy (EnergyMethodCreatorOP)
	Constructor, requiring an EnergyMethodCreator. No default constructor provided to force EnergyMethod writers to provide an energy-method-creator at construction time. More...

virtual	~TwoBodyEnergy ()

virtual bool	defines_score_for_residue_pair (conformation::Residue const &res1, conformation::Residue const &res2, bool res_moving_wrt_eachother) const
	During minimization, energy methods are allowed to decide that they say nothing about a particular residue pair (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default implementation returns "true" for all residue pairs. Context-dependent two-body energies have the option of behaving as if they are context-independent by returning "false" for residue pairs that do no move wrt each other. More...

virtual bool	defines_intrares_energy (EnergyMap const &weights) const =0
	Two body energies are able to define intra-residue energies, and to do so only in the presence of certain non-zero weights. The ScoreFunction will hand over its weight set as it asks whether the energy method defines an intraresidue energy or not. More...

virtual void	eval_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const =0
	Evaluate the intra-residue energy for a given residue. More...

virtual bool	defines_intrares_energy_for_residue (conformation::Residue const &res) const
	If a score function defines no intra-residue scores for a particular residue, then it may opt-out of being asked during minimization to evaluate the score for this residue. More...

virtual bool	defines_intrares_dof_derivatives (pose::Pose const &p) const
	Use the dof_derivative interface for this energy method when calculating derivatives? It is possible to define both dof_derivatives and atom-derivatives; they are not mutually exclusive. More...

virtual Real	eval_intraresidue_dof_derivative (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights) const
	Evaluate the DOF derivative for a particular residue. The Pose merely serves as context, and the input residue is not required to be a member of the Pose. More...

virtual void	evaluate_rotamer_intrares_energies (conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< core::PackerEnergy > &energies) const
	Batch computation of rotamer intrares energies. Need not be overriden in derived class – by default, iterates over all rotamers, and calls derived class's intrares _energy method. More...

virtual void	evaluate_rotamer_intrares_energy_maps (conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< EnergyMap > &emaps) const
	Batch computation of rotamer intrares energy map. Need not be overriden in derived class – by default, iterates over all rotamers, and calls derived class's intrares _energy method. More...

Public Member Functions inherited from core::scoring::methods::EnergyMethod
	EnergyMethod (EnergyMethodCreatorOP creator)
	Constructor with EnergyMethodCreator, which lists the score types that this energy method is responsible for. More...

	EnergyMethod (EnergyMethod const &src)
	Copy constructor copies over the score types of the source. More...

virtual	~EnergyMethod ()

virtual EnergyMethodOP	clone () const =0

virtual void	update_residue_for_packing (pose::Pose &, Size resid) const
	ensure this function gets called. The default behavior is to do nothing. More...

virtual void	finalize_after_derivatives (pose::Pose &, ScoreFunction const &) const
	called at the end of derivatives evaluation More...

virtual bool	defines_high_order_terms (pose::Pose const &) const
	Should this EnergyMethod have score and derivative evaluation evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta's get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns "false". More...

ScoreTypes const &	score_types () const
	Returns the score types that this energy method computes. More...

virtual core::Size	version () const =0
	Return the version of the energy method. More...

Public Attributes
	__pad0__:ContextIndependentTwoBodyEnergy parent

	__pad1__:EnergyMethodOP EnergyMethodOP

Protected Member Functions
trie::TrieCountPairBaseOP	get_count_pair_function_trie (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn) const
	Inline Methods For Trie-vs-Trie Algorithm. More...

trie::TrieCountPairBaseOP	get_count_pair_function_trie (conformation::Residue const &res1, conformation::Residue const &res2, trie::RotamerTrieBaseCOP trie1, trie::RotamerTrieBaseCOP trie2, pose::Pose const &pose, ScoreFunction const &sfxn) const

count_pair::CPCrossoverBehavior	determine_crossover_behavior (conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &, ScoreFunction const &sfxn) const

etrie::EtableRotamerTrieOP	create_rotamer_trie (conformation::RotamerSetBase const &rotset, pose::Pose const &pose) const
	create a rotamer trie for a particular set, deciding upon the kind of count pair data that needs to be contained by the trie. More...

etrie::EtableRotamerTrieOP	create_rotamer_trie (conformation::Residue const &residue, pose::Pose const &) const

etrie::EtableRotamerTrieOP	create_rotamer_trie_2 (conformation::RotamerSetBase const &rotset) const

etrie::EtableRotamerTrieOP	create_rotamer_trie_1 (conformation::RotamerSetBase const &rotset, Size connection_type) const

Real	eval_dE_dR_over_r_ (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const

void	derived_prepare_for_residue_pair (Size const, Size const, pose::Pose const &) const

bool	interpolate_bins (conformation::Atom const &atom1, conformation::Atom const &atom2, Real &d2, int &disbin, Real &frac) const

ScoreType	rep_scoretype () const

Etable const &	etable () const

trie::TrieCountPairBaseOP	get_count_pair_function_trie (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn) const

trie::TrieCountPairBaseOP	get_count_pair_function_trie (conformation::Residue const &res1, conformation::Residue const &res2, trie::RotamerTrieBaseCOP trie1, trie::RotamerTrieBaseCOP trie2, pose::Pose const &pose, ScoreFunction const &sfxn) const

count_pair::CPCrossoverBehavior	determine_crossover_behavior (conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &, ScoreFunction const &sfxn) const

etrie::EtableRotamerTrieOP	create_rotamer_trie (conformation::RotamerSetBase const &rotset, pose::Pose const &pose) const

etrie::EtableRotamerTrieOP	create_rotamer_trie_2 (conformation::RotamerSetBase const &rotset) const

etrie::EtableRotamerTrieOP	create_rotamer_trie_1 (conformation::RotamerSetBase const &rotset, Size connection_type) const

void	atom_pair_energy_ (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Real &atr, Real &rep, Real &solv, Real &bb, Real &dsq) const

void	memb_atom_pair_energy_ (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Real &atr, Real &rep, Real &solv, Real &bb, Real &dsq) const

void	fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const

void	pair_energy_H_ (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Real &atr, Real &rep, Real &solv, Real &bb) const

Real	eval_dE_dR_over_r_ (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const

Real	memb_eval_dE_dR_over_r_ (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
	pba More...

void	derived_prepare_for_residue_pair (Size const res1, Size const res2, pose::Pose const &) const

bool	interpolate_bins (conformation::Atom const &atom1, conformation::Atom const &atom2, Real &d2, int &disbin, Real &frac) const

void	set_scoretypes (ScoreType atr_type, ScoreType rep_type, ScoreType sol_type) const

ScoreType	rep_scoretype () const

trie::TrieCountPairBaseOP	get_count_pair_function_trie (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn) const

trie::TrieCountPairBaseOP	get_count_pair_function_trie (conformation::Residue const &res1, conformation::Residue const &res2, trie::RotamerTrieBaseCOP trie1, trie::RotamerTrieBaseCOP trie2, pose::Pose const &pose, ScoreFunction const &sfxn) const

count_pair::CPCrossoverBehavior	determine_crossover_behavior (conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &, ScoreFunction const &sfxn) const

etrie::EtableRotamerTrieOP	create_rotamer_trie (conformation::RotamerSetBase const &rotset, pose::Pose const &pose) const

etrie::EtableRotamerTrieOP	create_rotamer_trie_2 (conformation::RotamerSetBase const &rotset) const

etrie::EtableRotamerTrieOP	create_rotamer_trie_1 (conformation::RotamerSetBase const &rotset, Size connection_type) const

void	atom_pair_energy_ (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Real &atr, Real &rep, Real &solv, Real &bb, Real &dsq) const

void	memb_atom_pair_energy_ (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Real &atr, Real &rep, Real &solv, Real &bb, Real &dsq) const

void	fast_memb_env_energy (conformation::Atom const &atom1, int const attype1, Real &mbenvE) const

void	pair_energy_H_ (conformation::Atom const &atom1, conformation::Atom const &atom2, Real const weight, Real &atr, Real &rep, Real &solv, Real &bb) const

Real	eval_dE_dR_over_r_ (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const

Real	memb_eval_dE_dR_over_r_ (conformation::Atom const &atom1, conformation::Atom const &atom2, EnergyMap const &weights, Vector &f1, Vector &f2) const
	pba More...

void	derived_prepare_for_residue_pair (Size const res1, Size const res2, pose::Pose const &) const

bool	interpolate_bins (conformation::Atom const &atom1, conformation::Atom const &atom2, Real &d2, int &disbin, Real &frac) const

void	set_scoretypes (ScoreType atr_type, ScoreType rep_type, ScoreType sol_type) const

ScoreType	rep_scoretype () const

Private Attributes
Etable const &	etable_

Real	safe_max_dis2

Real	hydrogen_interaction_cutoff2_

bool	exclude_DNA_DNA

ObjexxFCL::FArray3D< Real > const &	ljatr_
	these guys are taken from the etable More...

ObjexxFCL::FArray3D< Real > const &	ljrep_

ObjexxFCL::FArray3D< Real > const &	solv1_

ObjexxFCL::FArray3D< Real > const &	solv2_

ObjexxFCL::FArray3D< Real > const &	dljatr_

ObjexxFCL::FArray3D< Real > const &	dljrep_

ObjexxFCL::FArray3D< Real > const &	dsolv_

ObjexxFCL::FArray3D< Real > const &	memb_solv1_

ObjexxFCL::FArray3D< Real > const &	memb_solv2_

ObjexxFCL::FArray3D< Real > const &	memb_dsolv_

int	etable_bins_per_A2

ScoreType	st_rep_

ScoreType	st_atr_

ScoreType	st_sol_

EnergyMap	weights_

Additional Inherited Members
Public Types inherited from core::scoring::methods::ContextIndependentTwoBodyEnergy
typedef ShortRangeTwoBodyEnergy	parent

Detailed Description

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

Definition at line 82 of file BaseEtableEnergy.hh.

Constructor & Destructor Documentation

template<class Derived >

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

construction with an etable

Definition at line 711 of file BaseEtableEnergy.tmpl.hh.

template<class Derived>

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

explicit copy constructor, since the BaseEtableEnergy now contains OP data

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

Definition at line 729 of file BaseEtableEnergy.tmpl.hh.

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

Definition at line 292 of file BaseMembEtableEnergy.hh.

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

Definition at line 292 of file BaseMembEtableEnergy.hh.

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.

Definition at line 349 of file BaseMembEtableEnergy.hh.

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.

Definition at line 349 of file BaseMembEtableEnergy.hh.

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

Definition at line 516 of file BaseEtableEnergy.hh.

Referenced by core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >::atom_pair_energy(), core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >::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.

Definition at line 531 of file BaseEtableEnergy.hh.

template<class Derived>

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

inline

APL – consider reinstating this function!

Definition at line 549 of file BaseEtableEnergy.hh.

template<class Derived>

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

inlineprotected

template<class Derived >

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

inlineprotected

Definition at line 758 of file BaseMembEtableEnergy.hh.

References protocols::antibody2::l1, protocols::antibody2::l2, and core::conformation::Atom::type().

Referenced by core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >::atom_pair_energy().

template<class Derived>

virtual Distance core::scoring::etable::BaseEtableEnergy< Derived >::atomic_interaction_cutoff ( ) const

virtual

Etable atomic distance cutoff is 5.5 A.

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

template<class Derived>

virtual Distance core::scoring::etable::BaseEtableEnergy< Derived >::atomic_interaction_cutoff ( ) const

virtual

Etable atomic distance cutoff is 5.5 A.

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

template<class Derived >

Distance core::scoring::etable::BaseEtableEnergy< Derived >::atomic_interaction_cutoff ( ) const

virtual

Etable atomic distance cutoff is 5.5 A.

return the Etables atomic distance cutoff

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

Definition at line 2049 of file BaseEtableEnergy.tmpl.hh.

References core::chemical::MAX_CHEMICAL_BOND_TO_HYDROGEN_LENGTH.

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.

Definition at line 1546 of file BaseEtableEnergy.tmpl.hh.

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

template<class Derived>

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

virtual

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

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

template<class Derived>

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

virtual

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

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

template<class Derived >

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

virtual

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

do not use this during minimization

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

Definition at line 1570 of file BaseEtableEnergy.tmpl.hh.

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

template<class Derived>

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

virtual

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

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.

Definition at line 1959 of file BaseEtableEnergy.tmpl.hh.

References core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function_and_invoke(), core::scoring::methods::determine_crossover_behavior(), and core::conformation::Residue::is_DNA().

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>

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.

Definition at line 1932 of file BaseEtableEnergy.tmpl.hh.

References core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function_and_invoke(), core::scoring::methods::determine_crossover_behavior(), and core::conformation::Residue::is_DNA().

template<class Derived>

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

protected

template<class Derived>

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

protected

template<class Derived >

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

protected

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

Definition at line 1858 of file BaseEtableEnergy.tmpl.hh.

References core::io::serialization::at(), 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 >

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

protected

Create a one-residue trie.

Definition at line 1892 of file BaseEtableEnergy.tmpl.hh.

References core::io::serialization::at(), 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>

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

protected

template<class Derived>

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

protected

template<class Derived>

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

protected

template<class Derived>

etrie::EtableRotamerTrieOP core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie_2 ( conformation::RotamerSetBase const & rotset) const

protected

template<class Derived>

etrie::EtableRotamerTrieOP core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie_2 ( conformation::RotamerSetBase const & rotset) const

protected

template<class Derived>

etrie::EtableRotamerTrieOP core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie_2 ( conformation::RotamerSetBase const & rotset) const

protected

template<class Derived>

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

inlineprotected

Definition at line 643 of file BaseMembEtableEnergy.hh.

template<class Derived>

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

inlineprotected

Definition at line 650 of file BaseMembEtableEnergy.hh.

template<class Derived>

void core::scoring::etable::BaseEtableEnergy< Derived >::derived_prepare_for_residue_pair	(	Size	const,
		Size	const,
		pose::Pose const &
	)		const

inlineprotected

Definition at line 798 of file BaseEtableEnergy.hh.

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

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

Definition at line 1142 of file BaseEtableEnergy.tmpl.hh.

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

inlinevirtual

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

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

Definition at line 460 of file BaseMembEtableEnergy.hh.

template<class Derived>

virtual bool core::scoring::etable::BaseEtableEnergy< Derived >::divides_backbone_and_sidechain_energetics ( ) const

inlinevirtual

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

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

Definition at line 631 of file BaseEtableEnergy.hh.

template<class Derived>

Etable const& core::scoring::etable::BaseEtableEnergy< Derived >::etable ( ) const

inlineprotected

Definition at line 831 of file BaseEtableEnergy.hh.

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>

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.

Definition at line 1989 of file BaseEtableEnergy.tmpl.hh.

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>

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

Definition at line 423 of file BaseMembEtableEnergy.hh.

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

Definition at line 423 of file BaseMembEtableEnergy.hh.

template<class Derived>

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

inlineprotected

template<class Derived>

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

inlineprotected

template<class Derived >

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

inlineprotected

Definition at line 975 of file BaseMembEtableEnergy.hh.

References protocols::antibody2::l1, protocols::antibody2::l2, core::conformation::Atom::type(), and core::conformation::Atom::xyz().

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

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.

Definition at line 1819 of file BaseEtableEnergy.tmpl.hh.

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.

Definition at line 1753 of file BaseEtableEnergy.tmpl.hh.

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.

Definition at line 1472 of file BaseEtableEnergy.tmpl.hh.

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.

Definition at line 1683 of file BaseEtableEnergy.tmpl.hh.

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

template<class Derived>

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

virtual

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

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

template<class Derived>

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

virtual

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

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

template<class Derived >

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

virtual

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

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

Definition at line 1617 of file BaseEtableEnergy.tmpl.hh.

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

template<class Derived>

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

inline

pba

Definition at line 336 of file BaseMembEtableEnergy.hh.

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

Definition at line 336 of file BaseMembEtableEnergy.hh.

Referenced by core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >::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

Definition at line 385 of file BaseMembEtableEnergy.hh.

template<class Derived>

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

inline

Definition at line 385 of file BaseMembEtableEnergy.hh.

template<class Derived>

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

inlineprotected

template<class Derived>

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

inlineprotected

template<class Derived>

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

virtual

called at the end of energy evaluation

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

template<class Derived>

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

virtual

called at the end of energy evaluation

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

template<class Derived >

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

virtual

called at the end of energy evaluation

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

Definition at line 742 of file BaseEtableEnergy.tmpl.hh.

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>

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

template<class Derived>

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

template<class Derived>

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

template<class Derived>

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

template<class Derived >

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

Definition at line 984 of file BaseEtableEnergy.tmpl.hh.

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

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.

Definition at line 998 of file BaseEtableEnergy.tmpl.hh.

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

template<class Derived>

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

protected

template<class Derived>

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

protected

template<class Derived>

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

protected

template<class Derived>

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

protected

template<class Derived >

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

protected

Inline Methods For Trie-vs-Trie Algorithm.

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

Definition at line 1041 of file BaseEtableEnergy.tmpl.hh.

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

Definition at line 1059 of file BaseEtableEnergy.tmpl.hh.

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

Definition at line 1018 of file BaseEtableEnergy.tmpl.hh.

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

Definition at line 471 of file BaseMembEtableEnergy.hh.

template<class Derived>

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

inline

Definition at line 478 of file BaseMembEtableEnergy.hh.

template<class Derived>

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

inline

Definition at line 483 of file BaseMembEtableEnergy.hh.

template<class Derived>

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

inline

Definition at line 490 of file BaseMembEtableEnergy.hh.

template<class Derived>

Real core::scoring::etable::BaseEtableEnergy< Derived >::hydrogen_interaction_cutoff2 ( ) const

inline

Definition at line 448 of file BaseMembEtableEnergy.hh.

template<class Derived>

Real core::scoring::etable::BaseEtableEnergy< Derived >::hydrogen_interaction_cutoff2 ( ) const

inline

Definition at line 448 of file BaseMembEtableEnergy.hh.

template<class Derived>

Real core::scoring::etable::BaseEtableEnergy< Derived >::hydrogen_interaction_cutoff2 ( ) const

inline

Definition at line 619 of file BaseEtableEnergy.hh.

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

template<class Derived>

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

inline

Definition at line 494 of file BaseMembEtableEnergy.hh.

template<class Derived>

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

inline

Definition at line 501 of file BaseMembEtableEnergy.hh.

template<class Derived>

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

inline

Definition at line 505 of file BaseMembEtableEnergy.hh.

template<class Derived>

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

inline

Definition at line 512 of file BaseMembEtableEnergy.hh.

template<class Derived>

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

virtual

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

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

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

template<class Derived>

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

virtual

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

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

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

template<class Derived >

void core::scoring::etable::BaseEtableEnergy< Derived >::indicate_required_context_graphs ( utility::vector1< bool > & context_graphs_required) const

virtual

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

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

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

Definition at line 1925 of file BaseEtableEnergy.tmpl.hh.

template<class Derived>

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

protected

template<class Derived>

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

protected

template<class Derived >

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

inlineprotected

Definition at line 730 of file BaseMembEtableEnergy.hh.

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

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

Definition at line 314 of file BaseMembEtableEnergy.hh.

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

Definition at line 314 of file BaseMembEtableEnergy.hh.

Referenced by core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >::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

Definition at line 368 of file BaseMembEtableEnergy.hh.

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

Definition at line 368 of file BaseMembEtableEnergy.hh.

template<class Derived>

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

inlineprotected

template<class Derived >

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

inlineprotected

Definition at line 828 of file BaseMembEtableEnergy.hh.

References protocols::antibody2::l1, protocols::antibody2::l2, core::scoring::MembraneEmbed_from_pose(), core::conformation::Atom::type(), and core::conformation::Atom::xyz().

Referenced by core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >::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

Definition at line 436 of file BaseMembEtableEnergy.hh.

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

Definition at line 436 of file BaseMembEtableEnergy.hh.

template<class Derived>

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

inlineprotected

pba

template<class Derived >

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

inlineprotected

pba

Definition at line 903 of file BaseMembEtableEnergy.hh.

References protocols::antibody2::l1, protocols::antibody2::l2, core::scoring::MembraneEmbed_from_pose(), core::conformation::Atom::type(), and core::conformation::Atom::xyz().

Referenced by core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >::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

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

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

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

Definition at line 825 of file BaseEtableEnergy.tmpl.hh.

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

Definition at line 396 of file BaseMembEtableEnergy.hh.

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

Definition at line 396 of file BaseMembEtableEnergy.hh.

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,
		EnergyMap &	emap
	)		const

inline

APL – Consider reinstating this function!

Definition at line 591 of file BaseEtableEnergy.hh.

Referenced by core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >::heavyatom_hydrogenatom_energy(), core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >::hydrogenatom_heavyatom_energy(), core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >::hydrogenatom_hydrogenatom_energy(), 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

inlineprotected

template<class Derived >

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

inlineprotected

Definition at line 1043 of file BaseMembEtableEnergy.hh.

References protocols::antibody2::l1, protocols::antibody2::l2, and core::conformation::Atom::type().

Referenced by core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >::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?

Definition at line 280 of file BaseMembEtableEnergy.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?

Definition at line 280 of file BaseMembEtableEnergy.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?

Definition at line 494 of file BaseEtableEnergy.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.

Definition at line 950 of file BaseEtableEnergy.tmpl.hh.

References core::scoring::methods::etable_method, and core::conformation::RotamerSetBase::store_trie().

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.

Definition at line 1342 of file BaseEtableEnergy.tmpl.hh.

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.

Definition at line 1404 of file BaseEtableEnergy.tmpl.hh.

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.

Definition at line 1316 of file BaseEtableEnergy.tmpl.hh.

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.

Definition at line 1366 of file BaseEtableEnergy.tmpl.hh.

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>

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.

Definition at line 1171 of file BaseEtableEnergy.tmpl.hh.

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 >

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.

Definition at line 1204 of file BaseEtableEnergy.tmpl.hh.

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>

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	(	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.

Definition at line 900 of file BaseEtableEnergy.tmpl.hh.

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 >

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.

Definition at line 1353 of file BaseEtableEnergy.tmpl.hh.

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.

Definition at line 1412 of file BaseEtableEnergy.tmpl.hh.

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.

Definition at line 833 of file BaseEtableEnergy.tmpl.hh.

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.

Definition at line 1782 of file BaseEtableEnergy.tmpl.hh.

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.

Definition at line 1258 of file BaseEtableEnergy.tmpl.hh.

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>

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.

Definition at line 923 of file BaseEtableEnergy.tmpl.hh.

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

virtual

check compatibility with atomtypeset

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.

Definition at line 882 of file BaseEtableEnergy.tmpl.hh.

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 >

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.

Definition at line 1327 of file BaseEtableEnergy.tmpl.hh.

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.

Definition at line 1375 of file BaseEtableEnergy.tmpl.hh.

template<class Derived>

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

virtual

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

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

template<class Derived>

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

virtual

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

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

template<class Derived >

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