elec¶

electrie

Bindings for core::scoring::elec namespace

class pyrosetta.rosetta.core.scoring.elec.CountPairRepMap¶

Bases: pybind11_object

A class to encapsulate the raw-pointer-based data caching

get_map(self: pyrosetta.rosetta.core.scoring.elec.CountPairRepMap, restype: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.std.map_unsigned_long_unsigned_long¶: C++: core::scoring::elec::CountPairRepMap::get_map(const class core::chemical::ResidueType &) –> const class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &

has(self: pyrosetta.rosetta.core.scoring.elec.CountPairRepMap, restype: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶: C++: core::scoring::elec::CountPairRepMap::has(const class core::chemical::ResidueType &) const –> bool

restype_destruction_observer(self: pyrosetta.rosetta.core.scoring.elec.CountPairRepMap, event: pyrosetta.rosetta.core.chemical.RestypeDestructionEvent) → None¶: C++: core::scoring::elec::CountPairRepMap::restype_destruction_observer(const struct core::chemical::RestypeDestructionEvent &) –> void

class pyrosetta.rosetta.core.scoring.elec.CountPairRepresentative¶

Bases: CountPairFunction

assign(self: pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction, : pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction) → pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction¶: C++: core::scoring::etable::count_pair::CountPairFunction::operator=(const class core::scoring::etable::count_pair::CountPairFunction &) –> class core::scoring::etable::count_pair::CountPairFunction &

count(self: pyrosetta.rosetta.core.scoring.elec.CountPairRepresentative, at1: int, at2: int, weight: float, path_dist: int) → bool¶: C++: core::scoring::elec::CountPairRepresentative::count(const int, const int, double &, unsigned long &) const –> bool

residue_atom_pair_energy(*args, **kwargs)¶

Overloaded function.

residue_atom_pair_energy(self: pyrosetta.rosetta.core.scoring.elec.CountPairRepresentative, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::scoring::etable::TableLookupEvaluator, : pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::elec::CountPairRepresentative::residue_atom_pair_energy(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::etable::TableLookupEvaluator &, class core::scoring::EMapVector &) const –> void

residue_atom_pair_energy(self: pyrosetta.rosetta.core.scoring.elec.CountPairRepresentative, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::scoring::etable::AnalyticEtableEvaluator, : pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::elec::CountPairRepresentative::residue_atom_pair_energy(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::etable::AnalyticEtableEvaluator &, class core::scoring::EMapVector &) const –> void

residue_atom_pair_energy_backbone_backbone(*args, **kwargs)¶

Overloaded function.

residue_atom_pair_energy_backbone_backbone(self: pyrosetta.rosetta.core.scoring.elec.CountPairRepresentative, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::scoring::etable::TableLookupEvaluator, : pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::elec::CountPairRepresentative::residue_atom_pair_energy_backbone_backbone(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::etable::TableLookupEvaluator &, class core::scoring::EMapVector &) const –> void

residue_atom_pair_energy_backbone_backbone(self: pyrosetta.rosetta.core.scoring.elec.CountPairRepresentative, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::scoring::etable::AnalyticEtableEvaluator, : pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::elec::CountPairRepresentative::residue_atom_pair_energy_backbone_backbone(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::etable::AnalyticEtableEvaluator &, class core::scoring::EMapVector &) const –> void

residue_atom_pair_energy_sidechain_backbone(*args, **kwargs)¶

Overloaded function.

residue_atom_pair_energy_sidechain_backbone(self: pyrosetta.rosetta.core.scoring.elec.CountPairRepresentative, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::scoring::etable::TableLookupEvaluator, : pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::elec::CountPairRepresentative::residue_atom_pair_energy_sidechain_backbone(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::etable::TableLookupEvaluator &, class core::scoring::EMapVector &) const –> void

residue_atom_pair_energy_sidechain_backbone(self: pyrosetta.rosetta.core.scoring.elec.CountPairRepresentative, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::scoring::etable::AnalyticEtableEvaluator, : pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::elec::CountPairRepresentative::residue_atom_pair_energy_sidechain_backbone(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::etable::AnalyticEtableEvaluator &, class core::scoring::EMapVector &) const –> void

residue_atom_pair_energy_sidechain_sidechain(*args, **kwargs)¶

Overloaded function.

residue_atom_pair_energy_sidechain_sidechain(self: pyrosetta.rosetta.core.scoring.elec.CountPairRepresentative, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::scoring::etable::TableLookupEvaluator, : pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::elec::CountPairRepresentative::residue_atom_pair_energy_sidechain_sidechain(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::etable::TableLookupEvaluator &, class core::scoring::EMapVector &) const –> void

residue_atom_pair_energy_sidechain_sidechain(self: pyrosetta.rosetta.core.scoring.elec.CountPairRepresentative, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::scoring::etable::AnalyticEtableEvaluator, : pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::elec::CountPairRepresentative::residue_atom_pair_energy_sidechain_sidechain(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::etable::AnalyticEtableEvaluator &, class core::scoring::EMapVector &) const –> void

residue_atom_pair_energy_sidechain_whole(*args, **kwargs)¶

Overloaded function.

residue_atom_pair_energy_sidechain_whole(self: pyrosetta.rosetta.core.scoring.elec.CountPairRepresentative, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::scoring::etable::TableLookupEvaluator, : pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::elec::CountPairRepresentative::residue_atom_pair_energy_sidechain_whole(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::etable::TableLookupEvaluator &, class core::scoring::EMapVector &) const –> void

residue_atom_pair_energy_sidechain_whole(self: pyrosetta.rosetta.core.scoring.elec.CountPairRepresentative, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::scoring::etable::AnalyticEtableEvaluator, : pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::elec::CountPairRepresentative::residue_atom_pair_energy_sidechain_whole(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::etable::AnalyticEtableEvaluator &, class core::scoring::EMapVector &) const –> void

class pyrosetta.rosetta.core.scoring.elec.ElecGroup¶

Bases: pybind11_object

property atms¶

property comatms¶

property n_acceptor¶

property n_donor¶

property qeps¶

class pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy¶

Bases: ContextIndependentTwoBodyEnergy

assign(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, : pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy) → pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy¶: C++: core::scoring::elec::FA_ElecEnergy::operator=(const class core::scoring::elec::FA_ElecEnergy &) –> class core::scoring::elec::FA_ElecEnergy &

atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy) → float¶: C++: core::scoring::elec::FA_ElecEnergy::atomic_interaction_cutoff() const –> double

atomistic_energy(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, atmno: int, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None¶

Evaluate the (one body) energy associated with a particular atom

This may be a “self” energy, or it may be the single atom contribution from a whole structure term. NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_energies()

This is return-by-reference in the EnergyMap - Implementations should accumulate, not replace.

C++: core::scoring::methods::EnergyMethod::atomistic_energy(unsigned long, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

atomistic_pair_energy(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, : int, : pyrosetta.rosetta.core.conformation.Residue, : int, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None¶: C++: core::scoring::elec::FA_ElecEnergy::atomistic_pair_energy(unsigned long, const class core::conformation::Residue &, unsigned long, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

backbone_backbone_energy(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None¶: C++: core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

backbone_sidechain_energy(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None¶: C++: core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

bump_energy_backbone(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None¶: C++: core::scoring::methods::TwoBodyEnergy::bump_energy_backbone(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

bump_energy_full(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None¶: C++: core::scoring::methods::TwoBodyEnergy::bump_energy_full(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

clone(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod¶

clone

C++: core::scoring::elec::FA_ElecEnergy::clone() const –> class std::shared_ptr<class core::scoring::methods::EnergyMethod>

coulomb(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy) → pyrosetta.rosetta.core.scoring.etable.coulomb.Coulomb¶: C++: core::scoring::elec::FA_ElecEnergy::coulomb() const –> const class core::scoring::etable::coulomb::Coulomb &

defines_high_order_terms(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose) → bool¶

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”.

C++: core::scoring::methods::EnergyMethod::defines_high_order_terms(const class core::pose::Pose &) const –> bool

defines_intrares_dof_derivatives(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, p: core::pose::Pose) → bool¶

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.

C++: core::scoring::methods::TwoBodyEnergy::defines_intrares_dof_derivatives(const class core::pose::Pose &) const –> bool

defines_intrares_energy(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, : core::scoring::EMapVector) → bool¶: C++: core::scoring::elec::FA_ElecEnergy::defines_intrares_energy(const class core::scoring::EMapVector &) const –> bool

defines_intrares_energy_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, res: pyrosetta.rosetta.core.conformation.Residue) → bool¶

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.

C++: core::scoring::methods::TwoBodyEnergy::defines_intrares_energy_for_residue(const class core::conformation::Residue &) const –> bool

defines_score_for_residue_pair(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, res_moving_wrt_eachother: bool) → bool¶: C++: core::scoring::elec::FA_ElecEnergy::defines_score_for_residue_pair(const class core::conformation::Residue &, const class core::conformation::Residue &, bool) const –> bool

divides_backbone_and_sidechain_energetics(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy) → bool¶: C++: core::scoring::elec::FA_ElecEnergy::divides_backbone_and_sidechain_energetics() const –> bool

elec_weight(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, intra_res: bool, at1isbb: bool, at2isbb: bool, wts: pyrosetta.rosetta.core.scoring.elec.weight_triple) → float¶: C++: core::scoring::elec::FA_ElecEnergy::elec_weight(bool, bool, bool, const struct core::scoring::elec::weight_triple &) const –> double

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, atom_id: pyrosetta.rosetta.core.id.AtomID, pose: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, : core::scoring::ScoreFunction, weights: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶

Evaluate the derivative vectors for a particular atom in a given: (asymmetric) pose when nblist_autoupdate is being used. nblist_autoupdate cannot be used with symmetric poses, in rtmin, or in minpack.

C++: core::scoring::elec::FA_ElecEnergy::eval_atom_derivative(const class core::id::AtomID &, const class core::pose::Pose &, const class ObjexxFCL::FArray1D<int> &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> void

eval_intrares_ST_only(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy) → bool¶: C++: core::scoring::elec::FA_ElecEnergy::eval_intrares_ST_only() const –> bool

eval_intrares_derivatives(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None¶: C++: core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, const class core::scoring::EMapVector &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &) const –> void

eval_intrares_energy(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sf: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None¶: C++: core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

eval_intrares_energy_ext(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, data_cache: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None¶

Evaluate the intra-residue energy for a given residue using the data held within the: ResSingleMinimizationData object. This function should be invoked only on derived instances of this class if they return “true” in a call to their use_extended_intrares_energy_interface method. This base class provides a noop implementation for classes that do not implement this interface, or that do not define intrares energies.

C++: core::scoring::methods::TwoBodyEnergy::eval_intrares_energy_ext(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

eval_intraresidue_dof_derivative(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, dof_id: pyrosetta.rosetta.core.id.DOF_ID, torsion_id: core::id::TorsionID, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector) → float¶

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.

C++: core::scoring::methods::TwoBodyEnergy::eval_intraresidue_dof_derivative(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::id::DOF_ID &, const class core::id::TorsionID &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &) const –> double

eval_residue_pair_derivatives(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, : core::scoring::ResSingleMinimizationData, : core::scoring::ResSingleMinimizationData, min_data: core::scoring::ResPairMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, r1_atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair, r2_atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None¶

Evaluate the atom derivative f1/f2 vectors for all atoms on rsd1: in response to the atoms on rsd2, and all the atoms on rsd2 as they in response to the atoms on rsd1. This method is used with the MinimizationGraph and when nblist_autoupdate is not in use.

C++: core::scoring::elec::FA_ElecEnergy::eval_residue_pair_derivatives(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::scoring::ResSingleMinimizationData &, const class core::scoring::ResPairMinimizationData &, const class core::pose::Pose &, const class core::scoring::EMapVector &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &) const –> void

evaluate_rotamer_background_energies(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, residue: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector, energy_vector: pyrosetta.rosetta.utility.vector1_float) → None¶: C++: core::scoring::elec::FA_ElecEnergy::evaluate_rotamer_background_energies(const class core::conformation::RotamerSetBase &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &, class utility::vector1<float, class std::allocator<float> > &) const –> void

evaluate_rotamer_background_energy_maps(self: pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, residue: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector, emaps: pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector) → None¶

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

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::evaluate_rotamer_background_energy_maps(const class core::conformation::RotamerSetBase &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &, class utility::vector1<class core::scoring::EMapVector, class std::allocator<class core::scoring::EMapVector> > &) const –> void

evaluate_rotamer_intrares_energies(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, energies: pyrosetta.rosetta.utility.vector1_float) → None¶: C++: core::scoring::elec::FA_ElecEnergy::evaluate_rotamer_intrares_energies(const class core::conformation::RotamerSetBase &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class utility::vector1<float, class std::allocator<float> > &) const –> void

evaluate_rotamer_intrares_energy_maps(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emaps: pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector) → None¶

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.

C++: core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_intrares_energy_maps(const class core::conformation::RotamerSetBase &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class utility::vector1<class core::scoring::EMapVector, class std::allocator<class core::scoring::EMapVector> > &) const –> void

evaluate_rotamer_pair_energies(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, set1: pyrosetta.rosetta.core.conformation.RotamerSetBase, set2: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector, energy_table: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) → None¶: C++: core::scoring::elec::FA_ElecEnergy::evaluate_rotamer_pair_energies(const class core::conformation::RotamerSetBase &, const class core::conformation::RotamerSetBase &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &, class ObjexxFCL::FArray2D<float> &) const –> void

finalize_after_derivatives(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None¶

called at the end of derivatives evaluation

C++: core::scoring::methods::EnergyMethod::finalize_after_derivatives(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

finalize_after_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose) → None¶

Called after minimization, allowing a derived class to do some

teardown steps.

Base class function does nothing. Derived classes may override.

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::methods::EnergyMethod::finalize_after_minimizing(class core::pose::Pose &) const –> void

finalize_total_energy(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, pose: core::pose::Pose, : core::scoring::ScoreFunction, totals: core::scoring::EMapVector) → None¶: C++: core::scoring::elec::FA_ElecEnergy::finalize_total_energy(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

get_count_pair_function(*args, **kwargs)¶

Overloaded function.

get_count_pair_function(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, : int, : int, : core::pose::Pose, : core::scoring::ScoreFunction) -> core::scoring::etable::count_pair::CountPairFunction

Interface function for class NeighborList.

C++: core::scoring::elec::FA_ElecEnergy::get_count_pair_function(const unsigned long, const unsigned long, const class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> class std::shared_ptr<const class core::scoring::etable::count_pair::CountPairFunction>

get_count_pair_function(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) -> core::scoring::etable::count_pair::CountPairFunction

C++: core::scoring::elec::FA_ElecEnergy::get_count_pair_function(const class core::conformation::Residue &, const class core::conformation::Residue &) const –> class std::shared_ptr<const class core::scoring::etable::count_pair::CountPairFunction>

get_countpair_representative_atom(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, restype: pyrosetta.rosetta.core.chemical.ResidueType, atm_i: int) → int¶: C++: core::scoring::elec::FA_ElecEnergy::get_countpair_representative_atom(const class core::chemical::ResidueType &, unsigned long) const –> unsigned long

get_intrares_countpair(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, sf: core::scoring::ScoreFunction) → core::scoring::etable::count_pair::CountPairFunction¶

Interface function for class NeighborList.

C++: core::scoring::elec::FA_ElecEnergy::get_intrares_countpair(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> class std::shared_ptr<const class core::scoring::etable::count_pair::CountPairFunction>

has_atomistic_energies(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → bool¶

Does this EnergyMethod have a non-trivial implementation of the (one body) atomistic energy method?: Note that this may return false even if the score term theoretically could support atomistic energies. And even if this function returns true, it’s not necessarily the case that all atoms will get assigned an energy, or that the sum over all atoms (or atom pairs) will result in the same energy as the residue-level approach. The atomistic functions are intended for supplemental informational purposes only. The residue-level energies are the main interface for EnergyMethods.

C++: core::scoring::methods::EnergyMethod::has_atomistic_energies() const –> bool

has_atomistic_pairwise_energies(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy) → bool¶

fa_elec has pairwise energies, but not single atom energies

C++: core::scoring::elec::FA_ElecEnergy::has_atomistic_pairwise_energies() const –> bool

hydrogen_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy) → float¶

How close two heavy atoms have to be such that their hydrogen atoms might interact

C++: core::scoring::elec::FA_ElecEnergy::hydrogen_interaction_cutoff() const –> double

hydrogen_interaction_cutoff2(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy) → float¶

How close two heavy atoms have to be such that their hydrogen atoms might interact, squared.

C++: core::scoring::elec::FA_ElecEnergy::hydrogen_interaction_cutoff2() const –> double

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, context_graphs_required: pyrosetta.rosetta.utility.vector1_bool) → None¶: C++: core::scoring::elec::FA_ElecEnergy::indicate_required_context_graphs(class utility::vector1<bool, class std::allocator<bool> > &) const –> void

initialize(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy) → None¶

Initilize constants.

C++: core::scoring::elec::FA_ElecEnergy::initialize() –> void

method_type(self: pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType¶: C++: core::scoring::methods::ContextIndependentTwoBodyEnergy::method_type() const –> enum core::scoring::methods::EnergyMethodType

minimize_in_whole_structure_context(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, pose: core::pose::Pose) → bool¶

Returns true if we’re using neighborlist-autoupdate

C++: core::scoring::elec::FA_ElecEnergy::minimize_in_whole_structure_context(const class core::pose::Pose &) const –> bool

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, pose: core::pose::Pose, set: pyrosetta.rosetta.core.conformation.RotamerSetBase) → None¶: C++: core::scoring::elec::FA_ElecEnergy::prepare_rotamers_for_packing(const class core::pose::Pose &, class core::conformation::RotamerSetBase &) const –> void

provide_citation_info(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by energy methods wishing to provide citation information.

C++: core::scoring::methods::EnergyMethod::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

requires_a_setup_for_derivatives_for_residue_opportunity(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, : core::pose::Pose) → bool¶: C++: core::scoring::elec::FA_ElecEnergy::requires_a_setup_for_derivatives_for_residue_opportunity(const class core::pose::Pose &) const –> bool

requires_a_setup_for_derivatives_for_residue_pair_opportunity(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, pose: core::pose::Pose) → bool¶

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.

C++: core::scoring::methods::TwoBodyEnergy::requires_a_setup_for_derivatives_for_residue_pair_opportunity(const class core::pose::Pose &) const –> bool

requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, : core::pose::Pose) → bool¶: C++: core::scoring::elec::FA_ElecEnergy::requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(const class core::pose::Pose &) const –> bool

requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose) → bool¶

Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not: all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false

C++: core::scoring::methods::EnergyMethod::requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(const class core::pose::Pose &) const –> bool

requires_a_setup_for_scoring_for_residue_pair_opportunity(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, pose: core::pose::Pose) → bool¶

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.

C++: core::scoring::methods::TwoBodyEnergy::requires_a_setup_for_scoring_for_residue_pair_opportunity(const class core::pose::Pose &) const –> bool

residue_pair_energy(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, : core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None¶: C++: core::scoring::elec::FA_ElecEnergy::residue_pair_energy(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

residue_pair_energy_ext(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResPairMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None¶: C++: core::scoring::elec::FA_ElecEnergy::residue_pair_energy_ext(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::ResPairMinimizationData &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

score_types(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType¶

Returns the score types that this energy method computes.

C++: core::scoring::methods::EnergyMethod::score_types() const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &

setup_for_derivatives(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, pose: core::pose::Pose, : core::scoring::ScoreFunction) → None¶: C++: core::scoring::elec::FA_ElecEnergy::setup_for_derivatives(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, : pyrosetta.rosetta.basic.datacache.BasicDataCache) → None¶: C++: core::scoring::elec::FA_ElecEnergy::setup_for_derivatives_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &, class basic::datacache::BasicDataCache &) const –> void

setup_for_derivatives_for_residue_pair(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, minsingle_data1: core::scoring::ResSingleMinimizationData, minsingle_data2: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, data_cache: core::scoring::ResPairMinimizationData) → None¶

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

C++: core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue_pair(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResPairMinimizationData &) const –> void

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_map: core::kinematics::MinimizerMapBase) → None¶

stashes nblist if use_nblist is true

C++: core::scoring::elec::FA_ElecEnergy::setup_for_minimizing(class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &) const –> void

setup_for_minimizing_for_residue(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, min_map: core::kinematics::MinimizerMapBase, : pyrosetta.rosetta.basic.datacache.BasicDataCache, resdata: core::scoring::ResSingleMinimizationData) → None¶: C++: core::scoring::elec::FA_ElecEnergy::setup_for_minimizing_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &, class basic::datacache::BasicDataCache &, class core::scoring::ResSingleMinimizationData &) const –> void

setup_for_minimizing_for_residue_pair(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, res1_data_cache: core::scoring::ResSingleMinimizationData, res2_data_cache: core::scoring::ResSingleMinimizationData, data_cache: core::scoring::ResPairMinimizationData) → None¶: C++: core::scoring::elec::FA_ElecEnergy::setup_for_minimizing_for_residue_pair(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &, const class core::scoring::ResSingleMinimizationData &, const class core::scoring::ResSingleMinimizationData &, class core::scoring::ResPairMinimizationData &) const –> void

setup_for_packing(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, pose: core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None¶: C++: core::scoring::elec::FA_ElecEnergy::setup_for_packing(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> void

setup_for_packing_with_rotsets(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose, rotsets: core::pack_basic::RotamerSetsBase, sfxn: core::scoring::ScoreFunction) → None¶

if an energy method needs to cache data in the Energies object,

before packing begins and requires access to the RotamerSets object, then it does so during this function. The default behavior is to do nothing.

The exact order of events when setting up for packing are as follows:

setup_for_packing() is called for all energy methods
rotamers are built
setup_for_packing_with_rotsets() is called for all energy methods
prepare_rotamers_for_packing() is called for all energy methods
The energy methods are asked to score all rotamers and rotamer pairs
Annealing

The pose is specifically non-const here so that energy methods can store data in it

: Used in ApproximateBuriedUnsatPenalty to pre-compute compatible rotamers

C++: core::scoring::methods::EnergyMethod::setup_for_packing_with_rotsets(class core::pose::Pose &, const class std::shared_ptr<class core::pack_basic::RotamerSetsBase> &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, pose: core::pose::Pose, : core::scoring::ScoreFunction) → None¶: C++: core::scoring::elec::FA_ElecEnergy::setup_for_scoring(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, sfxn: core::scoring::ScoreFunction, resdata: core::scoring::ResSingleMinimizationData) → None¶: C++: core::scoring::elec::FA_ElecEnergy::setup_for_scoring_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &) const –> void

setup_for_scoring_for_residue_pair(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, minsingle_data1: core::scoring::ResSingleMinimizationData, minsingle_data2: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, data_cache: core::scoring::ResPairMinimizationData) → None¶

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

C++: core::scoring::methods::TwoBodyEnergy::setup_for_scoring_for_residue_pair(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResPairMinimizationData &) const –> void

show_additional_info(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.std.ostream, : core::pose::Pose, : bool) → None¶

show additional information of the energy method

C++: core::scoring::methods::EnergyMethod::show_additional_info(std::ostream &, class core::pose::Pose &, bool) const –> void

sidechain_sidechain_energy(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None¶: C++: core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

update_residue_for_packing(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy, pose: core::pose::Pose, resid: int) → None¶: C++: core::scoring::elec::FA_ElecEnergy::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

use_extended_intrares_energy_interface(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy) → bool¶

Derived classes wishing to invoke the alternate, extended interface for eval_intrares_energy: during minimization routines should return “true” when this function is invoked on them. This class provides a default “return false” implementation so that classes not desiring to take advantage of this alternate interface need to do nothing.

C++: core::scoring::methods::TwoBodyEnergy::use_extended_intrares_energy_interface() const –> bool

use_extended_residue_pair_energy_interface(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy) → bool¶: C++: core::scoring::elec::FA_ElecEnergy::use_extended_residue_pair_energy_interface() const –> bool

version(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → int¶

Return the version of the energy method

C++: core::scoring::methods::EnergyMethod::version() const –> unsigned long

class pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergyCreator¶

Bases: EnergyMethodCreator

assign(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergyCreator, : pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergyCreator) → pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergyCreator¶: C++: core::scoring::elec::FA_ElecEnergyCreator::operator=(const class core::scoring::elec::FA_ElecEnergyCreator &) –> class core::scoring::elec::FA_ElecEnergyCreator &

create_energy_method(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod¶

Instantiate a new FA_ElecEnergy

C++: core::scoring::elec::FA_ElecEnergyCreator::create_energy_method(const class core::scoring::methods::EnergyMethodOptions &) const –> class std::shared_ptr<class core::scoring::methods::EnergyMethod>

score_types_for_method(self: pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergyCreator) → pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType¶

Return the set of score types claimed by the EnergyMethod: this EnergyMethodCreator creates in its create_energy_method() function

C++: core::scoring::elec::FA_ElecEnergyCreator::score_types_for_method() const –> class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> >

class pyrosetta.rosetta.core.scoring.elec.GroupElec¶

Bases: pybind11_object

eval_respair_group_coulomb(self: pyrosetta.rosetta.core.scoring.elec.GroupElec, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) → float¶: C++: core::scoring::elec::GroupElec::eval_respair_group_coulomb(const class core::conformation::Residue &, const class core::conformation::Residue &) const –> double

eval_respair_group_derivatives(self: pyrosetta.rosetta.core.scoring.elec.GroupElec, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, r1_atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair, r2_atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair, elec_weight: float, Erespair: float) → None¶: C++: core::scoring::elec::GroupElec::eval_respair_group_derivatives(const class core::conformation::Residue &, const class core::conformation::Residue &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &, const double, double &) const –> void

initialize(self: pyrosetta.rosetta.core.scoring.elec.GroupElec, coulomb: pyrosetta.rosetta.core.scoring.etable.coulomb.Coulomb) → None¶: C++: core::scoring::elec::GroupElec::initialize(const class core::scoring::etable::coulomb::Coulomb &) –> void

pyrosetta.rosetta.core.scoring.elec.read_cp_tables_from_db(filename: str) → pyrosetta.rosetta.std.map_std_string_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t_std_allocator_std_pair_const_std_string_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t¶

Read the CP tables from the database and return an owning pointer to the

new object created in memory.

Called by the ScoringManager to allow these data to be read in once and only once.

C++: core::scoring::elec::read_cp_tables_from_db(const std::string &) –> class std::shared_ptr<class std::map<std::string, class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > > > > >

class pyrosetta.rosetta.core.scoring.elec.weight_triple¶

Bases: pybind11_object

property w_intra_¶

property wbb_bb_¶

property wbb_sc_¶

property wsc_bb_¶

property wsc_sc_¶