etable

Bindings for core::scoring::etable namespace

class pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy

Bases: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t

assign(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, : pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy) pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy

C++: core::scoring::methods::ContextIndependentTwoBodyEnergy::operator=(const class core::scoring::methods::ContextIndependentTwoBodyEnergy &) –> class core::scoring::methods::ContextIndependentTwoBodyEnergy &

atom_pair_energy(*args, **kwargs)

Overloaded function.

  1. atom_pair_energy(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, emap: pyrosetta.rosetta.core.scoring.EMapVector, dsq: float) -> None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::atom_pair_energy(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, class core::scoring::EMapVector &, double &) const –> void

  1. atom_pair_energy(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, atr: float, rep: float, solv: float, bb: float, dsq: float) -> None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::atom_pair_energy(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, double &, double &, double &, double &, double &) const –> void

  1. atom_pair_energy(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, ape: pyrosetta.rosetta.core.scoring.etable.AtomPairEnergy) -> None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::atom_pair_energy(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, struct core::scoring::etable::AtomPairEnergy &) const –> void

atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t) float

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, : int, : pyrosetta.rosetta.core.conformation.Residue, : int, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, : pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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

calculate_interres(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::calculate_interres(const class core::conformation::Residue &, const class core::conformation::Residue &) const –> bool

calculate_intrares(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd: pyrosetta.rosetta.core.conformation.Residue) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::calculate_intrares(const class core::conformation::Residue &) const –> bool

clone(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy) pyrosetta.rosetta.core.scoring.methods.EnergyMethod

clone

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

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.etable.AnalyticEtableEnergy, : pyrosetta.rosetta.core.scoring.EMapVector) bool

C++: core::scoring::etable::AnalyticEtableEnergy::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.methods.TwoBodyEnergy, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, res_moving_wrt_eachother: bool) bool
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.

C++: core::scoring::methods::TwoBodyEnergy::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::divides_backbone_and_sidechain_energetics() const –> bool

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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_derivatives(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) None
eval_intrares_energy(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::AnalyticEtableEnergy::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.AnalyticEtableEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, : pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, min_data: pyrosetta.rosetta.core.scoring.ResPairMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector, r1_at_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair, r2_at_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) None
evaluate_rotamer_background_energies(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, residue: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, energy_vector: pyrosetta.rosetta.utility.vector1_float) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.methods.TwoBodyEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, energies: pyrosetta.rosetta.utility.vector1_float) None
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.

C++: core::scoring::methods::TwoBodyEnergy::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, set1: pyrosetta.rosetta.core.conformation.RotamerSetBase, set2: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, energy_table: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, totals: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.

  1. get_count_pair_function(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, res1: int, res2: int, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::get_count_pair_function(unsigned long, 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>

  1. get_count_pair_function(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::get_count_pair_function(const class core::conformation::Residue &, 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>

get_intrares_countpair(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, res: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::get_intrares_countpair(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> class std::shared_ptr<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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::has_atomistic_pairwise_energies() const –> bool

hydrogen_interaction_cutoff2(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t) float

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::hydrogen_interaction_cutoff2() const –> double

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, : pyrosetta.rosetta.utility.vector1_bool) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::indicate_required_context_graphs(class utility::vector1<bool, class std::allocator<bool> > &) const –> void

interres_evaluator(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy) pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator

C++: core::scoring::etable::AnalyticEtableEnergy::interres_evaluator() –> class core::scoring::etable::AnalyticEtableEvaluator &

intrares_evaluator(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy) pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator

C++: core::scoring::etable::AnalyticEtableEnergy::intrares_evaluator() –> class core::scoring::etable::AnalyticEtableEvaluator &

method_type(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t) pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

C++: core::scoring::methods::ContextIndependentTwoBodyEnergy::method_type() const –> enum core::scoring::methods::EnergyMethodType

min_pair_data_type(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t) pyrosetta.rosetta.core.scoring.min_pair_data

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::min_pair_data_type() const –> enum core::scoring::min_pair_data

min_single_data_type(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t) pyrosetta.rosetta.core.scoring.min_single_data

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::min_single_data_type() const –> enum core::scoring::min_single_data

minimize_in_whole_structure_context(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, : pyrosetta.rosetta.core.pose.Pose) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::minimize_in_whole_structure_context(const class core::pose::Pose &) const –> bool

nblist_type(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t) pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::nblist_type() const –> enum core::scoring::EnergiesCacheableDataType::Enum

nonprot_intrares_evaluator(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy) pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator

C++: core::scoring::etable::AnalyticEtableEnergy::nonprot_intrares_evaluator() –> class core::scoring::etable::AnalyticEtableEvaluator &

pair_energy_H(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::pair_energy_H(const class core::conformation::Atom &, const class core::conformation::Atom &, double, class core::scoring::EMapVector &) const –> void

prepare_for_residue_pair(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, res1: int, res2: int, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::prepare_for_residue_pair(const unsigned long, const unsigned long, const class core::pose::Pose &) const –> void

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, set: pyrosetta.rosetta.core.conformation.RotamerSetBase) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::requires_a_setup_for_scoring_for_residue_pair_opportunity(const class core::pose::Pose &) const –> bool

residue_pair_energy(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, min_data: pyrosetta.rosetta.core.scoring.ResPairMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::setup_for_derivatives(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, : pyrosetta.rosetta.basic.datacache.BasicDataCache) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, minsingle_data1: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, minsingle_data2: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, data_cache: pyrosetta.rosetta.core.scoring.ResPairMinimizationData) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, min_map: pyrosetta.rosetta.core.kinematics.MinimizerMapBase) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, minmap: pyrosetta.rosetta.core.kinematics.MinimizerMapBase, : pyrosetta.rosetta.basic.datacache.BasicDataCache, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, minmap: pyrosetta.rosetta.core.kinematics.MinimizerMapBase, res1_data_cache: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, res2_data_cache: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, min_data: pyrosetta.rosetta.core.scoring.ResPairMinimizationData) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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:
  1. setup_for_packing() is called for all energy methods

  2. rotamers are built

  3. setup_for_packing_with_rotsets() is called for all energy methods

  4. prepare_rotamers_for_packing() is called for all energy methods

  5. The energy methods are asked to score all rotamers and rotamer pairs

  6. 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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::setup_for_scoring(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring_(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::scoring::etable::AnalyticEtableEnergy::setup_for_scoring_(const class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, minsingle_data1: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, minsingle_data2: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, data_cache: pyrosetta.rosetta.core.scoring.ResPairMinimizationData) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, resid: int) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

use_extended_intrares_energy_interface(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::use_extended_intrares_energy_interface() const –> bool

use_extended_residue_pair_energy_interface(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.AnalyticEtableEvaluator

Bases: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator

assign(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, : pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) pyrosetta.rosetta.core.scoring.etable.EtableEvaluator

C++: core::scoring::etable::EtableEvaluator::operator=(const class core::scoring::etable::EtableEvaluator &) –> class core::scoring::etable::EtableEvaluator &

atom_pair_energy(*args, **kwargs)

Overloaded function.

  1. atom_pair_energy(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, emap: pyrosetta.rosetta.core.scoring.EMapVector, d2: float) -> None

A non-virtual function for the evaluation of an interaction energy of a

pair of atoms that is invoked directly by the atom-pair-energy-inline functions without any virtual-function overhead.

C++: core::scoring::etable::AnalyticEtableEvaluator::atom_pair_energy(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, class core::scoring::EMapVector &, double &) const –> void

  1. atom_pair_energy(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, atr: float, rep: float, solv: float, d2: float) -> None

A non-virtual function for the evaluation of an interaction energy of a

pair of atoms that is invoked by functions that are themselves invoked by the atom-pair-energy-inline functions without any virtual-function overhead.

C++: core::scoring::etable::AnalyticEtableEvaluator::atom_pair_energy(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, double &, double &, double &, double &) const –> void

atom_pair_energy_v(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, atrE: float, repE: float, solE: float, d2: float) None

C++: core::scoring::etable::AnalyticEtableEvaluator::atom_pair_energy_v(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, double &, double &, double &, double &) const –> void

atom_pair_lk_energy_and_deriv_v(*args, **kwargs)

Overloaded function.

  1. atom_pair_lk_energy_and_deriv_v(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, solE1: float, dsolE1: float) -> None

  2. atom_pair_lk_energy_and_deriv_v(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, solE1: float, dsolE1: float, eval_deriv: bool) -> None

C++: core::scoring::etable::AnalyticEtableEvaluator::atom_pair_lk_energy_and_deriv_v(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, const bool) const –> void

atom_pair_lk_energy_and_deriv_v_efficient(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, solE1: float, solE2: float, dsolE1: float, eval_deriv: bool) None

C++: core::scoring::etable::AnalyticEtableEvaluator::atom_pair_lk_energy_and_deriv_v_efficient(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, double &, const bool) const –> void

atr_weight(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) float

C++: core::scoring::etable::EtableEvaluator::atr_weight() const –> double

clone(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator) pyrosetta.rosetta.core.scoring.etable.EtableEvaluator

C++: core::scoring::etable::AnalyticEtableEvaluator::clone() const –> class std::shared_ptr<class core::scoring::etable::EtableEvaluator>

eval_dE_dR_over_r(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weights: pyrosetta.rosetta.core.scoring.EMapVector, f1: pyrosetta.rosetta.numeric.xyzVector_double_t, f2: pyrosetta.rosetta.numeric.xyzVector_double_t) float

C++: core::scoring::etable::AnalyticEtableEvaluator::eval_dE_dR_over_r(const class core::conformation::Atom &, const class core::conformation::Atom &, const class core::scoring::EMapVector &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> double

eval_dE_dR_over_r_v(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weights: pyrosetta.rosetta.core.scoring.EMapVector, f1: pyrosetta.rosetta.numeric.xyzVector_double_t, f2: pyrosetta.rosetta.numeric.xyzVector_double_t) float

C++: core::scoring::etable::AnalyticEtableEvaluator::eval_dE_dR_over_r_v(const class core::conformation::Atom &, const class core::conformation::Atom &, const class core::scoring::EMapVector &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> double

heavyatom_heavyatom_energy(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator, at1: pyrosetta.rosetta.core.scoring.etable.etrie.EtableAtom, at2: pyrosetta.rosetta.core.scoring.etable.etrie.EtableAtom, d2: float, : int) float

Inline Methods For Trie-vs-Trie Algorithm

C++: core::scoring::etable::AnalyticEtableEvaluator::heavyatom_heavyatom_energy(const class core::scoring::etable::etrie::EtableAtom &, const class core::scoring::etable::etrie::EtableAtom &, double &, unsigned long &) const –> double

heavyatom_hydrogenatom_energy(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator, at1: pyrosetta.rosetta.core.scoring.etable.etrie.EtableAtom, at2: pyrosetta.rosetta.core.scoring.etable.etrie.EtableAtom, : int, : core::scoring::trie::TrieVsTrieCachedDataContainerBase) float

C++: core::scoring::etable::AnalyticEtableEvaluator::heavyatom_hydrogenatom_energy(const class core::scoring::etable::etrie::EtableAtom &, const class core::scoring::etable::etrie::EtableAtom &, unsigned long &, const class core::scoring::trie::TrieVsTrieCachedDataContainerBase *const) const –> double

hydrogen_interaction_cutoff2(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) float

C++: core::scoring::etable::EtableEvaluator::hydrogen_interaction_cutoff2() const –> double

hydrogenatom_heavyatom_energy(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator, at1: pyrosetta.rosetta.core.scoring.etable.etrie.EtableAtom, at2: pyrosetta.rosetta.core.scoring.etable.etrie.EtableAtom, : int, : core::scoring::trie::TrieVsTrieCachedDataContainerBase) float

C++: core::scoring::etable::AnalyticEtableEvaluator::hydrogenatom_heavyatom_energy(const class core::scoring::etable::etrie::EtableAtom &, const class core::scoring::etable::etrie::EtableAtom &, unsigned long &, const class core::scoring::trie::TrieVsTrieCachedDataContainerBase *const) const –> double

hydrogenatom_hydrogenatom_energy(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator, at1: pyrosetta.rosetta.core.scoring.etable.etrie.EtableAtom, at2: pyrosetta.rosetta.core.scoring.etable.etrie.EtableAtom, : int, : core::scoring::trie::TrieVsTrieCachedDataContainerBase) float

C++: core::scoring::etable::AnalyticEtableEvaluator::hydrogenatom_hydrogenatom_energy(const class core::scoring::etable::etrie::EtableAtom &, const class core::scoring::etable::etrie::EtableAtom &, unsigned long &, const class core::scoring::trie::TrieVsTrieCachedDataContainerBase *const) const –> double

pair_energy_H(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, emap: pyrosetta.rosetta.core.scoring.EMapVector) None
A non-virtual function for the evaluation of an interaction energy of a

pair of atoms that is invoked directly by the atom-pair-energy-inline functions without any virtual-function overhead.

C++: core::scoring::etable::AnalyticEtableEvaluator::pair_energy_H(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, class core::scoring::EMapVector &) const –> void

pair_energy_H_v(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::AnalyticEtableEvaluator::pair_energy_H_v(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, class core::scoring::EMapVector &) const –> void

rep_weight(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) float

C++: core::scoring::etable::EtableEvaluator::rep_weight() const –> double

residue_atom_pair_energy(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, cp: pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

Atom pair energy inline type resolution function

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

residue_atom_pair_energy_backbone_backbone(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, cp: pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

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

residue_atom_pair_energy_sidechain_backbone(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, cp: pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

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

residue_atom_pair_energy_sidechain_sidechain(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, cp: pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

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

residue_atom_pair_energy_sidechain_whole(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, cp: pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

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

set_scoretypes(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, st_atr_in: pyrosetta.rosetta.core.scoring.ScoreType, st_rep_in: pyrosetta.rosetta.core.scoring.ScoreType, st_sol_in: pyrosetta.rosetta.core.scoring.ScoreType) None

C++: core::scoring::etable::EtableEvaluator::set_scoretypes(enum core::scoring::ScoreType, enum core::scoring::ScoreType, enum core::scoring::ScoreType) –> void

set_weights(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, weights: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::EtableEvaluator::set_weights(const class core::scoring::EMapVector &) –> void

sol_weight(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) float

C++: core::scoring::etable::EtableEvaluator::sol_weight() const –> double

st_atr(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) pyrosetta.rosetta.core.scoring.ScoreType

C++: core::scoring::etable::EtableEvaluator::st_atr() const –> enum core::scoring::ScoreType

st_rep(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) pyrosetta.rosetta.core.scoring.ScoreType

C++: core::scoring::etable::EtableEvaluator::st_rep() const –> enum core::scoring::ScoreType

st_sol(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) pyrosetta.rosetta.core.scoring.ScoreType

C++: core::scoring::etable::EtableEvaluator::st_sol() const –> enum core::scoring::ScoreType

sum_energies(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, atr: float, rep: float, solv: float) float

C++: core::scoring::etable::EtableEvaluator::sum_energies(double, double, double) const –> double

trie_vs_path(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator, trie1: pyrosetta.rosetta.core.scoring.trie.RotamerTrieBase, trie2: pyrosetta.rosetta.core.scoring.trie.RotamerTrieBase, cp: pyrosetta.rosetta.core.scoring.trie.TrieCountPairBase, pair_energy_vector: pyrosetta.rosetta.utility.vector1_float, temp_vector: pyrosetta.rosetta.utility.vector1_float) None

C++: core::scoring::etable::AnalyticEtableEvaluator::trie_vs_path(const class core::scoring::trie::RotamerTrieBase &, const class core::scoring::trie::RotamerTrieBase &, class core::scoring::trie::TrieCountPairBase &, class utility::vector1<float, class std::allocator<float> > &, class utility::vector1<float, class std::allocator<float> > &) const –> void

trie_vs_trie(self: pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator, trie1: pyrosetta.rosetta.core.scoring.trie.RotamerTrieBase, trie2: pyrosetta.rosetta.core.scoring.trie.RotamerTrieBase, cp: pyrosetta.rosetta.core.scoring.trie.TrieCountPairBase, pair_energy_table: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t, temp_table: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) None

Trie vs trie / trie vs path type resolution functions

C++: core::scoring::etable::AnalyticEtableEvaluator::trie_vs_trie(const class core::scoring::trie::RotamerTrieBase &, const class core::scoring::trie::RotamerTrieBase &, class core::scoring::trie::TrieCountPairBase &, class ObjexxFCL::FArray2D<float> &, class ObjexxFCL::FArray2D<float> &) const –> void

class pyrosetta.rosetta.core.scoring.etable.AtomPairEnergy

Bases: pybind11_builtins.pybind11_object

property attractive
property bead_bead_interaction
property distance_squared
property repulsive
property solvation
class pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t

Bases: pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy

assign(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, : pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy) pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy

C++: core::scoring::methods::ContextIndependentTwoBodyEnergy::operator=(const class core::scoring::methods::ContextIndependentTwoBodyEnergy &) –> class core::scoring::methods::ContextIndependentTwoBodyEnergy &

atom_pair_energy(*args, **kwargs)

Overloaded function.

  1. atom_pair_energy(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, emap: pyrosetta.rosetta.core.scoring.EMapVector, dsq: float) -> None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::atom_pair_energy(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, class core::scoring::EMapVector &, double &) const –> void

  1. atom_pair_energy(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, atr: float, rep: float, solv: float, bb: float, dsq: float) -> None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::atom_pair_energy(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, double &, double &, double &, double &, double &) const –> void

  1. atom_pair_energy(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, ape: pyrosetta.rosetta.core.scoring.etable.AtomPairEnergy) -> None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::atom_pair_energy(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, struct core::scoring::etable::AtomPairEnergy &) const –> void

atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t) float

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, : int, : pyrosetta.rosetta.core.conformation.Residue, : int, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, : pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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

calculate_interres(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::calculate_interres(const class core::conformation::Residue &, const class core::conformation::Residue &) const –> bool

calculate_intrares(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd: pyrosetta.rosetta.core.conformation.Residue) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::calculate_intrares(const class core::conformation::Residue &) const –> bool

clone(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) pyrosetta.rosetta.core.scoring.methods.EnergyMethod

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

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.methods.TwoBodyEnergy, weights: core::scoring::EMapVector) bool
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.

For example, the Etable method defines intra-residue energies only when one or more of the fa_intra_{atr,rep,sol} weights are non-zero.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, res_moving_wrt_eachother: bool) bool
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.

C++: core::scoring::methods::TwoBodyEnergy::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::divides_backbone_and_sidechain_energetics() const –> bool

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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_derivatives(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) None

Evaluate the intra-residue energy for a given residue

C++: core::scoring::methods::TwoBodyEnergy::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, : pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, min_data: pyrosetta.rosetta.core.scoring.ResPairMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector, r1_at_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair, r2_at_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, residue: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, energy_vector: pyrosetta.rosetta.utility.vector1_float) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.methods.TwoBodyEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, energies: pyrosetta.rosetta.utility.vector1_float) None
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.

C++: core::scoring::methods::TwoBodyEnergy::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, set1: pyrosetta.rosetta.core.conformation.RotamerSetBase, set2: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, energy_table: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, totals: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.

  1. get_count_pair_function(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, res1: int, res2: int, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::get_count_pair_function(unsigned long, 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>

  1. get_count_pair_function(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::get_count_pair_function(const class core::conformation::Residue &, 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>

get_intrares_countpair(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, res: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::get_intrares_countpair(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> class std::shared_ptr<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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::has_atomistic_pairwise_energies() const –> bool

hydrogen_interaction_cutoff2(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t) float

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::hydrogen_interaction_cutoff2() const –> double

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, : pyrosetta.rosetta.utility.vector1_bool) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::indicate_required_context_graphs(class utility::vector1<bool, class std::allocator<bool> > &) const –> void

method_type(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t) pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

C++: core::scoring::methods::ContextIndependentTwoBodyEnergy::method_type() const –> enum core::scoring::methods::EnergyMethodType

min_pair_data_type(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t) pyrosetta.rosetta.core.scoring.min_pair_data

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::min_pair_data_type() const –> enum core::scoring::min_pair_data

min_single_data_type(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t) pyrosetta.rosetta.core.scoring.min_single_data

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::min_single_data_type() const –> enum core::scoring::min_single_data

minimize_in_whole_structure_context(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, : pyrosetta.rosetta.core.pose.Pose) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::minimize_in_whole_structure_context(const class core::pose::Pose &) const –> bool

nblist_type(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t) pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::nblist_type() const –> enum core::scoring::EnergiesCacheableDataType::Enum

pair_energy_H(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::pair_energy_H(const class core::conformation::Atom &, const class core::conformation::Atom &, double, class core::scoring::EMapVector &) const –> void

prepare_for_residue_pair(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, res1: int, res2: int, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::prepare_for_residue_pair(const unsigned long, const unsigned long, const class core::pose::Pose &) const –> void

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, set: pyrosetta.rosetta.core.conformation.RotamerSetBase) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::requires_a_setup_for_scoring_for_residue_pair_opportunity(const class core::pose::Pose &) const –> bool

residue_pair_energy(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, min_data: pyrosetta.rosetta.core.scoring.ResPairMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::setup_for_derivatives(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, : pyrosetta.rosetta.basic.datacache.BasicDataCache) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, minsingle_data1: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, minsingle_data2: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, data_cache: pyrosetta.rosetta.core.scoring.ResPairMinimizationData) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, min_map: pyrosetta.rosetta.core.kinematics.MinimizerMapBase) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, minmap: pyrosetta.rosetta.core.kinematics.MinimizerMapBase, : pyrosetta.rosetta.basic.datacache.BasicDataCache, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, minmap: pyrosetta.rosetta.core.kinematics.MinimizerMapBase, res1_data_cache: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, res2_data_cache: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, min_data: pyrosetta.rosetta.core.scoring.ResPairMinimizationData) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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:
  1. setup_for_packing() is called for all energy methods

  2. rotamers are built

  3. setup_for_packing_with_rotsets() is called for all energy methods

  4. prepare_rotamers_for_packing() is called for all energy methods

  5. The energy methods are asked to score all rotamers and rotamer pairs

  6. 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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::setup_for_scoring(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, minsingle_data1: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, minsingle_data2: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, data_cache: pyrosetta.rosetta.core.scoring.ResPairMinimizationData) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, resid: int) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

use_extended_intrares_energy_interface(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::use_extended_intrares_energy_interface() const –> bool

use_extended_residue_pair_energy_interface(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::AnalyticEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t

Bases: pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy

assign(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, : pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy) pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy

C++: core::scoring::methods::ContextIndependentTwoBodyEnergy::operator=(const class core::scoring::methods::ContextIndependentTwoBodyEnergy &) –> class core::scoring::methods::ContextIndependentTwoBodyEnergy &

atom_pair_energy(*args, **kwargs)

Overloaded function.

  1. atom_pair_energy(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, emap: pyrosetta.rosetta.core.scoring.EMapVector, dsq: float) -> None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::atom_pair_energy(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, class core::scoring::EMapVector &, double &) const –> void

  1. atom_pair_energy(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, atr: float, rep: float, solv: float, bb: float, dsq: float) -> None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::atom_pair_energy(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, double &, double &, double &, double &, double &) const –> void

  1. atom_pair_energy(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, ape: pyrosetta.rosetta.core.scoring.etable.AtomPairEnergy) -> None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::atom_pair_energy(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, struct core::scoring::etable::AtomPairEnergy &) const –> void

atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t) float

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, : int, : pyrosetta.rosetta.core.conformation.Residue, : int, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, : pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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

calculate_interres(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::calculate_interres(const class core::conformation::Residue &, const class core::conformation::Residue &) const –> bool

calculate_intrares(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd: pyrosetta.rosetta.core.conformation.Residue) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::calculate_intrares(const class core::conformation::Residue &) const –> bool

clone(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) pyrosetta.rosetta.core.scoring.methods.EnergyMethod

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

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.methods.TwoBodyEnergy, weights: core::scoring::EMapVector) bool
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.

For example, the Etable method defines intra-residue energies only when one or more of the fa_intra_{atr,rep,sol} weights are non-zero.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, res_moving_wrt_eachother: bool) bool
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.

C++: core::scoring::methods::TwoBodyEnergy::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::divides_backbone_and_sidechain_energetics() const –> bool

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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_derivatives(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) None

Evaluate the intra-residue energy for a given residue

C++: core::scoring::methods::TwoBodyEnergy::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, : pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, min_data: pyrosetta.rosetta.core.scoring.ResPairMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector, r1_at_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair, r2_at_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, residue: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, energy_vector: pyrosetta.rosetta.utility.vector1_float) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.methods.TwoBodyEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, energies: pyrosetta.rosetta.utility.vector1_float) None
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.

C++: core::scoring::methods::TwoBodyEnergy::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, set1: pyrosetta.rosetta.core.conformation.RotamerSetBase, set2: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, energy_table: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, totals: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.

  1. get_count_pair_function(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, res1: int, res2: int, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::get_count_pair_function(unsigned long, 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>

  1. get_count_pair_function(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::get_count_pair_function(const class core::conformation::Residue &, 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>

get_intrares_countpair(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, res: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::get_intrares_countpair(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> class std::shared_ptr<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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::has_atomistic_pairwise_energies() const –> bool

hydrogen_interaction_cutoff2(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t) float

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::hydrogen_interaction_cutoff2() const –> double

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, : pyrosetta.rosetta.utility.vector1_bool) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::indicate_required_context_graphs(class utility::vector1<bool, class std::allocator<bool> > &) const –> void

method_type(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t) pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

C++: core::scoring::methods::ContextIndependentTwoBodyEnergy::method_type() const –> enum core::scoring::methods::EnergyMethodType

min_pair_data_type(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t) pyrosetta.rosetta.core.scoring.min_pair_data

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::min_pair_data_type() const –> enum core::scoring::min_pair_data

min_single_data_type(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t) pyrosetta.rosetta.core.scoring.min_single_data

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::min_single_data_type() const –> enum core::scoring::min_single_data

minimize_in_whole_structure_context(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, : pyrosetta.rosetta.core.pose.Pose) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::minimize_in_whole_structure_context(const class core::pose::Pose &) const –> bool

nblist_type(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t) pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::nblist_type() const –> enum core::scoring::EnergiesCacheableDataType::Enum

pair_energy_H(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::pair_energy_H(const class core::conformation::Atom &, const class core::conformation::Atom &, double, class core::scoring::EMapVector &) const –> void

prepare_for_residue_pair(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, res1: int, res2: int, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::prepare_for_residue_pair(const unsigned long, const unsigned long, const class core::pose::Pose &) const –> void

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, set: pyrosetta.rosetta.core.conformation.RotamerSetBase) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::requires_a_setup_for_scoring_for_residue_pair_opportunity(const class core::pose::Pose &) const –> bool

residue_pair_energy(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, min_data: pyrosetta.rosetta.core.scoring.ResPairMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::setup_for_derivatives(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, : pyrosetta.rosetta.basic.datacache.BasicDataCache) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, minsingle_data1: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, minsingle_data2: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, data_cache: pyrosetta.rosetta.core.scoring.ResPairMinimizationData) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, min_map: pyrosetta.rosetta.core.kinematics.MinimizerMapBase) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, minmap: pyrosetta.rosetta.core.kinematics.MinimizerMapBase, : pyrosetta.rosetta.basic.datacache.BasicDataCache, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, minmap: pyrosetta.rosetta.core.kinematics.MinimizerMapBase, res1_data_cache: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, res2_data_cache: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, min_data: pyrosetta.rosetta.core.scoring.ResPairMinimizationData) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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:
  1. setup_for_packing() is called for all energy methods

  2. rotamers are built

  3. setup_for_packing_with_rotsets() is called for all energy methods

  4. prepare_rotamers_for_packing() is called for all energy methods

  5. The energy methods are asked to score all rotamers and rotamer pairs

  6. 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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::setup_for_scoring(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, minsingle_data1: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, minsingle_data2: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, data_cache: pyrosetta.rosetta.core.scoring.ResPairMinimizationData) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, resid: int) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

use_extended_intrares_energy_interface(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::use_extended_intrares_energy_interface() const –> bool

use_extended_residue_pair_energy_interface(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.Etable

Bases: pybind11_builtins.pybind11_object

Class definition for Etable

Wradius(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::Wradius() const –> double

add_long_range_damping(self: pyrosetta.rosetta.core.scoring.etable.Etable) bool

C++: core::scoring::etable::Etable::add_long_range_damping() const –> bool

analytic_etable_derivatives(self: pyrosetta.rosetta.core.scoring.etable.Etable, at1: pyrosetta.rosetta.core.conformation.Atom, at2: pyrosetta.rosetta.core.conformation.Atom, dljatrE_ddis: float, dljrepE_ddis: float, dfasolE_ddis: float, inv_d: float) None

Analytically evaluate the energy derivatives for a pair of atoms

C++: core::scoring::etable::Etable::analytic_etable_derivatives(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, double &, double &) const –> void

analytic_etable_evaluation(self: pyrosetta.rosetta.core.scoring.etable.Etable, at1: pyrosetta.rosetta.core.conformation.Atom, at2: pyrosetta.rosetta.core.conformation.Atom, lj_atrE: float, lj_repE: float, fa_solE: float, d2: float) None
Use an analytic functional form of the etable to evaluate an atom-pair energy

without reading from the enormous and uncachable tables.

C++: core::scoring::etable::Etable::analytic_etable_evaluation(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, double &, double &) const –> void

analytic_lk_derivatives(self: pyrosetta.rosetta.core.scoring.etable.Etable, at1: pyrosetta.rosetta.core.conformation.Atom, at2: pyrosetta.rosetta.core.conformation.Atom, dfasolE1_ddis: float, dfasolE2_ddis: float, inv_d: float) None
Analytically evaluate the LK solvation derivatives for a pair of atoms, separately

computing the derivative for atom2’s desolvation of atom1 (dfasolE1_ddis) and atom1’s desolvation of atom2 (dfasolE2_ddis).

C++: core::scoring::etable::Etable::analytic_lk_derivatives(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, double &) const –> void

analytic_lk_energy(self: pyrosetta.rosetta.core.scoring.etable.Etable, at1: pyrosetta.rosetta.core.conformation.Atom, at2: pyrosetta.rosetta.core.conformation.Atom, fa_solE1: float, fa_solE2: float) None
Use an analytic functional form of the etable to evaluate only the LK atom-pair energy

computing the desolvation of atom1 by atom2 separately from the desolvation of atom2 by atom1.

C++: core::scoring::etable::Etable::analytic_lk_energy(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &) const –> void

analytic_params_for_pair(self: pyrosetta.rosetta.core.scoring.etable.Etable, atype1: int, atype2: int) pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair

C++: core::scoring::etable::Etable::analytic_params_for_pair(unsigned long, unsigned long) const –> const struct core::scoring::etable::EtableParamsOnePair &

atom_set(self: pyrosetta.rosetta.core.scoring.etable.Etable) pyrosetta.rosetta.std.weak_ptr_const_core_chemical_AtomTypeSet_t

C++: core::scoring::etable::Etable::atom_set() const –> class std::weak_ptr<const class core::chemical::AtomTypeSet>

atom_type(self: pyrosetta.rosetta.core.scoring.etable.Etable, type: int) pyrosetta.rosetta.core.chemical.AtomType

C++: core::scoring::etable::Etable::atom_type(const int) –> const class core::chemical::AtomType &

dljatr(self: pyrosetta.rosetta.core.scoring.etable.Etable) pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

const access to the deriv arrays

C++: core::scoring::etable::Etable::dljatr() const –> const class ObjexxFCL::FArray3D<double> &

dljrep(self: pyrosetta.rosetta.core.scoring.etable.Etable) pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

C++: core::scoring::etable::Etable::dljrep() const –> const class ObjexxFCL::FArray3D<double> &

dsolv(self: pyrosetta.rosetta.core.scoring.etable.Etable) pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

return the solvation derivative table that combines atom1 and atom2’s desolvations

C++: core::scoring::etable::Etable::dsolv() const –> const class ObjexxFCL::FArray3D<double> &

dsolv1(self: pyrosetta.rosetta.core.scoring.etable.Etable) pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

return the solvation derivative table for the desolvation of atom1 by atom2

C++: core::scoring::etable::Etable::dsolv1() const –> const class ObjexxFCL::FArray3D<double> &

epsilon(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::epsilon() const –> double

etable_disbins(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::etable_disbins() const –> double

fa_hatr(self: pyrosetta.rosetta.core.scoring.etable.Etable) bool

Do hydrogens provide attractive forces or do they only repell?

C++: core::scoring::etable::Etable::fa_hatr() const –> bool

fasol_cubic_poly_far_xhi(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::fasol_cubic_poly_far_xhi() const –> double

fasol_cubic_poly_far_xlo(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::fasol_cubic_poly_far_xlo() const –> double

get_bins_per_A2(self: pyrosetta.rosetta.core.scoring.etable.Etable) int

C++: core::scoring::etable::Etable::get_bins_per_A2() const –> int

get_lj_hbond_OH_donor_dis(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::get_lj_hbond_OH_donor_dis() const –> double

get_lj_hbond_dis(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::get_lj_hbond_dis() const –> double

get_lj_hbond_hdis(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::get_lj_hbond_hdis() const –> double

get_safe_max_dis2(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::get_safe_max_dis2() const –> double

hydrogen_interaction_cutoff2(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::hydrogen_interaction_cutoff2() const –> double

input_etable(self: pyrosetta.rosetta.core.scoring.etable.Etable, etable: pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t, label: str, in: pyrosetta.rosetta.std.istream) None

C++: core::scoring::etable::Etable::input_etable(class ObjexxFCL::FArray3D<double> &, const std::string &, std::istream &) –> void

interpolated_analytic_etable_evaluation(self: pyrosetta.rosetta.core.scoring.etable.Etable, at1: pyrosetta.rosetta.core.conformation.Atom, at2: pyrosetta.rosetta.core.conformation.Atom, lj_atrE: float, lj_repE: float, fa_solE: float, d2: float) None
Use the analytic_etable_evaluation function to evaluate the energy

of two atoms, but evaluate the function at the old grid points and then interpolate between them the way the existing etable does (in square distance space). Useful for comparing the original etable evaluation with the analytic evaluation.

C++: core::scoring::etable::Etable::interpolated_analytic_etable_evaluation(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, double &, double &) const –> void

lj_radius(self: pyrosetta.rosetta.core.scoring.etable.Etable, i: int) float

Return the Lennard-Jones radius for an atom.

C++: core::scoring::etable::Etable::lj_radius(const int) const –> double

lj_slope_intercept(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::lj_slope_intercept() const –> double

lj_switch_dis2sigma(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::lj_switch_dis2sigma() const –> double

lj_use_hbond_radii(self: pyrosetta.rosetta.core.scoring.etable.Etable) bool

C++: core::scoring::etable::Etable::lj_use_hbond_radii() const –> bool

lj_use_lj_deriv_slope(self: pyrosetta.rosetta.core.scoring.etable.Etable) bool

C++: core::scoring::etable::Etable::lj_use_lj_deriv_slope() const –> bool

lj_use_water_radii(self: pyrosetta.rosetta.core.scoring.etable.Etable) bool

C++: core::scoring::etable::Etable::lj_use_water_radii() const –> bool

lj_water_dis(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::lj_water_dis() const –> double

lj_water_hdis(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::lj_water_hdis() const –> double

lj_wdepth(self: pyrosetta.rosetta.core.scoring.etable.Etable, i: int) float

Return the Lennard-Jones well depth for an atom

C++: core::scoring::etable::Etable::lj_wdepth(const int) const –> double

ljatr(self: pyrosetta.rosetta.core.scoring.etable.Etable) pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

const access to the arrays

C++: core::scoring::etable::Etable::ljatr() const –> const class ObjexxFCL::FArray3D<double> &

ljrep(self: pyrosetta.rosetta.core.scoring.etable.Etable) pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

C++: core::scoring::etable::Etable::ljrep() const –> const class ObjexxFCL::FArray3D<double> &

lk_dgfree(self: pyrosetta.rosetta.core.scoring.etable.Etable, i: int) float

Return the Lazardis Karplus DGFree value for an atom

C++: core::scoring::etable::Etable::lk_dgfree(const int) const –> double

lk_inv_lambda2(self: pyrosetta.rosetta.core.scoring.etable.Etable, i: int) float

C++: core::scoring::etable::Etable::lk_inv_lambda2(const int) const –> double

lk_lambda(self: pyrosetta.rosetta.core.scoring.etable.Etable, i: int) float

Return the Lazaridis Karplus “lambda” value (correlation distance) for an atom

C++: core::scoring::etable::Etable::lk_lambda(const int) const –> double

lk_min_dis2sigma(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::lk_min_dis2sigma() const –> double

lk_volume(self: pyrosetta.rosetta.core.scoring.etable.Etable, i: int) float

Return the Lazaridis Karplus volume for an atom

C++: core::scoring::etable::Etable::lk_volume(const int) const –> double

long_range_damping_length(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::long_range_damping_length() const –> double

max_dis(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::max_dis() const –> double

max_dis2(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::max_dis2() const –> double

max_heavy_heavy_cutoff(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::max_heavy_heavy_cutoff() const –> double

max_heavy_hydrogen_cutoff(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::max_heavy_hydrogen_cutoff() const –> double

max_hydrogen_hydrogen_cutoff(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::max_hydrogen_hydrogen_cutoff() const –> double

max_hydrogen_lj_radius(self: pyrosetta.rosetta.core.scoring.etable.Etable) float
Returns the maximum lj radius for any hydrogen atom as

defined by the input atom-type-set used to create this Etable.

C++: core::scoring::etable::Etable::max_hydrogen_lj_radius() const –> double

max_non_hydrogen_lj_radius(self: pyrosetta.rosetta.core.scoring.etable.Etable) float
Returns the maximum lj radius for any non-hydrogen

atom as defined by the atom-type-set used to create this Etable.

C++: core::scoring::etable::Etable::max_non_hydrogen_lj_radius() const –> double

min_dis(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::min_dis() const –> double

min_dis2(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::min_dis2() const –> double

n_atomtypes(self: pyrosetta.rosetta.core.scoring.etable.Etable) int

C++: core::scoring::etable::Etable::n_atomtypes() const –> int

nblist_dis2_cutoff_HH(self: pyrosetta.rosetta.core.scoring.etable.Etable) float
The square distance cutoff beyond which any hydrogen/hydrogen pair is guaranteed

to have an interaction energy of zero. This function is used by the NeighborList

C++: core::scoring::etable::Etable::nblist_dis2_cutoff_HH() const –> double

nblist_dis2_cutoff_XH(self: pyrosetta.rosetta.core.scoring.etable.Etable) float
The square distance cutoff beyond which a hydrogen/heavy-atom pair is

guaranteed to have an interaction energy of zero. This function is used by the NeighborList

C++: core::scoring::etable::Etable::nblist_dis2_cutoff_XH() const –> double

nblist_dis2_cutoff_XX(self: pyrosetta.rosetta.core.scoring.etable.Etable) float
The square distance cutoff beyond which any pair of heavy-atoms is

guaranteed to have an interaction energy of zero. This function is used by the NeighborList

C++: core::scoring::etable::Etable::nblist_dis2_cutoff_XX() const –> double

output_etable(self: pyrosetta.rosetta.core.scoring.etable.Etable, etable: pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t, label: str, out: pyrosetta.rosetta.std.ostream) None

C++: core::scoring::etable::Etable::output_etable(class ObjexxFCL::FArray3D<double> &, std::string, std::ostream &) –> void

solv1(self: pyrosetta.rosetta.core.scoring.etable.Etable) pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

C++: core::scoring::etable::Etable::solv1() const –> const class ObjexxFCL::FArray3D<double> &

solv2(self: pyrosetta.rosetta.core.scoring.etable.Etable) pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

C++: core::scoring::etable::Etable::solv2() const –> const class ObjexxFCL::FArray3D<double> &

class pyrosetta.rosetta.core.scoring.etable.EtableClassicIntraEnergyCreator

Bases: pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator

assign(self: pyrosetta.rosetta.core.scoring.etable.EtableClassicIntraEnergyCreator, : pyrosetta.rosetta.core.scoring.etable.EtableClassicIntraEnergyCreator) pyrosetta.rosetta.core.scoring.etable.EtableClassicIntraEnergyCreator

C++: core::scoring::etable::EtableClassicIntraEnergyCreator::operator=(const class core::scoring::etable::EtableClassicIntraEnergyCreator &) –> class core::scoring::etable::EtableClassicIntraEnergyCreator &

create_energy_method(self: pyrosetta.rosetta.core.scoring.etable.EtableClassicIntraEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) pyrosetta.rosetta.core.scoring.methods.EnergyMethod

Instantiate a new EtableEnergy

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

class pyrosetta.rosetta.core.scoring.etable.EtableEnergyCreator

Bases: pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator

assign(self: pyrosetta.rosetta.core.scoring.etable.EtableEnergyCreator, : pyrosetta.rosetta.core.scoring.etable.EtableEnergyCreator) pyrosetta.rosetta.core.scoring.etable.EtableEnergyCreator

C++: core::scoring::etable::EtableEnergyCreator::operator=(const class core::scoring::etable::EtableEnergyCreator &) –> class core::scoring::etable::EtableEnergyCreator &

create_energy_method(self: pyrosetta.rosetta.core.scoring.etable.EtableEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) pyrosetta.rosetta.core.scoring.methods.EnergyMethod

Instantiate a new EtableEnergy

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

class pyrosetta.rosetta.core.scoring.etable.EtableEvaluator

Bases: pybind11_builtins.pybind11_object

///////////////// Evaluators ///////////////////////////////

assign(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, : pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) pyrosetta.rosetta.core.scoring.etable.EtableEvaluator

C++: core::scoring::etable::EtableEvaluator::operator=(const class core::scoring::etable::EtableEvaluator &) –> class core::scoring::etable::EtableEvaluator &

atom_pair_energy_v(*args, **kwargs)

Overloaded function.

  1. atom_pair_energy_v(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, atrE: float, repE: float, solE: float, d2: float) -> None

C++: core::scoring::etable::EtableEvaluator::atom_pair_energy_v(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, double &, double &, double &, double &) const –> void

  1. atom_pair_energy_v(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, emap: pyrosetta.rosetta.core.scoring.EMapVector, d2: float) -> None

C++: core::scoring::etable::EtableEvaluator::atom_pair_energy_v(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, class core::scoring::EMapVector &, double &) const –> void

atom_pair_lk_energy_and_deriv_v(*args, **kwargs)

Overloaded function.

  1. atom_pair_lk_energy_and_deriv_v(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, solE1: float, dsolE1: float) -> None

  2. atom_pair_lk_energy_and_deriv_v(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, solE1: float, dsolE1: float, eval_deriv: bool) -> None

C++: core::scoring::etable::EtableEvaluator::atom_pair_lk_energy_and_deriv_v(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, const bool) const –> void

atom_pair_lk_energy_and_deriv_v_efficient(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, solE1: float, solE2: float, dsolE1: float, eval_deriv: bool) None

C++: core::scoring::etable::EtableEvaluator::atom_pair_lk_energy_and_deriv_v_efficient(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, double &, const bool) const –> void

atr_weight(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) float

C++: core::scoring::etable::EtableEvaluator::atr_weight() const –> double

clone(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) pyrosetta.rosetta.core.scoring.etable.EtableEvaluator

C++: core::scoring::etable::EtableEvaluator::clone() const –> class std::shared_ptr<class core::scoring::etable::EtableEvaluator>

eval_dE_dR_over_r_v(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weights: pyrosetta.rosetta.core.scoring.EMapVector, f1: pyrosetta.rosetta.numeric.xyzVector_double_t, f2: pyrosetta.rosetta.numeric.xyzVector_double_t) float

C++: core::scoring::etable::EtableEvaluator::eval_dE_dR_over_r_v(const class core::conformation::Atom &, const class core::conformation::Atom &, const class core::scoring::EMapVector &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> double

hydrogen_interaction_cutoff2(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) float

C++: core::scoring::etable::EtableEvaluator::hydrogen_interaction_cutoff2() const –> double

pair_energy_H_v(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, emap: pyrosetta.rosetta.core.scoring.EMapVector) None
A Virtual function for the evaluation of an interaction energy of an atom with

a hydrogen atom. Not to be confused with the importantly non-virtual function defined in each of the subclasses that templated atom-pair-energy-inline functions invoke (avoiding any virtual-function overhead).

C++: core::scoring::etable::EtableEvaluator::pair_energy_H_v(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, class core::scoring::EMapVector &) const –> void

rep_weight(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) float

C++: core::scoring::etable::EtableEvaluator::rep_weight() const –> double

set_scoretypes(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, st_atr_in: pyrosetta.rosetta.core.scoring.ScoreType, st_rep_in: pyrosetta.rosetta.core.scoring.ScoreType, st_sol_in: pyrosetta.rosetta.core.scoring.ScoreType) None

C++: core::scoring::etable::EtableEvaluator::set_scoretypes(enum core::scoring::ScoreType, enum core::scoring::ScoreType, enum core::scoring::ScoreType) –> void

set_weights(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, weights: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::EtableEvaluator::set_weights(const class core::scoring::EMapVector &) –> void

sol_weight(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) float

C++: core::scoring::etable::EtableEvaluator::sol_weight() const –> double

st_atr(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) pyrosetta.rosetta.core.scoring.ScoreType

C++: core::scoring::etable::EtableEvaluator::st_atr() const –> enum core::scoring::ScoreType

st_rep(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) pyrosetta.rosetta.core.scoring.ScoreType

C++: core::scoring::etable::EtableEvaluator::st_rep() const –> enum core::scoring::ScoreType

st_sol(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) pyrosetta.rosetta.core.scoring.ScoreType

C++: core::scoring::etable::EtableEvaluator::st_sol() const –> enum core::scoring::ScoreType

sum_energies(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, atr: float, rep: float, solv: float) float

C++: core::scoring::etable::EtableEvaluator::sum_energies(double, double, double) const –> double

class pyrosetta.rosetta.core.scoring.etable.EtableOptions

Bases: pybind11_builtins.pybind11_object

property Wradius
property analytic_etable_evaluation
property analytic_membetable_evaluation
static append_schema_attributes(attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) None

C++: core::scoring::etable::EtableOptions::append_schema_attributes(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

assign(self: pyrosetta.rosetta.core.scoring.etable.EtableOptions, src: pyrosetta.rosetta.core.scoring.etable.EtableOptions) pyrosetta.rosetta.core.scoring.etable.EtableOptions

C++: core::scoring::etable::EtableOptions::operator=(const class core::scoring::etable::EtableOptions &) –> class core::scoring::etable::EtableOptions &

property bins_per_A2
property enlarge_h_lj_wdepth
property etable_type
property fa_hatr
initialize_from_options(*args, **kwargs)

Overloaded function.

  1. initialize_from_options(self: pyrosetta.rosetta.core.scoring.etable.EtableOptions) -> None

C++: core::scoring::etable::EtableOptions::initialize_from_options() –> void

  1. initialize_from_options(self: pyrosetta.rosetta.core.scoring.etable.EtableOptions, options: pyrosetta.rosetta.utility.options.OptionCollection) -> None

C++: core::scoring::etable::EtableOptions::initialize_from_options(const class utility::options::OptionCollection &) –> void

static list_options_read(option_list: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) None

C++: core::scoring::etable::EtableOptions::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) –> void

property lj_hbond_OH_donor_dis
property lj_hbond_hdis
property lj_switch_dis2sigma
property max_dis
property no_lk_polar_desolvation
parse_my_tag(self: pyrosetta.rosetta.core.scoring.etable.EtableOptions, tag: utility::tag::Tag) None

C++: core::scoring::etable::EtableOptions::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

property proline_N_is_lk_nonpolar
show(self: pyrosetta.rosetta.core.scoring.etable.EtableOptions, out: pyrosetta.rosetta.std.ostream) None

C++: core::scoring::etable::EtableOptions::show(std::ostream &) const –> void

class pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair

Bases: pybind11_builtins.pybind11_object

%EtableParamsOnePair describes all of the parameters for a particular pair of atom types necessary to evaluate the Lennard-Jones and LK solvation energies.

property fasol_cubic_poly1_close
property fasol_cubic_poly1_close_flat
property fasol_cubic_poly1_far
property fasol_cubic_poly2_close
property fasol_cubic_poly2_close_flat
property fasol_cubic_poly2_far
property fasol_cubic_poly_close
property fasol_cubic_poly_close_end
property fasol_cubic_poly_close_flat
property fasol_cubic_poly_close_start
property fasol_cubic_poly_far
property fasol_final_weight
property hydrogen_interaction
property lj_minimum
property lj_r12_coeff
property lj_r6_coeff
property lj_switch_intercept
property lj_switch_slope
property lj_val_at_minimum
property ljatr_cubic_poly_parameters
property ljatr_cubic_poly_xhi
property ljatr_cubic_poly_xlo
property ljatr_final_weight
property ljrep_extra_repulsion
property ljrep_from_negcrossing
property ljrep_linear_ramp_d2_cutoff
property lk_coeff1
property lk_coeff2
property lk_min_dis2sigma_value
property maxd2
class pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion

Bases: pybind11_builtins.pybind11_object

the ExtraQuadraticRepulsion class is used to add in extra repulsion for particular atom pairs, if needed, (e.g. for OCbb/OCbb) where the functional form is: fa_rep += (xhi - x)^2 * slope for values of x between xlo and xhi, and fa_rep += (x - xlo ) * extrapolated_slope + ylo where extrapolated slope can be anything, but, to defined a function with continuous derivatives, should be extrapolated_slope = (xhi-xlo)^2*slope. This is the analytical implementation of the “modify_pot” behavior.

property extrapolated_slope
property slope
property xhi
property xlo
property ylo
class pyrosetta.rosetta.core.scoring.etable.MembEtable

Bases: pyrosetta.rosetta.core.scoring.etable.Etable

Table of pre-computed LK membrane solvation energies

Wradius(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::Wradius() const –> double

add_long_range_damping(self: pyrosetta.rosetta.core.scoring.etable.Etable) bool

C++: core::scoring::etable::Etable::add_long_range_damping() const –> bool

analytic_etable_derivatives(self: pyrosetta.rosetta.core.scoring.etable.Etable, at1: pyrosetta.rosetta.core.conformation.Atom, at2: pyrosetta.rosetta.core.conformation.Atom, dljatrE_ddis: float, dljrepE_ddis: float, dfasolE_ddis: float, inv_d: float) None

Analytically evaluate the energy derivatives for a pair of atoms

C++: core::scoring::etable::Etable::analytic_etable_derivatives(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, double &, double &) const –> void

analytic_etable_evaluation(self: pyrosetta.rosetta.core.scoring.etable.Etable, at1: pyrosetta.rosetta.core.conformation.Atom, at2: pyrosetta.rosetta.core.conformation.Atom, lj_atrE: float, lj_repE: float, fa_solE: float, d2: float) None
Use an analytic functional form of the etable to evaluate an atom-pair energy

without reading from the enormous and uncachable tables.

C++: core::scoring::etable::Etable::analytic_etable_evaluation(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, double &, double &) const –> void

analytic_lk_derivatives(self: pyrosetta.rosetta.core.scoring.etable.Etable, at1: pyrosetta.rosetta.core.conformation.Atom, at2: pyrosetta.rosetta.core.conformation.Atom, dfasolE1_ddis: float, dfasolE2_ddis: float, inv_d: float) None
Analytically evaluate the LK solvation derivatives for a pair of atoms, separately

computing the derivative for atom2’s desolvation of atom1 (dfasolE1_ddis) and atom1’s desolvation of atom2 (dfasolE2_ddis).

C++: core::scoring::etable::Etable::analytic_lk_derivatives(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, double &) const –> void

analytic_lk_energy(self: pyrosetta.rosetta.core.scoring.etable.Etable, at1: pyrosetta.rosetta.core.conformation.Atom, at2: pyrosetta.rosetta.core.conformation.Atom, fa_solE1: float, fa_solE2: float) None
Use an analytic functional form of the etable to evaluate only the LK atom-pair energy

computing the desolvation of atom1 by atom2 separately from the desolvation of atom2 by atom1.

C++: core::scoring::etable::Etable::analytic_lk_energy(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &) const –> void

analytic_params_for_pair(self: pyrosetta.rosetta.core.scoring.etable.Etable, atype1: int, atype2: int) pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair

C++: core::scoring::etable::Etable::analytic_params_for_pair(unsigned long, unsigned long) const –> const struct core::scoring::etable::EtableParamsOnePair &

atom_set(self: pyrosetta.rosetta.core.scoring.etable.Etable) pyrosetta.rosetta.std.weak_ptr_const_core_chemical_AtomTypeSet_t

C++: core::scoring::etable::Etable::atom_set() const –> class std::weak_ptr<const class core::chemical::AtomTypeSet>

atom_type(self: pyrosetta.rosetta.core.scoring.etable.Etable, type: int) pyrosetta.rosetta.core.chemical.AtomType

C++: core::scoring::etable::Etable::atom_type(const int) –> const class core::chemical::AtomType &

dljatr(self: pyrosetta.rosetta.core.scoring.etable.Etable) pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

const access to the deriv arrays

C++: core::scoring::etable::Etable::dljatr() const –> const class ObjexxFCL::FArray3D<double> &

dljrep(self: pyrosetta.rosetta.core.scoring.etable.Etable) pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

C++: core::scoring::etable::Etable::dljrep() const –> const class ObjexxFCL::FArray3D<double> &

dsolv(self: pyrosetta.rosetta.core.scoring.etable.Etable) pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

return the solvation derivative table that combines atom1 and atom2’s desolvations

C++: core::scoring::etable::Etable::dsolv() const –> const class ObjexxFCL::FArray3D<double> &

dsolv1(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

Return the solvation derivative table for the desolvation of atom1 by atom2

C++: core::scoring::etable::MembEtable::dsolv1() const –> const class ObjexxFCL::FArray3D<double> &

dsolv2(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

Return the solvation derivative table that combines atom1 and atom2’s desolvations

C++: core::scoring::etable::MembEtable::dsolv2() const –> const class ObjexxFCL::FArray3D<double> &

epsilon(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::epsilon() const –> double

etable_disbins(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::etable_disbins() const –> double

fa_hatr(self: pyrosetta.rosetta.core.scoring.etable.Etable) bool

Do hydrogens provide attractive forces or do they only repell?

C++: core::scoring::etable::Etable::fa_hatr() const –> bool

fasol_cubic_poly_far_xhi(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::fasol_cubic_poly_far_xhi() const –> double

fasol_cubic_poly_far_xlo(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::fasol_cubic_poly_far_xlo() const –> double

get_bins_per_A2(self: pyrosetta.rosetta.core.scoring.etable.Etable) int

C++: core::scoring::etable::Etable::get_bins_per_A2() const –> int

get_lj_hbond_OH_donor_dis(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::get_lj_hbond_OH_donor_dis() const –> double

get_lj_hbond_dis(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::get_lj_hbond_dis() const –> double

get_lj_hbond_hdis(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::get_lj_hbond_hdis() const –> double

get_safe_max_dis2(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::get_safe_max_dis2() const –> double

hydrogen_interaction_cutoff2(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::hydrogen_interaction_cutoff2() const –> double

input_etable(self: pyrosetta.rosetta.core.scoring.etable.MembEtable, etable: pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t, label: str, in: pyrosetta.rosetta.std.istream) None

C++: core::scoring::etable::MembEtable::input_etable(class ObjexxFCL::FArray3D<double> &, const std::string &, std::istream &) –> void

interpolated_analytic_etable_evaluation(self: pyrosetta.rosetta.core.scoring.etable.Etable, at1: pyrosetta.rosetta.core.conformation.Atom, at2: pyrosetta.rosetta.core.conformation.Atom, lj_atrE: float, lj_repE: float, fa_solE: float, d2: float) None
Use the analytic_etable_evaluation function to evaluate the energy

of two atoms, but evaluate the function at the old grid points and then interpolate between them the way the existing etable does (in square distance space). Useful for comparing the original etable evaluation with the analytic evaluation.

C++: core::scoring::etable::Etable::interpolated_analytic_etable_evaluation(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, double &, double &) const –> void

lj_radius(*args, **kwargs)

Overloaded function.

  1. lj_radius(self: pyrosetta.rosetta.core.scoring.etable.MembEtable, i: int) -> float

set these up in the ctor

C++: core::scoring::etable::MembEtable::lj_radius(const int) const –> double

  1. lj_radius(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) -> pyrosetta.rosetta.utility.vector1_double

C++: core::scoring::etable::MembEtable::lj_radius() const –> const class utility::vector1<double, class std::allocator<double> > &

lj_sigma(self: pyrosetta.rosetta.core.scoring.etable.MembEtable, i: int, j: int) float

C++: core::scoring::etable::MembEtable::lj_sigma(const int, const int) const –> double

lj_slope_intercept(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::lj_slope_intercept() const –> double

lj_switch_dis2sigma(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::lj_switch_dis2sigma() const –> double

lj_use_hbond_radii(self: pyrosetta.rosetta.core.scoring.etable.Etable) bool

C++: core::scoring::etable::Etable::lj_use_hbond_radii() const –> bool

lj_use_lj_deriv_slope(self: pyrosetta.rosetta.core.scoring.etable.Etable) bool

C++: core::scoring::etable::Etable::lj_use_lj_deriv_slope() const –> bool

lj_use_water_radii(self: pyrosetta.rosetta.core.scoring.etable.Etable) bool

C++: core::scoring::etable::Etable::lj_use_water_radii() const –> bool

lj_water_dis(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::lj_water_dis() const –> double

lj_water_hdis(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::lj_water_hdis() const –> double

lj_wdepth(self: pyrosetta.rosetta.core.scoring.etable.Etable, i: int) float

Return the Lennard-Jones well depth for an atom

C++: core::scoring::etable::Etable::lj_wdepth(const int) const –> double

ljatr(self: pyrosetta.rosetta.core.scoring.etable.Etable) pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

const access to the arrays

C++: core::scoring::etable::Etable::ljatr() const –> const class ObjexxFCL::FArray3D<double> &

ljrep(self: pyrosetta.rosetta.core.scoring.etable.Etable) pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

C++: core::scoring::etable::Etable::ljrep() const –> const class ObjexxFCL::FArray3D<double> &

lk_dgfree(*args, **kwargs)

Overloaded function.

  1. lk_dgfree(self: pyrosetta.rosetta.core.scoring.etable.MembEtable, i: int) -> float

C++: core::scoring::etable::MembEtable::lk_dgfree(const int) const –> double

  1. lk_dgfree(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) -> pyrosetta.rosetta.utility.vector1_double

C++: core::scoring::etable::MembEtable::lk_dgfree() const –> const class utility::vector1<double, class std::allocator<double> > &

lk_dgrefce(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t

C++: core::scoring::etable::MembEtable::lk_dgrefce() const –> const class ObjexxFCL::FArray1D<double> &

lk_inv_lambda2(self: pyrosetta.rosetta.core.scoring.etable.Etable, i: int) float

C++: core::scoring::etable::Etable::lk_inv_lambda2(const int) const –> double

lk_lambda(*args, **kwargs)

Overloaded function.

  1. lk_lambda(self: pyrosetta.rosetta.core.scoring.etable.MembEtable, i: int) -> float

C++: core::scoring::etable::MembEtable::lk_lambda(const int) const –> double

  1. lk_lambda(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) -> pyrosetta.rosetta.utility.vector1_double

C++: core::scoring::etable::MembEtable::lk_lambda() const –> const class utility::vector1<double, class std::allocator<double> > &

lk_min_dis2sigma(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::lk_min_dis2sigma() const –> double

lk_volume(*args, **kwargs)

Overloaded function.

  1. lk_volume(self: pyrosetta.rosetta.core.scoring.etable.MembEtable, i: int) -> float

C++: core::scoring::etable::MembEtable::lk_volume(const int) const –> double

  1. lk_volume(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) -> pyrosetta.rosetta.utility.vector1_double

C++: core::scoring::etable::MembEtable::lk_volume() const –> const class utility::vector1<double, class std::allocator<double> > &

long_range_damping_length(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::long_range_damping_length() const –> double

max_dis(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::max_dis() const –> double

max_dis2(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::max_dis2() const –> double

max_heavy_heavy_cutoff(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::max_heavy_heavy_cutoff() const –> double

max_heavy_hydrogen_cutoff(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::max_heavy_hydrogen_cutoff() const –> double

max_hydrogen_hydrogen_cutoff(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::max_hydrogen_hydrogen_cutoff() const –> double

max_hydrogen_lj_radius(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) float
Returns the maximum lj radius for any hydrogen atom as

defined by the input atom-type-set used to create this Etable.

C++: core::scoring::etable::MembEtable::max_hydrogen_lj_radius() const –> double

max_non_hydrogen_lj_radius(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) float
Returns the maximum lj radius for any non-hydrogen

atom as defined by the atom-type-set used to create this Etable.

C++: core::scoring::etable::MembEtable::max_non_hydrogen_lj_radius() const –> double

memb_dsolv1(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

Return the solvation derivative table for the desolvation of atom1 by atom2

C++: core::scoring::etable::MembEtable::memb_dsolv1() const –> const class ObjexxFCL::FArray3D<double> &

memb_dsolv2(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

return the solvation derivative table that combines atom1 and atom2’s desolvations

C++: core::scoring::etable::MembEtable::memb_dsolv2() const –> const class ObjexxFCL::FArray3D<double> &

memb_lk_dgfree(*args, **kwargs)

Overloaded function.

  1. memb_lk_dgfree(self: pyrosetta.rosetta.core.scoring.etable.MembEtable, i: int) -> float

C++: core::scoring::etable::MembEtable::memb_lk_dgfree(const int) const –> double

  1. memb_lk_dgfree(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) -> pyrosetta.rosetta.utility.vector1_double

C++: core::scoring::etable::MembEtable::memb_lk_dgfree() const –> const class utility::vector1<double, class std::allocator<double> > &

memb_lk_dgrefce(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t

C++: core::scoring::etable::MembEtable::memb_lk_dgrefce() const –> const class ObjexxFCL::FArray1D<double> &

memb_solv1(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

C++: core::scoring::etable::MembEtable::memb_solv1() const –> const class ObjexxFCL::FArray3D<double> &

memb_solv2(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

C++: core::scoring::etable::MembEtable::memb_solv2() const –> const class ObjexxFCL::FArray3D<double> &

min_dis(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::min_dis() const –> double

min_dis2(self: pyrosetta.rosetta.core.scoring.etable.Etable) float

C++: core::scoring::etable::Etable::min_dis2() const –> double

n_atomtypes(self: pyrosetta.rosetta.core.scoring.etable.Etable) int

C++: core::scoring::etable::Etable::n_atomtypes() const –> int

nblist_dis2_cutoff_HH(self: pyrosetta.rosetta.core.scoring.etable.Etable) float
The square distance cutoff beyond which any hydrogen/hydrogen pair is guaranteed

to have an interaction energy of zero. This function is used by the NeighborList

C++: core::scoring::etable::Etable::nblist_dis2_cutoff_HH() const –> double

nblist_dis2_cutoff_XH(self: pyrosetta.rosetta.core.scoring.etable.Etable) float
The square distance cutoff beyond which a hydrogen/heavy-atom pair is

guaranteed to have an interaction energy of zero. This function is used by the NeighborList

C++: core::scoring::etable::Etable::nblist_dis2_cutoff_XH() const –> double

nblist_dis2_cutoff_XX(self: pyrosetta.rosetta.core.scoring.etable.Etable) float
The square distance cutoff beyond which any pair of heavy-atoms is

guaranteed to have an interaction energy of zero. This function is used by the NeighborList

C++: core::scoring::etable::Etable::nblist_dis2_cutoff_XX() const –> double

output_etable(self: pyrosetta.rosetta.core.scoring.etable.MembEtable, etable: pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t, label: str, out: pyrosetta.rosetta.std.ostream) None

C++: core::scoring::etable::MembEtable::output_etable(class ObjexxFCL::FArray3D<double> &, std::string, std::ostream &) –> void

solv1(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

Provide Constnat Access to Arrays

C++: core::scoring::etable::MembEtable::solv1() const –> const class ObjexxFCL::FArray3D<double> &

solv2(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

C++: core::scoring::etable::MembEtable::solv2() const –> const class ObjexxFCL::FArray3D<double> &

class pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy

Bases: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t

assign(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, : pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy) pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy

C++: core::scoring::methods::ContextIndependentTwoBodyEnergy::operator=(const class core::scoring::methods::ContextIndependentTwoBodyEnergy &) –> class core::scoring::methods::ContextIndependentTwoBodyEnergy &

atom_pair_energy(*args, **kwargs)

Overloaded function.

  1. atom_pair_energy(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, emap: pyrosetta.rosetta.core.scoring.EMapVector, dsq: float) -> None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::atom_pair_energy(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, class core::scoring::EMapVector &, double &) const –> void

  1. atom_pair_energy(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, atr: float, rep: float, solv: float, bb: float, dsq: float) -> None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::atom_pair_energy(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, double &, double &, double &, double &, double &) const –> void

  1. atom_pair_energy(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, ape: pyrosetta.rosetta.core.scoring.etable.AtomPairEnergy) -> None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::atom_pair_energy(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, struct core::scoring::etable::AtomPairEnergy &) const –> void

atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t) float

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, : int, : pyrosetta.rosetta.core.conformation.Residue, : int, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, : pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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

calculate_interres(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::calculate_interres(const class core::conformation::Residue &, const class core::conformation::Residue &) const –> bool

calculate_intrares(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd: pyrosetta.rosetta.core.conformation.Residue) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::calculate_intrares(const class core::conformation::Residue &) const –> bool

clone(self: pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy) pyrosetta.rosetta.core.scoring.methods.EnergyMethod

clone

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

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.etable.TableLookupEtableEnergy, : pyrosetta.rosetta.core.scoring.EMapVector) bool

C++: core::scoring::etable::TableLookupEtableEnergy::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.methods.TwoBodyEnergy, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, res_moving_wrt_eachother: bool) bool
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.

C++: core::scoring::methods::TwoBodyEnergy::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::divides_backbone_and_sidechain_energetics() const –> bool

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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_derivatives(self: pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) None
eval_intrares_energy(self: pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::TableLookupEtableEnergy::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.TableLookupEtableEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, : pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, min_data: pyrosetta.rosetta.core.scoring.ResPairMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector, r1_at_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair, r2_at_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) None
evaluate_rotamer_background_energies(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, residue: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, energy_vector: pyrosetta.rosetta.utility.vector1_float) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.methods.TwoBodyEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, energies: pyrosetta.rosetta.utility.vector1_float) None
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.

C++: core::scoring::methods::TwoBodyEnergy::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, set1: pyrosetta.rosetta.core.conformation.RotamerSetBase, set2: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, energy_table: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, totals: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.

  1. get_count_pair_function(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, res1: int, res2: int, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::get_count_pair_function(unsigned long, 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>

  1. get_count_pair_function(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::get_count_pair_function(const class core::conformation::Residue &, 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>

get_intrares_countpair(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, res: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::get_intrares_countpair(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> class std::shared_ptr<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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::has_atomistic_pairwise_energies() const –> bool

hydrogen_interaction_cutoff2(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t) float

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::hydrogen_interaction_cutoff2() const –> double

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, : pyrosetta.rosetta.utility.vector1_bool) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::indicate_required_context_graphs(class utility::vector1<bool, class std::allocator<bool> > &) const –> void

interres_evaluator(self: pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy) pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator

C++: core::scoring::etable::TableLookupEtableEnergy::interres_evaluator() –> class core::scoring::etable::TableLookupEvaluator &

intrares_evaluator(self: pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy) pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator

C++: core::scoring::etable::TableLookupEtableEnergy::intrares_evaluator() –> class core::scoring::etable::TableLookupEvaluator &

method_type(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t) pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

C++: core::scoring::methods::ContextIndependentTwoBodyEnergy::method_type() const –> enum core::scoring::methods::EnergyMethodType

min_pair_data_type(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t) pyrosetta.rosetta.core.scoring.min_pair_data

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::min_pair_data_type() const –> enum core::scoring::min_pair_data

min_single_data_type(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t) pyrosetta.rosetta.core.scoring.min_single_data

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::min_single_data_type() const –> enum core::scoring::min_single_data

minimize_in_whole_structure_context(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, : pyrosetta.rosetta.core.pose.Pose) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::minimize_in_whole_structure_context(const class core::pose::Pose &) const –> bool

nblist_type(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t) pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::nblist_type() const –> enum core::scoring::EnergiesCacheableDataType::Enum

nonprot_intrares_evaluator(self: pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy) pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator

C++: core::scoring::etable::TableLookupEtableEnergy::nonprot_intrares_evaluator() –> class core::scoring::etable::TableLookupEvaluator &

pair_energy_H(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::pair_energy_H(const class core::conformation::Atom &, const class core::conformation::Atom &, double, class core::scoring::EMapVector &) const –> void

prepare_for_residue_pair(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, res1: int, res2: int, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::prepare_for_residue_pair(const unsigned long, const unsigned long, const class core::pose::Pose &) const –> void

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, set: pyrosetta.rosetta.core.conformation.RotamerSetBase) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::requires_a_setup_for_scoring_for_residue_pair_opportunity(const class core::pose::Pose &) const –> bool

residue_pair_energy(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, min_data: pyrosetta.rosetta.core.scoring.ResPairMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::setup_for_derivatives(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, : pyrosetta.rosetta.basic.datacache.BasicDataCache) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, minsingle_data1: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, minsingle_data2: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, data_cache: pyrosetta.rosetta.core.scoring.ResPairMinimizationData) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, min_map: pyrosetta.rosetta.core.kinematics.MinimizerMapBase) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, minmap: pyrosetta.rosetta.core.kinematics.MinimizerMapBase, : pyrosetta.rosetta.basic.datacache.BasicDataCache, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, minmap: pyrosetta.rosetta.core.kinematics.MinimizerMapBase, res1_data_cache: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, res2_data_cache: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, min_data: pyrosetta.rosetta.core.scoring.ResPairMinimizationData) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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:
  1. setup_for_packing() is called for all energy methods

  2. rotamers are built

  3. setup_for_packing_with_rotsets() is called for all energy methods

  4. prepare_rotamers_for_packing() is called for all energy methods

  5. The energy methods are asked to score all rotamers and rotamer pairs

  6. 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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::setup_for_scoring(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring_(self: pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::scoring::etable::TableLookupEtableEnergy::setup_for_scoring_(const class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, minsingle_data1: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, minsingle_data2: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, data_cache: pyrosetta.rosetta.core.scoring.ResPairMinimizationData) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t, pose: pyrosetta.rosetta.core.pose.Pose, resid: int) None

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

use_extended_intrares_energy_interface(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::use_extended_intrares_energy_interface() const –> bool

use_extended_residue_pair_energy_interface(self: pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t) bool

C++: core::scoring::etable::BaseEtableEnergy<core::scoring::etable::TableLookupEtableEnergy>::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.etable.TableLookupEvaluator

Bases: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator

assign(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, : pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) pyrosetta.rosetta.core.scoring.etable.EtableEvaluator

C++: core::scoring::etable::EtableEvaluator::operator=(const class core::scoring::etable::EtableEvaluator &) –> class core::scoring::etable::EtableEvaluator &

atom_pair_energy(*args, **kwargs)

Overloaded function.

  1. atom_pair_energy(self: pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, emap: pyrosetta.rosetta.core.scoring.EMapVector, d2: float) -> None

A non-virtual function for the evaluation of an interaction energy of a

pair of atoms that is invoked directly by the atom-pair-energy-inline functions without any virtual-function overhead.

C++: core::scoring::etable::TableLookupEvaluator::atom_pair_energy(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, class core::scoring::EMapVector &, double &) const –> void

  1. atom_pair_energy(self: pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, atr: float, rep: float, solv: float, d2: float) -> None

C++: core::scoring::etable::TableLookupEvaluator::atom_pair_energy(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, double &, double &, double &, double &) const –> void

atom_pair_energy_v(*args, **kwargs)

Overloaded function.

  1. atom_pair_energy_v(self: pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, emap: pyrosetta.rosetta.core.scoring.EMapVector, d2: float) -> None

C++: core::scoring::etable::TableLookupEvaluator::atom_pair_energy_v(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, class core::scoring::EMapVector &, double &) const –> void

  1. atom_pair_energy_v(self: pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, atrE: float, repE: float, solE: float, d2: float) -> None

C++: core::scoring::etable::TableLookupEvaluator::atom_pair_energy_v(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, double &, double &, double &, double &) const –> void

atom_pair_lk_energy_and_deriv_v(*args, **kwargs)

Overloaded function.

  1. atom_pair_lk_energy_and_deriv_v(self: pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, solE1: float, dsolE1: float) -> None

  2. atom_pair_lk_energy_and_deriv_v(self: pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, solE1: float, dsolE1: float, eval_deriv: bool) -> None

C++: core::scoring::etable::TableLookupEvaluator::atom_pair_lk_energy_and_deriv_v(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, const bool) const –> void

atom_pair_lk_energy_and_deriv_v_efficient(self: pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, solE1: float, solE2: float, dsolE1: float, eval_deriv: bool) None

C++: core::scoring::etable::TableLookupEvaluator::atom_pair_lk_energy_and_deriv_v_efficient(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, double &, const bool) const –> void

atr_weight(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) float

C++: core::scoring::etable::EtableEvaluator::atr_weight() const –> double

clone(self: pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator) pyrosetta.rosetta.core.scoring.etable.EtableEvaluator

C++: core::scoring::etable::TableLookupEvaluator::clone() const –> class std::shared_ptr<class core::scoring::etable::EtableEvaluator>

eval_dE_dR_over_r(self: pyrosetta.rosetta.core.s