methods

• dfire

Bindings for core::scoring::methods namespace

class pyrosetta.rosetta.core.scoring.methods.BBDepCartBondedParameters

Bases: CartBondedParameters

K(self: pyrosetta.rosetta.core.scoring.methods.BBDepCartBondedParameters, phi: float, psi: float) → float

C++: core::scoring::methods::BBDepCartBondedParameters::K(double, double) const –> double

assign(self: pyrosetta.rosetta.core.scoring.methods.BBDepCartBondedParameters, : pyrosetta.rosetta.core.scoring.methods.BBDepCartBondedParameters) → pyrosetta.rosetta.core.scoring.methods.BBDepCartBondedParameters

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

dK_dphi(self: pyrosetta.rosetta.core.scoring.methods.BBDepCartBondedParameters, phi: float, psi: float) → float

C++: core::scoring::methods::BBDepCartBondedParameters::dK_dphi(double, double) const –> double

dK_dpsi(self: pyrosetta.rosetta.core.scoring.methods.BBDepCartBondedParameters, phi: float, psi: float) → float

C++: core::scoring::methods::BBDepCartBondedParameters::dK_dpsi(double, double) const –> double

dmu_dphi(self: pyrosetta.rosetta.core.scoring.methods.BBDepCartBondedParameters, phi: float, psi: float) → float

C++: core::scoring::methods::BBDepCartBondedParameters::dmu_dphi(double, double) const –> double

dmu_dpsi(self: pyrosetta.rosetta.core.scoring.methods.BBDepCartBondedParameters, phi: float, psi: float) → float

C++: core::scoring::methods::BBDepCartBondedParameters::dmu_dpsi(double, double) const –> double

init(*args, **kwargs)

Overloaded function.

1. init(self: pyrosetta.rosetta.core.scoring.methods.BBDepCartBondedParameters, mu: pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t, Ks: pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t) -> None

C++: core::scoring::methods::BBDepCartBondedParameters::init(const class ObjexxFCL::FArray2D<double> &, const class ObjexxFCL::FArray2D<double> &) –> void

2. init(self: pyrosetta.rosetta.core.scoring.methods.BBDepCartBondedParameters, x: pyrosetta.rosetta.numeric.MathMatrix_double_t, x_spline: pyrosetta.rosetta.numeric.interpolation.spline.BicubicSpline) -> None

C++: core::scoring::methods::BBDepCartBondedParameters::init(const class numeric::MathMatrix<double> &, class numeric::interpolation::spline::BicubicSpline &) –> void

is_null(self: pyrosetta.rosetta.core.scoring.methods.CartBondedParameters) → bool

C++: core::scoring::methods::CartBondedParameters::is_null() const –> bool

mu(self: pyrosetta.rosetta.core.scoring.methods.BBDepCartBondedParameters, phi: float, psi: float) → float

C++: core::scoring::methods::BBDepCartBondedParameters::mu(double, double) const –> double

period(self: pyrosetta.rosetta.core.scoring.methods.BBDepCartBondedParameters) → int

C++: core::scoring::methods::BBDepCartBondedParameters::period() const –> unsigned long

class pyrosetta.rosetta.core.scoring.methods.BBIndepCartBondedParameters

Bases: CartBondedParameters

K(self: pyrosetta.rosetta.core.scoring.methods.BBIndepCartBondedParameters, : float, : float) → float

C++: core::scoring::methods::BBIndepCartBondedParameters::K(double, double) const –> double

assign(self: pyrosetta.rosetta.core.scoring.methods.BBIndepCartBondedParameters, : pyrosetta.rosetta.core.scoring.methods.BBIndepCartBondedParameters) → pyrosetta.rosetta.core.scoring.methods.BBIndepCartBondedParameters

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

dK_dphi(self: pyrosetta.rosetta.core.scoring.methods.CartBondedParameters, : float, : float) → float

C++: core::scoring::methods::CartBondedParameters::dK_dphi(double, double) const –> double

dK_dpsi(self: pyrosetta.rosetta.core.scoring.methods.CartBondedParameters, : float, : float) → float

C++: core::scoring::methods::CartBondedParameters::dK_dpsi(double, double) const –> double

dmu_dphi(self: pyrosetta.rosetta.core.scoring.methods.CartBondedParameters, : float, : float) → float

C++: core::scoring::methods::CartBondedParameters::dmu_dphi(double, double) const –> double

dmu_dpsi(self: pyrosetta.rosetta.core.scoring.methods.CartBondedParameters, : float, : float) → float

C++: core::scoring::methods::CartBondedParameters::dmu_dpsi(double, double) const –> double

is_null(self: pyrosetta.rosetta.core.scoring.methods.BBIndepCartBondedParameters) → bool

C++: core::scoring::methods::BBIndepCartBondedParameters::is_null() const –> bool

mu(self: pyrosetta.rosetta.core.scoring.methods.BBIndepCartBondedParameters, : float, : float) → float

C++: core::scoring::methods::BBIndepCartBondedParameters::mu(double, double) const –> double

period(self: pyrosetta.rosetta.core.scoring.methods.BBIndepCartBondedParameters) → int

C++: core::scoring::methods::BBIndepCartBondedParameters::period() const –> unsigned long

class pyrosetta.rosetta.core.scoring.methods.CartBondedParameters

Bases: pybind11_object

K(self: pyrosetta.rosetta.core.scoring.methods.CartBondedParameters, phi: float, psi: float) → float

C++: core::scoring::methods::CartBondedParameters::K(double, double) const –> double

assign(self: pyrosetta.rosetta.core.scoring.methods.CartBondedParameters, : pyrosetta.rosetta.core.scoring.methods.CartBondedParameters) → pyrosetta.rosetta.core.scoring.methods.CartBondedParameters

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

dK_dphi(self: pyrosetta.rosetta.core.scoring.methods.CartBondedParameters, : float, : float) → float

C++: core::scoring::methods::CartBondedParameters::dK_dphi(double, double) const –> double

dK_dpsi(self: pyrosetta.rosetta.core.scoring.methods.CartBondedParameters, : float, : float) → float

C++: core::scoring::methods::CartBondedParameters::dK_dpsi(double, double) const –> double

dmu_dphi(self: pyrosetta.rosetta.core.scoring.methods.CartBondedParameters, : float, : float) → float

C++: core::scoring::methods::CartBondedParameters::dmu_dphi(double, double) const –> double

dmu_dpsi(self: pyrosetta.rosetta.core.scoring.methods.CartBondedParameters, : float, : float) → float

C++: core::scoring::methods::CartBondedParameters::dmu_dpsi(double, double) const –> double

is_null(self: pyrosetta.rosetta.core.scoring.methods.CartBondedParameters) → bool

C++: core::scoring::methods::CartBondedParameters::is_null() const –> bool

mu(self: pyrosetta.rosetta.core.scoring.methods.CartBondedParameters, phi: float, psi: float) → float

C++: core::scoring::methods::CartBondedParameters::mu(double, double) const –> double

period(self: pyrosetta.rosetta.core.scoring.methods.CartBondedParameters) → int

C++: core::scoring::methods::CartBondedParameters::period() const –> unsigned long

class pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy

Bases: LongRangeTwoBodyEnergy

assign(self: pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy, : pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy

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

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.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers 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_pairwise_energies()

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

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

backbone of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the weighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

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

bump_energy_backbone(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None

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

bump_energy_full(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None

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

clone(self: pyrosetta.rosetta.core.scoring.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_residue_pair_energy(self: pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy, pose: core::pose::Pose, res1: int, res2: int) → bool

C++: core::scoring::methods::LongRangeTwoBodyEnergy::defines_residue_pair_energy(const class core::pose::Pose &, unsigned long, unsigned long) 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

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Evaluate the XYZ derivative for an atom in the pose.

Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom’s XYZ derivative

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) “Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations” Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

Evaluate the derivative for the intra-residue component of this energy method

for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd.

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

Evaluate the intra-residue energy for a given residue using the data held within the

ResSingleMinimizationData object. This function should be invoked only on derived instances of this class if they return “true” in a call to their use_extended_intrares_energy_interface method. This base class provides a noop implementation for classes that do not implement this interface, or that do not define intrares energies.

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

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

Evaluate the DOF derivative for a particular residue. The Pose merely serves as context,

and the input residue is not required to be a member of the Pose.

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

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

Evaluate the derivatives for all atoms on rsd1 and rsd2 with respect

to each other and increment the derivatives in atom-derivatives vector1s. The calling function must guarantee that the r1_atom_derivs vector1 holds at least as many entries as there are atoms in rsd1, and that the r2_atom_derivs vector1 holds at least as many entries as there are atoms in rsd2.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, residue: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector, energy_vector: pyrosetta.rosetta.utility.vector1_float) → None

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 rotamr

C++: core::scoring::methods::TwoBodyEnergy::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.TwoBodyEnergy, 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 rotamr

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

Batch computation of rotamer pair energies. Need not be overriden in

derived class – by default, iterates over all pairs of rotamers, and calls the derived class’s residue_pair_energy method.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, total_energy: core::scoring::EMapVector) → None

called by the ScoreFunction at the end of energy evaluation.

The derived class has the opportunity to accumulate a score into the pose’s total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

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

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.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

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

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, context_graphs_required: pyrosetta.rosetta.utility.vector1_bool) → None

Indicate in the context-graphs-required list which

context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed

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

long_range_type(self: pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType

C++: core::scoring::methods::LongRangeTwoBodyEnergy::long_range_type() const –> enum core::scoring::methods::LongRangeEnergyType

method_type(self: pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

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

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

Should this EnergyMethod have score and derivative evaluation

evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that’s serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return “true” will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction’s traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return “true” cannot be included in RTMin.

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

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Evaluate the interaction between a given residue pair

accumulating the unweighted energies in an EnergyMap

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResPairMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the two-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those two body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residues in a call to setup_for_minimizing_for_residue_pair before this function is invoked. This function should not be called unless the use_extended_residue_pair_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit().

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction) → None

Called immediately before atom- and DOF-derivatives are calculated

allowing the derived class a chance to prepare for future calls.

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

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

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

C++: core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &, class basic::datacache::BasicDataCache &) const –> void

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

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

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

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) → None

Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache, res_data_cache: core::scoring::ResSingleMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, res1_data_cache: core::scoring::ResSingleMinimizationData, res2_data_cache: core::scoring::ResSingleMinimizationData, data_cache: core::scoring::ResPairMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

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

before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None

if an energy method needs to cache something in the pose (e.g. in pose.energies()),

before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

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

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue (who is still guaranteed to be

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

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

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

Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

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

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

show additional information of the energy method

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

sidechain_sidechain_energy(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the sidechain of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, : core::pose::Pose, resid: int) → None

If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

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

Derived classes wishing to invoke the alternate, extended interface for eval_intrares_energy

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

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

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

Rely on the extended version of the residue_pair_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResPairMinimizationData in which the derived base class has (or should have) cached a piece of data that will make residue-pair energy evaluation faster than its absense (e.g. a neighbor list). Derived energy methods should return ‘true’ from this function to use the extended interface. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::TwoBodyEnergy::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.methods.ContextDependentOneBodyEnergy

Bases: OneBodyEnergy

assign(self: pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy, : pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy

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

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.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers 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_pairwise_energies()

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

C++: core::scoring::methods::EnergyMethod::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

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_dof_derivatives(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, 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::OneBodyEnergy::defines_dof_derivatives(const class core::pose::Pose &) const –> bool

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_score_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue) → bool

During minimization, energy methods are allowed to decide that they say nothing

about a particular residue (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default behavior is to return “true” for all residues.

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

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Evaluate the XYZ derivative for an atom in the pose.

Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom’s XYZ derivative

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) “Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations” Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

C++: core::scoring::methods::EnergyMethod::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_residue_derivatives(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

Evaluate the derivatives for all atoms on this residue and increment them

into the input atom_derivs vector1. The calling function must guarantee that setup for derivatives is called before this function is, and that the atom_derivs vector contains at least as many entries as there are atoms in the input Residue. This base class provides a default noop implementation of this function.

C++: core::scoring::methods::OneBodyEnergy::eval_residue_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_residue_dof_derivative(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, 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::OneBodyEnergy::eval_residue_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

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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, total_energy: core::scoring::EMapVector) → None

called by the ScoreFunction at the end of energy evaluation.

The derived class has the opportunity to accumulate a score into the pose’s total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

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

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.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

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

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, context_graphs_required: pyrosetta.rosetta.utility.vector1_bool) → None

Indicate in the context-graphs-required list which

context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed

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

method_type(self: pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

Returns the cd_1b element of the EnergyMethodType enumeration; this method

should NOT be overridden by derived classes.

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

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

Should this EnergyMethod have score and derivative evaluation

evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that’s serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return “true” will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction’s traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return “true” cannot be included in RTMin.

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

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.OneBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

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

requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

C++: core::scoring::methods::OneBodyEnergy::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

residue_energy(self: pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, emap: core::scoring::EMapVector) → None

C++: core::scoring::methods::ContextDependentOneBodyEnergy::residue_energy(const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

residue_energy_ext(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, emap: core::scoring::EMapVector) → None

Evaluate the one-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those one body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to setup_for_minimizing_for_residue before this function is invoked. This function should not be called unless the use_extended_residue_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit(). The Pose merely serves as context, and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::OneBodyEnergy::residue_energy_ext(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, 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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction) → None

Called immediately before atom- and DOF-derivatives are calculated

allowing the derived class a chance to prepare for future calls.

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

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

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

C++: core::scoring::methods::OneBodyEnergy::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_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) → None

Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

C++: core::scoring::methods::EnergyMethod::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.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase, : pyrosetta.rosetta.basic.datacache.BasicDataCache, : core::scoring::ResSingleMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResSingleMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. The Pose merely serves as context, and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::OneBodyEnergy::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_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

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

before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None

if an energy method needs to cache something in the pose (e.g. in pose.energies()),

before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

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

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue, who is still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

C++: core::scoring::methods::OneBodyEnergy::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

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

update_residue_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, resid: int) → None

If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

use_extended_residue_energy_interface(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy) → bool

Rely on the extended version of the residue_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResSingleMinimizationData. Return ‘true’ for the extended version. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::OneBodyEnergy::use_extended_residue_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.methods.ContextDependentTwoBodyEnergy

Bases: ShortRangeTwoBodyEnergy

assign(self: pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy, : pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy

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

atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy) → float

how far apart must two heavy atoms be to have a zero interaction energy?

If hydrogen atoms interact at the same range as heavy atoms, then this distance should build-in a 2 * max-bound-h-distance-cutoff buffer. There is an improper mixing here between run-time aquired chemical knowledge (max-bound-h-distance-cutoff) and compile time aquired scoring knowledge (max atom cutoff); this could be resolved by adding a boolean uses_hydrogen_interaction_distance() to the SRTBEnergy class along with a method of the ChemicalManager max_bound_h_distance_cutoff().

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::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.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers 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_pairwise_energies()

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

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

backbone of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the weighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

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

bump_energy_backbone(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None

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

bump_energy_full(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None

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

clone(self: pyrosetta.rosetta.core.scoring.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.methods.ShortRangeTwoBodyEnergy) → bool

A derived class should return true for this function if it implements its own

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

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::divides_backbone_and_sidechain_energetics() const –> bool

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Evaluate the XYZ derivative for an atom in the pose.

Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom’s XYZ derivative

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) “Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations” Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

Evaluate the derivative for the intra-residue component of this energy method

for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd.

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

Evaluate the intra-residue energy for a given residue using the data held within the

ResSingleMinimizationData object. This function should be invoked only on derived instances of this class if they return “true” in a call to their use_extended_intrares_energy_interface method. This base class provides a noop implementation for classes that do not implement this interface, or that do not define intrares energies.

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

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

Evaluate the DOF derivative for a particular residue. The Pose merely serves as context,

and the input residue is not required to be a member of the Pose.

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

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

Evaluate the derivatives for all atoms on rsd1 and rsd2 with respect

to each other and increment the derivatives in atom-derivatives vector1s. The calling function must guarantee that the r1_atom_derivs vector1 holds at least as many entries as there are atoms in rsd1, and that the r2_atom_derivs vector1 holds at least as many entries as there are atoms in rsd2.

C++: core::scoring::methods::TwoBodyEnergy::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.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, energy_vector: pyrosetta.rosetta.utility.vector1_float) → 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_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.methods.ShortRangeTwoBodyEnergy, set1: pyrosetta.rosetta.core.conformation.RotamerSetBase, set2: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector, energy_table: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) → None

Batch computation of rotamer pair energies. Need not be overriden in

derived class – by default, iterates over all pairs of rotamers, and calls derived class’s residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, total_energy: core::scoring::EMapVector) → None

called by the ScoreFunction at the end of energy evaluation.

The derived class has the opportunity to accumulate a score into the pose’s total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

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

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.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

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

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, context_graphs_required: pyrosetta.rosetta.utility.vector1_bool) → None

Indicate in the context-graphs-required list which

context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed

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

method_type(self: pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

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

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

Should this EnergyMethod have score and derivative evaluation

evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that’s serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return “true” will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction’s traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return “true” cannot be included in RTMin.

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

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Evaluate the interaction between a given residue pair

accumulating the unweighted energies in an EnergyMap

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResPairMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the two-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those two body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residues in a call to setup_for_minimizing_for_residue_pair before this function is invoked. This function should not be called unless the use_extended_residue_pair_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit().

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction) → None

Called immediately before atom- and DOF-derivatives are calculated

allowing the derived class a chance to prepare for future calls.

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

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

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

C++: core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &, class basic::datacache::BasicDataCache &) const –> void

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

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

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

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) → None

Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache, res_data_cache: core::scoring::ResSingleMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, res1_data_cache: core::scoring::ResSingleMinimizationData, res2_data_cache: core::scoring::ResSingleMinimizationData, data_cache: core::scoring::ResPairMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

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

before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None

if an energy method needs to cache something in the pose (e.g. in pose.energies()),

before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

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

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue (who is still guaranteed to be

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

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

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

Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

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

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

show additional information of the energy method

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

sidechain_sidechain_energy(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the sidechain of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, : core::pose::Pose, resid: int) → None

If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

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

Derived classes wishing to invoke the alternate, extended interface for eval_intrares_energy

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

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

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

Rely on the extended version of the residue_pair_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResPairMinimizationData in which the derived base class has (or should have) cached a piece of data that will make residue-pair energy evaluation faster than its absense (e.g. a neighbor list). Derived energy methods should return ‘true’ from this function to use the extended interface. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::TwoBodyEnergy::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.methods.ContextIndependentLRTwoBodyEnergy

Bases: LongRangeTwoBodyEnergy

assign(self: pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy, : pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy

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

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.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers 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_pairwise_energies()

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

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

backbone of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the weighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

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

bump_energy_backbone(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None

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

bump_energy_full(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None

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

clone(self: pyrosetta.rosetta.core.scoring.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_residue_pair_energy(self: pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy, pose: core::pose::Pose, res1: int, res2: int) → bool

C++: core::scoring::methods::LongRangeTwoBodyEnergy::defines_residue_pair_energy(const class core::pose::Pose &, unsigned long, unsigned long) 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

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Evaluate the XYZ derivative for an atom in the pose.

Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom’s XYZ derivative

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) “Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations” Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

Evaluate the derivative for the intra-residue component of this energy method

for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd.

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

Evaluate the intra-residue energy for a given residue using the data held within the

ResSingleMinimizationData object. This function should be invoked only on derived instances of this class if they return “true” in a call to their use_extended_intrares_energy_interface method. This base class provides a noop implementation for classes that do not implement this interface, or that do not define intrares energies.

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

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

Evaluate the DOF derivative for a particular residue. The Pose merely serves as context,

and the input residue is not required to be a member of the Pose.

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

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

Evaluate the derivatives for all atoms on rsd1 and rsd2 with respect

to each other and increment the derivatives in atom-derivatives vector1s. The calling function must guarantee that the r1_atom_derivs vector1 holds at least as many entries as there are atoms in rsd1, and that the r2_atom_derivs vector1 holds at least as many entries as there are atoms in rsd2.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, residue: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector, energy_vector: pyrosetta.rosetta.utility.vector1_float) → None

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 rotamr

C++: core::scoring::methods::TwoBodyEnergy::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.TwoBodyEnergy, 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 rotamr

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

Batch computation of rotamer pair energies. Need not be overriden in

derived class – by default, iterates over all pairs of rotamers, and calls the derived class’s residue_pair_energy method.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, total_energy: core::scoring::EMapVector) → None

called by the ScoreFunction at the end of energy evaluation.

The derived class has the opportunity to accumulate a score into the pose’s total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

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

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.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

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

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, context_graphs_required: pyrosetta.rosetta.utility.vector1_bool) → None

Indicate in the context-graphs-required list which

context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed

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

long_range_type(self: pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType

C++: core::scoring::methods::LongRangeTwoBodyEnergy::long_range_type() const –> enum core::scoring::methods::LongRangeEnergyType

method_type(self: pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

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

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

Should this EnergyMethod have score and derivative evaluation

evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that’s serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return “true” will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction’s traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return “true” cannot be included in RTMin.

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

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Evaluate the interaction between a given residue pair

accumulating the unweighted energies in an EnergyMap

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResPairMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the two-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those two body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residues in a call to setup_for_minimizing_for_residue_pair before this function is invoked. This function should not be called unless the use_extended_residue_pair_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit().

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction) → None

Called immediately before atom- and DOF-derivatives are calculated

allowing the derived class a chance to prepare for future calls.

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

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

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

C++: core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &, class basic::datacache::BasicDataCache &) const –> void

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

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

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

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) → None

Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache, res_data_cache: core::scoring::ResSingleMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, res1_data_cache: core::scoring::ResSingleMinimizationData, res2_data_cache: core::scoring::ResSingleMinimizationData, data_cache: core::scoring::ResPairMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

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

before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None

if an energy method needs to cache something in the pose (e.g. in pose.energies()),

before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

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

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue (who is still guaranteed to be

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

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

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

Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

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

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

show additional information of the energy method

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

sidechain_sidechain_energy(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the sidechain of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, : core::pose::Pose, resid: int) → None

If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

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

Derived classes wishing to invoke the alternate, extended interface for eval_intrares_energy

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

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

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

Rely on the extended version of the residue_pair_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResPairMinimizationData in which the derived base class has (or should have) cached a piece of data that will make residue-pair energy evaluation faster than its absense (e.g. a neighbor list). Derived energy methods should return ‘true’ from this function to use the extended interface. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::TwoBodyEnergy::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.methods.ContextIndependentOneBodyEnergy

Bases: OneBodyEnergy

assign(self: pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy, : pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy

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

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.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers 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_pairwise_energies()

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

C++: core::scoring::methods::EnergyMethod::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

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_dof_derivatives(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, 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::OneBodyEnergy::defines_dof_derivatives(const class core::pose::Pose &) const –> bool

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_score_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue) → bool

During minimization, energy methods are allowed to decide that they say nothing

about a particular residue (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default behavior is to return “true” for all residues.

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

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Evaluate the XYZ derivative for an atom in the pose.

Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom’s XYZ derivative

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) “Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations” Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

C++: core::scoring::methods::EnergyMethod::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_residue_derivatives(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

Evaluate the derivatives for all atoms on this residue and increment them

into the input atom_derivs vector1. The calling function must guarantee that setup for derivatives is called before this function is, and that the atom_derivs vector contains at least as many entries as there are atoms in the input Residue. This base class provides a default noop implementation of this function.

C++: core::scoring::methods::OneBodyEnergy::eval_residue_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_residue_dof_derivative(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, 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::OneBodyEnergy::eval_residue_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

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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, total_energy: core::scoring::EMapVector) → None

called by the ScoreFunction at the end of energy evaluation.

The derived class has the opportunity to accumulate a score into the pose’s total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

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

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.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

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

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, context_graphs_required: pyrosetta.rosetta.utility.vector1_bool) → None

Indicate in the context-graphs-required list which

context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed

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

method_type(self: pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

Returns the ci_1b element of the EnergyMethodType enumeration; this

method should NOT be overridden by derived classes.

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

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

Should this EnergyMethod have score and derivative evaluation

evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that’s serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return “true” will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction’s traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return “true” cannot be included in RTMin.

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

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.OneBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

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

requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

C++: core::scoring::methods::OneBodyEnergy::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

residue_energy(self: pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, emap: core::scoring::EMapVector) → None

C++: core::scoring::methods::ContextIndependentOneBodyEnergy::residue_energy(const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

residue_energy_ext(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, emap: core::scoring::EMapVector) → None

Evaluate the one-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those one body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to setup_for_minimizing_for_residue before this function is invoked. This function should not be called unless the use_extended_residue_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit(). The Pose merely serves as context, and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::OneBodyEnergy::residue_energy_ext(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, 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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction) → None

Called immediately before atom- and DOF-derivatives are calculated

allowing the derived class a chance to prepare for future calls.

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

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

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

C++: core::scoring::methods::OneBodyEnergy::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_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) → None

Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

C++: core::scoring::methods::EnergyMethod::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.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase, : pyrosetta.rosetta.basic.datacache.BasicDataCache, : core::scoring::ResSingleMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResSingleMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. The Pose merely serves as context, and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::OneBodyEnergy::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_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

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

before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None

if an energy method needs to cache something in the pose (e.g. in pose.energies()),

before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

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

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue, who is still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

C++: core::scoring::methods::OneBodyEnergy::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

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

update_residue_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, resid: int) → None

If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

use_extended_residue_energy_interface(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy) → bool

Rely on the extended version of the residue_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResSingleMinimizationData. Return ‘true’ for the extended version. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::OneBodyEnergy::use_extended_residue_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.methods.ContextIndependentTwoBodyEnergy

Bases: ShortRangeTwoBodyEnergy

assign(self: pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy, : 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 &

atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy) → float

how far apart must two heavy atoms be to have a zero interaction energy?

If hydrogen atoms interact at the same range as heavy atoms, then this distance should build-in a 2 * max-bound-h-distance-cutoff buffer. There is an improper mixing here between run-time aquired chemical knowledge (max-bound-h-distance-cutoff) and compile time aquired scoring knowledge (max atom cutoff); this could be resolved by adding a boolean uses_hydrogen_interaction_distance() to the SRTBEnergy class along with a method of the ChemicalManager max_bound_h_distance_cutoff().

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::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.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers 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_pairwise_energies()

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

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

backbone of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the weighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

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

bump_energy_backbone(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None

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

bump_energy_full(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None

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

clone(self: pyrosetta.rosetta.core.scoring.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.methods.ShortRangeTwoBodyEnergy) → bool

A derived class should return true for this function if it implements its own

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

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::divides_backbone_and_sidechain_energetics() const –> bool

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Evaluate the XYZ derivative for an atom in the pose.

Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom’s XYZ derivative

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) “Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations” Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

Evaluate the derivative for the intra-residue component of this energy method

for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd.

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

Evaluate the intra-residue energy for a given residue using the data held within the

ResSingleMinimizationData object. This function should be invoked only on derived instances of this class if they return “true” in a call to their use_extended_intrares_energy_interface method. This base class provides a noop implementation for classes that do not implement this interface, or that do not define intrares energies.

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

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

Evaluate the DOF derivative for a particular residue. The Pose merely serves as context,

and the input residue is not required to be a member of the Pose.

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

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

Evaluate the derivatives for all atoms on rsd1 and rsd2 with respect

to each other and increment the derivatives in atom-derivatives vector1s. The calling function must guarantee that the r1_atom_derivs vector1 holds at least as many entries as there are atoms in rsd1, and that the r2_atom_derivs vector1 holds at least as many entries as there are atoms in rsd2.

C++: core::scoring::methods::TwoBodyEnergy::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.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, energy_vector: pyrosetta.rosetta.utility.vector1_float) → 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_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.methods.ShortRangeTwoBodyEnergy, set1: pyrosetta.rosetta.core.conformation.RotamerSetBase, set2: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector, energy_table: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) → None

Batch computation of rotamer pair energies. Need not be overriden in

derived class – by default, iterates over all pairs of rotamers, and calls derived class’s residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, total_energy: core::scoring::EMapVector) → None

called by the ScoreFunction at the end of energy evaluation.

The derived class has the opportunity to accumulate a score into the pose’s total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

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

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.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

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

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, context_graphs_required: pyrosetta.rosetta.utility.vector1_bool) → None

Indicate in the context-graphs-required list which

context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed

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

method_type(self: pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

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

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

Should this EnergyMethod have score and derivative evaluation

evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that’s serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return “true” will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction’s traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return “true” cannot be included in RTMin.

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

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Evaluate the interaction between a given residue pair

accumulating the unweighted energies in an EnergyMap

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResPairMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the two-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those two body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residues in a call to setup_for_minimizing_for_residue_pair before this function is invoked. This function should not be called unless the use_extended_residue_pair_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit().

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction) → None

Called immediately before atom- and DOF-derivatives are calculated

allowing the derived class a chance to prepare for future calls.

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

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

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

C++: core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &, class basic::datacache::BasicDataCache &) const –> void

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

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

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

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) → None

Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache, res_data_cache: core::scoring::ResSingleMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, res1_data_cache: core::scoring::ResSingleMinimizationData, res2_data_cache: core::scoring::ResSingleMinimizationData, data_cache: core::scoring::ResPairMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

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

before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None

if an energy method needs to cache something in the pose (e.g. in pose.energies()),

before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

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

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue (who is still guaranteed to be

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

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

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

Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

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

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

show additional information of the energy method

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

sidechain_sidechain_energy(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the sidechain of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, : core::pose::Pose, resid: int) → None

If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

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

Derived classes wishing to invoke the alternate, extended interface for eval_intrares_energy

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

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

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

Rely on the extended version of the residue_pair_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResPairMinimizationData in which the derived base class has (or should have) cached a piece of data that will make residue-pair energy evaluation faster than its absense (e.g. a neighbor list). Derived energy methods should return ‘true’ from this function to use the extended interface. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod

Bases: pybind11_object

base class for the energy method hierarchy

assign(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

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

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.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers 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_pairwise_energies()

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

C++: core::scoring::methods::EnergyMethod::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

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

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Evaluate the XYZ derivative for an atom in the pose.

Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom’s XYZ derivative

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) “Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations” Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

C++: core::scoring::methods::EnergyMethod::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

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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, total_energy: core::scoring::EMapVector) → None

called by the ScoreFunction at the end of energy evaluation.

The derived class has the opportunity to accumulate a score into the pose’s total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

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

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.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

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

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, context_graphs_required: pyrosetta.rosetta.utility.vector1_bool) → None

Indicate in the context-graphs-required list which

context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed

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

method_type(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

Return one of the 7 kinds of energy methods that exist:

e.g. context-dependent-one-body vs whole-structure.

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

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

Should this EnergyMethod have score and derivative evaluation

evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that’s serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return “true” will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction’s traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return “true” cannot be included in RTMin.

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

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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_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

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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction) → None

Called immediately before atom- and DOF-derivatives are calculated

allowing the derived class a chance to prepare for future calls.

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

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) → None

Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

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

setup_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

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

before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None

if an energy method needs to cache something in the pose (e.g. in pose.energies()),

before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

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

setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

Do any setup work before scoring, caching any slow-to-compute data that will be used during

energy evaluation inside of the input Residue object’s data cache. (The Residue on the whole is given as a constant reference, but non-constant access to its data cache is granted.)

C++: core::scoring::methods::EnergyMethod::setup_for_scoring_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class basic::datacache::BasicDataCache &) 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

update_residue_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, resid: int) → None

If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

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.methods.EnergyMethodCreator

Bases: pybind11_object

The EnergyMethodCreator class’s responsibilities are to create on demand a new EnergyMethod class, and to tell the ScoringManager singleton which ScoreTypes the EnergyMethod it creates is responsible for. The EnergyMethodCreator must register itself with the ScoringManager at load time (before main() begins) so that the ScoringManager is ready to start creating EnergyMethods by the time the first ScoreFunction requests one.

assign(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator

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

create_energy_method(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator, options: core::scoring::methods::EnergyMethodOptions) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

Instantiate a new EnergyMethod given a set of energy-method options

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

class pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions

Bases: pybind11_object

add more options here NOTE: If you add an option, make sure you also update the constructor, the assignment operator, the == comparison operator, and the show method in the .cc file! right now this class should be pretty light-weight since a copy is held inside ScoreFunctionInfo

aa_composition_setup_file(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, index: int) → str

Get the nth aa_composition setup file name from the list of setup files.

C++: core::scoring::methods::EnergyMethodOptions::aa_composition_setup_file(const unsigned long) const –> const std::string &

aa_composition_setup_file_count(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → int

Get the number of aa_composition setup files.

C++: core::scoring::methods::EnergyMethodOptions::aa_composition_setup_file_count() const –> unsigned long

analytic_etable_evaluation(*args, **kwargs)

Overloaded function.

1. analytic_etable_evaluation(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

C++: core::scoring::methods::EnergyMethodOptions::analytic_etable_evaluation() const –> bool

2. analytic_etable_evaluation(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

C++: core::scoring::methods::EnergyMethodOptions::analytic_etable_evaluation(bool) –> void

analytic_membetable_evaluation(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → bool

C++: core::scoring::methods::EnergyMethodOptions::analytic_membetable_evaluation() const –> bool

append_aa_composition_setup_files(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, input_filenames: pyrosetta.rosetta.utility.vector1_std_string) → None

Appends additional files to the aa_composition setup file names.

Does not override existing.

C++: core::scoring::methods::EnergyMethodOptions::append_aa_composition_setup_files(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

append_mhc_epitope_setup_files(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, input_filenames: pyrosetta.rosetta.utility.vector1_std_string) → None

Appends additional files to the mhc_epitope setup file names.

Does not override existing.

C++: core::scoring::methods::EnergyMethodOptions::append_mhc_epitope_setup_files(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

append_netcharge_setup_files(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, input_filenames: pyrosetta.rosetta.utility.vector1_std_string) → None

Appends additional files to the netcharge setup file names.

Does not override existing.

C++: core::scoring::methods::EnergyMethodOptions::append_netcharge_setup_files(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

approximate_buried_unsat_penalty_assume_const_backbone(*args, **kwargs)

Overloaded function.

1. approximate_buried_unsat_penalty_assume_const_backbone(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

Set the assume const backbone for approximate_buried_unsat_penalty.

Used by the ApproximateBuriedUnsatPenalty energy.

C++: core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_assume_const_backbone(const bool) –> void

2. approximate_buried_unsat_penalty_assume_const_backbone(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

Get the assume const backbone for approximate_buried_unsat_penalty.

Used by the ApproximateBuriedUnsatPenalty energy.

C++: core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_assume_const_backbone() const –> bool

approximate_buried_unsat_penalty_burial_atomic_depth(*args, **kwargs)

Overloaded function.

1. approximate_buried_unsat_penalty_burial_atomic_depth(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

Set the atomic depth above which an atom is considered buried.

Used by the ApproximateBuriedUnsatPenalty energy.

C++: core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_burial_atomic_depth(const double) –> void

2. approximate_buried_unsat_penalty_burial_atomic_depth(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

Get the atomic depth above which an atom is considered buried.

Used by the ApproximateBuriedUnsatPenalty energy.

C++: core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_burial_atomic_depth() const –> double

approximate_buried_unsat_penalty_burial_probe_radius(*args, **kwargs)

Overloaded function.

1. approximate_buried_unsat_penalty_burial_probe_radius(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

Set the probe radius for the atomic depth calculation.

Used by the ApproximateBuriedUnsatPenalty energy.

C++: core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_burial_probe_radius(const double) –> void

2. approximate_buried_unsat_penalty_burial_probe_radius(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

Get the probe radius for the atomic depth calculation.

Used by the ApproximateBuriedUnsatPenalty energy.

C++: core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_burial_probe_radius() const –> double

approximate_buried_unsat_penalty_burial_resolution(*args, **kwargs)

Overloaded function.

1. approximate_buried_unsat_penalty_burial_resolution(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

Set the resolution for the atomic depth calculation.

Used by the ApproximateBuriedUnsatPenalty energy.

C++: core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_burial_resolution(const double) –> void

2. approximate_buried_unsat_penalty_burial_resolution(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

Get the resolution for the atomic depth calculation.

Used by the ApproximateBuriedUnsatPenalty energy.

C++: core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_burial_resolution() const –> double

approximate_buried_unsat_penalty_hbond_bonus_cross_chain(*args, **kwargs)

Overloaded function.

1. approximate_buried_unsat_penalty_hbond_bonus_cross_chain(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

Set the hbond_bonus_cross_chain for approximate_buried_unsat_penalty.

Used by the ApproximateBuriedUnsatPenalty energy.

C++: core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_hbond_bonus_cross_chain(const double) –> void

2. approximate_buried_unsat_penalty_hbond_bonus_cross_chain(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

Get the hbond_bonus_cross_chain for approximate_buried_unsat_penalty.

Used by the ApproximateBuriedUnsatPenalty energy.

C++: core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_hbond_bonus_cross_chain() const –> double

approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb(*args, **kwargs)

Overloaded function.

1. approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

Set the hbond_bonus_ser_to_helix_bb for approximate_buried_unsat_penalty.

Used by the ApproximateBuriedUnsatPenalty energy.

C++: core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb(const double) –> void

2. approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

Get the hbond_bonus_ser_to_helix_bb for approximate_buried_unsat_penalty.

Used by the ApproximateBuriedUnsatPenalty energy.

C++: core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb() const –> double

approximate_buried_unsat_penalty_hbond_energy_threshold(*args, **kwargs)

Overloaded function.

1. approximate_buried_unsat_penalty_hbond_energy_threshold(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

Set the energy threshold above which a hydrogen bond is not counted.

Used by the ApproximateBuriedUnsatPenalty energy.

C++: core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_hbond_energy_threshold(const double) –> void

2. approximate_buried_unsat_penalty_hbond_energy_threshold(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

Get the energy threshold above which a hydrogen bond is not counted.

Used by the ApproximateBuriedUnsatPenalty energy.

C++: core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_hbond_energy_threshold() const –> double

approximate_buried_unsat_penalty_lys_ok_with_1(*args, **kwargs)

Overloaded function.

1. approximate_buried_unsat_penalty_lys_ok_with_1(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

Set the lys_ok_with_1 for approximate_buried_unsat_penalty.

Used by the ApproximateBuriedUnsatPenalty energy.

C++: core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_lys_ok_with_1(const bool) –> void

2. approximate_buried_unsat_penalty_lys_ok_with_1(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

Get the lys_ok_with_1 for approximate_buried_unsat_penalty.

Used by the ApproximateBuriedUnsatPenalty energy.

C++: core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_lys_ok_with_1() const –> bool

approximate_buried_unsat_penalty_natural_corrections1(*args, **kwargs)

Overloaded function.

1. approximate_buried_unsat_penalty_natural_corrections1(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

Set the natural corrections 1 for approximate_buried_unsat_penalty.

Used by the ApproximateBuriedUnsatPenalty energy.

C++: core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_natural_corrections1(const bool) –> void

2. approximate_buried_unsat_penalty_natural_corrections1(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

Get the natural corrections 1 for approximate_buried_unsat_penalty.

Used by the ApproximateBuriedUnsatPenalty energy.

C++: core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_natural_corrections1() const –> bool

approximate_buried_unsat_penalty_oversat_penalty(*args, **kwargs)

Overloaded function.

1. approximate_buried_unsat_penalty_oversat_penalty(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

Set the oversat penalty for approximate_buried_unsat_penalty.

Used by the ApproximateBuriedUnsatPenalty energy.

C++: core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_oversat_penalty(const double) –> void

2. approximate_buried_unsat_penalty_oversat_penalty(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

Get the oversat penalty for approximate_buried_unsat_penalty.

Used by the ApproximateBuriedUnsatPenalty energy.

C++: core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_oversat_penalty() const –> double

arg_cation_pi_his_can_be_pi(*args, **kwargs)

Overloaded function.

1. arg_cation_pi_his_can_be_pi(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

For the arg_cation_pi scoreterm. Can histidine be the pi-side of an Arginine cation-pi interaction?

C++: core::scoring::methods::EnergyMethodOptions::arg_cation_pi_his_can_be_pi() const –> bool

2. arg_cation_pi_his_can_be_pi(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

For the arg_cation_pi scoreterm. Can histidine be the pi-side of an Arginine cation-pi interaction?

C++: core::scoring::methods::EnergyMethodOptions::arg_cation_pi_his_can_be_pi(const bool) –> void

aspartimide_penalty_value(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → float

Get the penalty for each aspartimide-forming two-residue sequence.

Used by the aspartimide_penalty score term.

C++: core::scoring::methods::EnergyMethodOptions::aspartimide_penalty_value() const –> const double &

assign(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, src: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions

copy operator

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

atom_vdw_atom_type_set_name(*args, **kwargs)

Overloaded function.

1. atom_vdw_atom_type_set_name(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> str

This is used in the construction of the VDW_Energy’s AtomVDW object

C++: core::scoring::methods::EnergyMethodOptions::atom_vdw_atom_type_set_name() const –> const std::string &

2. atom_vdw_atom_type_set_name(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: str) -> None

C++: core::scoring::methods::EnergyMethodOptions::atom_vdw_atom_type_set_name(const std::string &) –> void

bond_angle_central_atoms_to_score(*args, **kwargs)

Overloaded function.

1. bond_angle_central_atoms_to_score(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> pyrosetta.rosetta.utility.vector1_std_string

deprecated

C++: core::scoring::methods::EnergyMethodOptions::bond_angle_central_atoms_to_score() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

2. bond_angle_central_atoms_to_score(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, atom_names: pyrosetta.rosetta.utility.vector1_std_string) -> None

depricated

C++: core::scoring::methods::EnergyMethodOptions::bond_angle_central_atoms_to_score(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

bond_angle_residue_type_param_set(*args, **kwargs)

Overloaded function.

1. bond_angle_residue_type_param_set(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> core::scoring::mm::MMBondAngleResidueTypeParamSet

C++: core::scoring::methods::EnergyMethodOptions::bond_angle_residue_type_param_set() –> class std::shared_ptr<class core::scoring::mm::MMBondAngleResidueTypeParamSet>

2. bond_angle_residue_type_param_set(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, param_set: core::scoring::mm::MMBondAngleResidueTypeParamSet) -> None

C++: core::scoring::methods::EnergyMethodOptions::bond_angle_residue_type_param_set(class std::shared_ptr<class core::scoring::mm::MMBondAngleResidueTypeParamSet>) –> void

buried_unsatisfied_penalty_burial_threshold(*args, **kwargs)

Overloaded function.

1. buried_unsatisfied_penalty_burial_threshold(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

Set the number of cones in which a point must lie to be considered “buried”

by the method of sidechain neighbor cones.

Used by the BuriedUnsatPenalty energy.

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::methods::EnergyMethodOptions::buried_unsatisfied_penalty_burial_threshold(const double) –> void

2. buried_unsatisfied_penalty_burial_threshold(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

Get the number of cones in which a point must lie to be considered “buried”

by the method of sidechain neighbor cones.

Used by the BuriedUnsatPenalty energy.

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::methods::EnergyMethodOptions::buried_unsatisfied_penalty_burial_threshold() const –> double

buried_unsatisfied_penalty_cone_angle_exponent(*args, **kwargs)

Overloaded function.

1. buried_unsatisfied_penalty_cone_angle_exponent(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

Set the angle exponent for calculating burial by the method of sidechain neighbor cones.

Used by the BuriedUnsatPenalty energy.

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::methods::EnergyMethodOptions::buried_unsatisfied_penalty_cone_angle_exponent(const double) –> void

2. buried_unsatisfied_penalty_cone_angle_exponent(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

Get the angle exponent for calculating burial by the method of sidechain neighbor cones.

Used by the BuriedUnsatPenalty energy.

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::methods::EnergyMethodOptions::buried_unsatisfied_penalty_cone_angle_exponent() const –> double

buried_unsatisfied_penalty_cone_angle_shift_factor(*args, **kwargs)

Overloaded function.

1. buried_unsatisfied_penalty_cone_angle_shift_factor(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

Set the angle shift factor for calculating burial by the method of sidechain neighbor cones.

Used by the BuriedUnsatPenalty energy.

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::methods::EnergyMethodOptions::buried_unsatisfied_penalty_cone_angle_shift_factor(const double) –> void

2. buried_unsatisfied_penalty_cone_angle_shift_factor(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

Get the angle shift factor for calculating burial by the method of sidechain neighbor cones.

Used by the BuriedUnsatPenalty energy.

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::methods::EnergyMethodOptions::buried_unsatisfied_penalty_cone_angle_shift_factor() const –> double

buried_unsatisfied_penalty_cone_dist_exponent(*args, **kwargs)

Overloaded function.

1. buried_unsatisfied_penalty_cone_dist_exponent(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

Set the distance exponent for calculating burial by the method of sidechain neighbor cones.

Used by the BuriedUnsatPenalty energy.

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::methods::EnergyMethodOptions::buried_unsatisfied_penalty_cone_dist_exponent(const double) –> void

2. buried_unsatisfied_penalty_cone_dist_exponent(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

Get the distance exponent for calculating burial by the method of sidechain neighbor cones.

Used by the BuriedUnsatPenalty energy.

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::methods::EnergyMethodOptions::buried_unsatisfied_penalty_cone_dist_exponent() const –> double

buried_unsatisfied_penalty_cone_dist_midpoint(*args, **kwargs)

Overloaded function.

1. buried_unsatisfied_penalty_cone_dist_midpoint(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

Set the distance midpoint for calculating burial by the method of sidechain neighbor cones.

Used by the BuriedUnsatPenalty energy.

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::methods::EnergyMethodOptions::buried_unsatisfied_penalty_cone_dist_midpoint(const double) –> void

2. buried_unsatisfied_penalty_cone_dist_midpoint(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

Get the distance midpoint for calculating burial by the method of sidechain neighbor cones.

Used by the BuriedUnsatPenalty energy.

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::methods::EnergyMethodOptions::buried_unsatisfied_penalty_cone_dist_midpoint() const –> double

buried_unsatisfied_penalty_hbond_energy_threshold(*args, **kwargs)

Overloaded function.

1. buried_unsatisfied_penalty_hbond_energy_threshold(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

Set the energy threshold above which a hydrogen bond is not counted.

Used by the BuriedUnsatPenalty energy.

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::methods::EnergyMethodOptions::buried_unsatisfied_penalty_hbond_energy_threshold(const double) –> void

2. buried_unsatisfied_penalty_hbond_energy_threshold(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

Get the energy threshold above which a hydrogen bond is not counted.

Used by the BuriedUnsatPenalty energy.

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::methods::EnergyMethodOptions::buried_unsatisfied_penalty_hbond_energy_threshold() const –> double

clone(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions

clone

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

count_pair_full(*args, **kwargs)

Overloaded function.

1. count_pair_full(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

Take full-1-5 countpairs for any residue type

C++: core::scoring::methods::EnergyMethodOptions::count_pair_full() const –> bool

2. count_pair_full(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

C++: core::scoring::methods::EnergyMethodOptions::count_pair_full(const bool) –> void

count_pair_hybrid(*args, **kwargs)

Overloaded function.

1. count_pair_hybrid(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

Take full-1-5 countpairs for LIGAND/non-(POLYMER_or_PROTEIN) type

C++: core::scoring::methods::EnergyMethodOptions::count_pair_hybrid() const –> bool

2. count_pair_hybrid(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

C++: core::scoring::methods::EnergyMethodOptions::count_pair_hybrid(const bool) –> void

covalent_labeling_fa_input(*args, **kwargs)

Overloaded function.

1. covalent_labeling_fa_input(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> str

C++: core::scoring::methods::EnergyMethodOptions::covalent_labeling_fa_input() const –> std::string

2. covalent_labeling_fa_input(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: str) -> None

C++: core::scoring::methods::EnergyMethodOptions::covalent_labeling_fa_input(const std::string &) –> void

covalent_labeling_input(*args, **kwargs)

Overloaded function.

1. covalent_labeling_input(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> str

C++: core::scoring::methods::EnergyMethodOptions::covalent_labeling_input() const –> std::string

2. covalent_labeling_input(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: str) -> None

C++: core::scoring::methods::EnergyMethodOptions::covalent_labeling_input(const std::string &) –> void

cst_max_seq_sep(*args, **kwargs)

Overloaded function.

1. cst_max_seq_sep(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> int

C++: core::scoring::methods::EnergyMethodOptions::cst_max_seq_sep() const –> unsigned long

2. cst_max_seq_sep(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: int) -> None

C++: core::scoring::methods::EnergyMethodOptions::cst_max_seq_sep(const unsigned long) –> void

depc_ms_input(*args, **kwargs)

Overloaded function.

1. depc_ms_input(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> str

C++: core::scoring::methods::EnergyMethodOptions::depc_ms_input() const –> std::string

2. depc_ms_input(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: str) -> None

C++: core::scoring::methods::EnergyMethodOptions::depc_ms_input(const std::string &) –> void

dump_trajectory_gz(*args, **kwargs)

Overloaded function.

1. dump_trajectory_gz(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

Set whether the dump_trajectory energy produces g-zipped output.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::dump_trajectory_gz(const bool) –> void

2. dump_trajectory_gz(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

Get whether the dump_trajectory energy produces g-zipped output.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::dump_trajectory_gz() const –> bool

dump_trajectory_prefix(*args, **kwargs)

Overloaded function.

1. dump_trajectory_prefix(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: str) -> None

Set the prefix for the dump_trajectory energy’s output.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::dump_trajectory_prefix(const std::string &) –> void

2. dump_trajectory_prefix(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> str

Get the prefix for the dump_trajectory energy’s output.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::dump_trajectory_prefix() const –> const std::string &

dump_trajectory_stride(*args, **kwargs)

Overloaded function.

1. dump_trajectory_stride(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: int) -> None

Set the number of function evaluations that elapse before the dump_trajectory mover produces output.

Vikram K. Mulligan (vmulligan.org).

The input must be greater than zero. There’s a check for this. (The function signature takes a signed long because the options system parses signed integers, so we need to check that the user hasn’t provided a negative number.)

C++: core::scoring::methods::EnergyMethodOptions::dump_trajectory_stride(long) –> void

2. dump_trajectory_stride(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> int

Get the number of function evaluations that elapse before the dump_trajectory mover produces output.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::dump_trajectory_stride() const –> unsigned long

elec_die(*args, **kwargs)

Overloaded function.

1. elec_die(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

The dielectric used for the fa_elec term

C++: core::scoring::methods::EnergyMethodOptions::elec_die() const –> double

2. elec_die(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

C++: core::scoring::methods::EnergyMethodOptions::elec_die(double) –> void

elec_group_file(*args, **kwargs)

Overloaded function.

1. elec_group_file(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> str

C++: core::scoring::methods::EnergyMethodOptions::elec_group_file() const –> std::string

2. elec_group_file(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: str) -> None

C++: core::scoring::methods::EnergyMethodOptions::elec_group_file(std::string) –> void

elec_max_dis(*args, **kwargs)

Overloaded function.

1. elec_max_dis(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

The maximum (all atom) distance at which fa_elec is non-zero

C++: core::scoring::methods::EnergyMethodOptions::elec_max_dis() const –> double

2. elec_max_dis(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

C++: core::scoring::methods::EnergyMethodOptions::elec_max_dis(double) –> void

elec_min_dis(*args, **kwargs)

Overloaded function.

1. elec_min_dis(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

The minimium (all atom) distance for which fa_elec changes with distances

C++: core::scoring::methods::EnergyMethodOptions::elec_min_dis() const –> double

2. elec_min_dis(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

C++: core::scoring::methods::EnergyMethodOptions::elec_min_dis(double) –> void

elec_no_dis_dep_die(*args, **kwargs)

Overloaded function.

1. elec_no_dis_dep_die(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

Should fa_elec use a constant (non-distance dependant) dielectric?

C++: core::scoring::methods::EnergyMethodOptions::elec_no_dis_dep_die() const –> bool

2. elec_no_dis_dep_die(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

C++: core::scoring::methods::EnergyMethodOptions::elec_no_dis_dep_die(bool) –> void

elec_sigmoidal_die(*args, **kwargs)

Overloaded function.

1. elec_sigmoidal_die(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

Should fa_elec/gpelec use a sigmoidal dielectric?

C++: core::scoring::methods::EnergyMethodOptions::elec_sigmoidal_die() const –> bool

2. elec_sigmoidal_die(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

C++: core::scoring::methods::EnergyMethodOptions::elec_sigmoidal_die(const bool) –> void

elec_sigmoidal_die_params(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, D: float, D0: float, S: float) → None

C++: core::scoring::methods::EnergyMethodOptions::elec_sigmoidal_die_params(double &, double &, double &) const –> void

envsmooth_zero_negatives(*args, **kwargs)

Overloaded function.

1. envsmooth_zero_negatives(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

C++: core::scoring::methods::EnergyMethodOptions::envsmooth_zero_negatives() const –> bool

2. envsmooth_zero_negatives(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

C++: core::scoring::methods::EnergyMethodOptions::envsmooth_zero_negatives(const bool) –> void

etable_options(*args, **kwargs)

Overloaded function.

1. etable_options(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> core::scoring::etable::EtableOptions

non-const access to the etable options object

C++: core::scoring::methods::EnergyMethodOptions::etable_options() –> class core::scoring::etable::EtableOptions &

2. etable_options(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, opts: core::scoring::etable::EtableOptions) -> None

Set the etable options object – makes a deep copy

C++: core::scoring::methods::EnergyMethodOptions::etable_options(const class core::scoring::etable::EtableOptions &) –> void

etable_type(*args, **kwargs)

Overloaded function.

1. etable_type(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> str

C++: core::scoring::methods::EnergyMethodOptions::etable_type() const –> const std::string &

2. etable_type(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, type: str) -> None

C++: core::scoring::methods::EnergyMethodOptions::etable_type(const std::string &) –> void

eval_intrares_elec_ST_only(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → bool

C++: core::scoring::methods::EnergyMethodOptions::eval_intrares_elec_ST_only() const –> bool

eval_intrsres_elec_ST_only(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) → None

C++: core::scoring::methods::EnergyMethodOptions::eval_intrsres_elec_ST_only(bool) –> void

exclude_DNA_DNA(*args, **kwargs)

Overloaded function.

1. exclude_DNA_DNA(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

C++: core::scoring::methods::EnergyMethodOptions::exclude_DNA_DNA() const –> bool

2. exclude_DNA_DNA(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

C++: core::scoring::methods::EnergyMethodOptions::exclude_DNA_DNA(const bool) –> void

exclude_RNA_RNA_fa_elec(*args, **kwargs)

Overloaded function.

1. exclude_RNA_RNA_fa_elec(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

C++: core::scoring::methods::EnergyMethodOptions::exclude_RNA_RNA_fa_elec() const –> bool

2. exclude_RNA_RNA_fa_elec(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

C++: core::scoring::methods::EnergyMethodOptions::exclude_RNA_RNA_fa_elec(const bool) –> void

exclude_RNA_protein_fa_elec(*args, **kwargs)

Overloaded function.

1. exclude_RNA_protein_fa_elec(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

C++: core::scoring::methods::EnergyMethodOptions::exclude_RNA_protein_fa_elec() const –> bool

2. exclude_RNA_protein_fa_elec(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

C++: core::scoring::methods::EnergyMethodOptions::exclude_RNA_protein_fa_elec(const bool) –> void

exclude_intra_res_protein(*args, **kwargs)

Overloaded function.

1. exclude_intra_res_protein(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

C++: core::scoring::methods::EnergyMethodOptions::exclude_intra_res_protein() const –> bool

2. exclude_intra_res_protein(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

C++: core::scoring::methods::EnergyMethodOptions::exclude_intra_res_protein(const bool) –> void

exclude_monomer_fa_elec(*args, **kwargs)

Overloaded function.

1. exclude_monomer_fa_elec(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

C++: core::scoring::methods::EnergyMethodOptions::exclude_monomer_fa_elec() const –> bool

2. exclude_monomer_fa_elec(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

C++: core::scoring::methods::EnergyMethodOptions::exclude_monomer_fa_elec(const bool) –> void

exclude_protein_protein_fa_elec(*args, **kwargs)

Overloaded function.

1. exclude_protein_protein_fa_elec(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

C++: core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_fa_elec() const –> bool

2. exclude_protein_protein_fa_elec(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

C++: core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_fa_elec(const bool) –> void

fa_stack_base_all(*args, **kwargs)

Overloaded function.

1. fa_stack_base_all(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

C++: core::scoring::methods::EnergyMethodOptions::fa_stack_base_all() const –> bool

2. fa_stack_base_all(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

C++: core::scoring::methods::EnergyMethodOptions::fa_stack_base_all(const bool) –> void

free_dof_options(*args, **kwargs)

Overloaded function.

1. free_dof_options(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> core::scoring::methods::FreeDOF_Options

non-const access to the FreeDOF options object

C++: core::scoring::methods::EnergyMethodOptions::free_dof_options() –> class core::scoring::methods::FreeDOF_Options &

2. free_dof_options(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, opts: core::scoring::methods::FreeDOF_Options) -> None

Set the FreeDOF options object – makes a deep copy

C++: core::scoring::methods::EnergyMethodOptions::free_dof_options(const class core::scoring::methods::FreeDOF_Options &) –> void

genbonded_score_full(*args, **kwargs)

Overloaded function.

1. genbonded_score_full(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

allow scoring all (i.e. canonical aas) with gen_bonded

C++: core::scoring::methods::EnergyMethodOptions::genbonded_score_full() const –> bool

2. genbonded_score_full(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

allow scoring all (i.e. canonical aas) with gen_bonded

C++: core::scoring::methods::EnergyMethodOptions::genbonded_score_full(bool) –> void

genbonded_score_hybrid(*args, **kwargs)

Overloaded function.

1. genbonded_score_hybrid(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

allow scoring torsions lack of any preference term with gen_bonded

C++: core::scoring::methods::EnergyMethodOptions::genbonded_score_hybrid() const –> bool

2. genbonded_score_hybrid(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

allow scoring torsions lack of any preference term with gen_bonded

C++: core::scoring::methods::EnergyMethodOptions::genbonded_score_hybrid(bool) –> void

geom_sol_interres_path_distance_cutoff(*args, **kwargs)

Overloaded function.

1. geom_sol_interres_path_distance_cutoff(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> int

C++: core::scoring::methods::EnergyMethodOptions::geom_sol_interres_path_distance_cutoff() const –> unsigned long

2. geom_sol_interres_path_distance_cutoff(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: int) -> None

C++: core::scoring::methods::EnergyMethodOptions::geom_sol_interres_path_distance_cutoff(const unsigned long) –> void

geom_sol_intrares_path_distance_cutoff(*args, **kwargs)

Overloaded function.

1. geom_sol_intrares_path_distance_cutoff(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> int

C++: core::scoring::methods::EnergyMethodOptions::geom_sol_intrares_path_distance_cutoff() const –> unsigned long

2. geom_sol_intrares_path_distance_cutoff(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: int) -> None

C++: core::scoring::methods::EnergyMethodOptions::geom_sol_intrares_path_distance_cutoff(const unsigned long) –> void

get_cartesian_bonded_linear(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → bool

get the harmonic bond angle and bond-length spring constants

C++: core::scoring::methods::EnergyMethodOptions::get_cartesian_bonded_linear() const –> bool

get_cartesian_bonded_parameters(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, len: float, ang: float, tors: float, proton: float, imp: float) → None

get the harmonic bond angle and bond-length spring constants

C++: core::scoring::methods::EnergyMethodOptions::get_cartesian_bonded_parameters(double &, double &, double &, double &, double &) const –> void

get_cartesian_bonded_skip_cutpoints(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → bool

get the harmonic bond angle and bond-length spring constants

C++: core::scoring::methods::EnergyMethodOptions::get_cartesian_bonded_skip_cutpoints() const –> bool

get_density_sc_scale_byres(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → pyrosetta.rosetta.utility.vector1_double

C++: core::scoring::methods::EnergyMethodOptions::get_density_sc_scale_byres() const –> const class utility::vector1<double, class std::allocator<double> > &

grp_cpfxn(*args, **kwargs)

Overloaded function.

1. grp_cpfxn(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

C++: core::scoring::methods::EnergyMethodOptions::grp_cpfxn() const –> bool

2. grp_cpfxn(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

C++: core::scoring::methods::EnergyMethodOptions::grp_cpfxn(bool) –> void

grpelec_context_dependent(*args, **kwargs)

Overloaded function.

1. grpelec_context_dependent(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

C++: core::scoring::methods::EnergyMethodOptions::grpelec_context_dependent() const –> bool

2. grpelec_context_dependent(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

C++: core::scoring::methods::EnergyMethodOptions::grpelec_context_dependent(bool) –> void

grpelec_fade_hbond(*args, **kwargs)

Overloaded function.

1. grpelec_fade_hbond(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

C++: core::scoring::methods::EnergyMethodOptions::grpelec_fade_hbond() const –> bool

2. grpelec_fade_hbond(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

C++: core::scoring::methods::EnergyMethodOptions::grpelec_fade_hbond(bool) –> void

grpelec_fade_param1(*args, **kwargs)

Overloaded function.

1. grpelec_fade_param1(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

C++: core::scoring::methods::EnergyMethodOptions::grpelec_fade_param1() const –> double

2. grpelec_fade_param1(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

C++: core::scoring::methods::EnergyMethodOptions::grpelec_fade_param1(double) –> void

grpelec_fade_param2(*args, **kwargs)

Overloaded function.

1. grpelec_fade_param2(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

C++: core::scoring::methods::EnergyMethodOptions::grpelec_fade_param2() const –> double

2. grpelec_fade_param2(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

C++: core::scoring::methods::EnergyMethodOptions::grpelec_fade_param2(double) –> void

grpelec_fade_type(*args, **kwargs)

Overloaded function.

1. grpelec_fade_type(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> str

C++: core::scoring::methods::EnergyMethodOptions::grpelec_fade_type() const –> std::string

2. grpelec_fade_type(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: str) -> None

C++: core::scoring::methods::EnergyMethodOptions::grpelec_fade_type(std::string) –> void

has_method_weights(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, type: pyrosetta.rosetta.core.scoring.ScoreType) → bool

C++: core::scoring::methods::EnergyMethodOptions::has_method_weights(const enum core::scoring::ScoreType &) const –> bool

hb_cen_soft(*args, **kwargs)

Overloaded function.

1. hb_cen_soft(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

Set whether the CenHBEnergy will use a softened version of its potential. Default false.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::hb_cen_soft(const bool) –> void

2. hb_cen_soft(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

Get whether the CenHBEnergy should use a softened version of its potential. Default false.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::hb_cen_soft() const –> bool

hbnet_bonus_function_ramping(*args, **kwargs)

Overloaded function.

1. hbnet_bonus_function_ramping(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> str

Get the bonus function shape for the hbnet energy term.

Vikram K. Mulligan (vmullig.edu)

C++: core::scoring::methods::EnergyMethodOptions::hbnet_bonus_function_ramping() const –> const std::string &

2. hbnet_bonus_function_ramping(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: str) -> None

Set the bonus function shape for the hbnet energy term.

Vikram K. Mulligan (vmullig.edu)

C++: core::scoring::methods::EnergyMethodOptions::hbnet_bonus_function_ramping(const std::string &) –> void

hbnet_max_network_size(*args, **kwargs)

Overloaded function.

1. hbnet_max_network_size(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> int

Get the maximum hydrogen bond network size, beyond which the hbnet score term yields no futher bonus.

Vikram K. Mulligan (vmullig.edu)

C++: core::scoring::methods::EnergyMethodOptions::hbnet_max_network_size() const –> unsigned long

2. hbnet_max_network_size(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: int) -> None

Set the maximum hydrogen bond network size, beyond which the hbnet score term yields no futher bonus.

Vikram K. Mulligan (vmullig.edu)

C++: core::scoring::methods::EnergyMethodOptions::hbnet_max_network_size(const unsigned long) –> void

hbond_options(*args, **kwargs)

Overloaded function.

1. hbond_options(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> core::scoring::hbonds::HBondOptions

non-const access to the hbond options object

C++: core::scoring::methods::EnergyMethodOptions::hbond_options() –> class core::scoring::hbonds::HBondOptions &

2. hbond_options(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, opts: core::scoring::hbonds::HBondOptions) -> None

Set the hbond options object – makes a deep copy

C++: core::scoring::methods::EnergyMethodOptions::hbond_options(const class core::scoring::hbonds::HBondOptions &) –> void

hrf_dynamics_input(*args, **kwargs)

Overloaded function.

1. hrf_dynamics_input(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> str

C++: core::scoring::methods::EnergyMethodOptions::hrf_dynamics_input() const –> std::string

2. hrf_dynamics_input(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: str) -> None

C++: core::scoring::methods::EnergyMethodOptions::hrf_dynamics_input(const std::string &) –> void

initialize_from_options(*args, **kwargs)

Overloaded function.

1. initialize_from_options(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> None

Initialize a new EnergyMethodOptions with defaults from the global option collection

C++: core::scoring::methods::EnergyMethodOptions::initialize_from_options() –> void

2. initialize_from_options(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, options: pyrosetta.rosetta.utility.options.OptionCollection) -> None

Initialize a new EnergyMethodOptions with defaults from a (possibly local) option collection

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

insert_score_function_method_options_rows(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, batch_id: int, score_function_name: str, db_session: pyrosetta.rosetta.utility.sql_database.session) → None

C++: core::scoring::methods::EnergyMethodOptions::insert_score_function_method_options_rows(unsigned long, const std::string &, class std::shared_ptr<class utility::sql_database::session>) const –> void

static list_options_read(read_options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None

Append the option keys read by the initialize_from_options method to the input option-key list

C++: core::scoring::methods::EnergyMethodOptions::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

loop_close_use_6D_potential(*args, **kwargs)

Overloaded function.

1. loop_close_use_6D_potential(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

C++: core::scoring::methods::EnergyMethodOptions::loop_close_use_6D_potential() const –> bool

2. loop_close_use_6D_potential(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

C++: core::scoring::methods::EnergyMethodOptions::loop_close_use_6D_potential(const bool) –> void

method_weights(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, type: pyrosetta.rosetta.core.scoring.ScoreType) → pyrosetta.rosetta.utility.vector1_double

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

mhc_epitope_setup_file(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, index: int) → str

Get the nth mhc_epitope setup file name from the list of setup files.

C++: core::scoring::methods::EnergyMethodOptions::mhc_epitope_setup_file(const unsigned long) const –> const std::string &

mhc_epitope_setup_file_count(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → int

Get the number of mhc_epitope setup files.

C++: core::scoring::methods::EnergyMethodOptions::mhc_epitope_setup_file_count() const –> unsigned long

netcharge_setup_file(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, index: int) → str

Get the nth netcharge setup file name from the list of setup files.

C++: core::scoring::methods::EnergyMethodOptions::netcharge_setup_file(const unsigned long) const –> const std::string &

netcharge_setup_file_count(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → int

Get the number of netcharge setup files.

C++: core::scoring::methods::EnergyMethodOptions::netcharge_setup_file_count() const –> unsigned long

nmer_ref_seq_length(*args, **kwargs)

Overloaded function.

1. nmer_ref_seq_length(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> int

Get reference sequence length.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_ref_seq_length() const –> unsigned long

2. nmer_ref_seq_length(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: int) -> None

Set reference sequence length.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_ref_seq_length(const unsigned long) –> void

nmer_svm(*args, **kwargs)

Overloaded function.

1. nmer_svm(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> str

Get SVM file provided by the user.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm() const –> const std::string &

2. nmer_svm(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, filename: str) -> None

Set SVM file.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm(const std::string &) –> void

nmer_svm_aa_matrix(*args, **kwargs)

Overloaded function.

1. nmer_svm_aa_matrix(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> str

Get the user-specified AA matrix filename.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm_aa_matrix() const –> const std::string &

2. nmer_svm_aa_matrix(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, filename: str) -> None

Set the user-specified AA matrix filename.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm_aa_matrix(const std::string &) –> void

nmer_svm_aa_matrix_defined(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → bool

Get whether we have a user-specified AA matrix.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm_aa_matrix_defined() const –> bool

nmer_svm_avg_rank_as_energy(*args, **kwargs)

Overloaded function.

1. nmer_svm_avg_rank_as_energy(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

Get whether the SVM average rank should be treated as an energy.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm_avg_rank_as_energy() const –> bool

2. nmer_svm_avg_rank_as_energy(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

Set whether the SVM average rank should be treated as an energy.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm_avg_rank_as_energy(const bool) –> void

nmer_svm_defined(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → bool

Get whether SVM is provided by the user.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm_defined() const –> bool

nmer_svm_list(*args, **kwargs)

Overloaded function.

1. nmer_svm_list(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> str

Get SVM filename list file.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm_list() const –> const std::string &

2. nmer_svm_list(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, filename: str) -> None

Set SVM filename list file.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm_list(const std::string &) –> void

nmer_svm_list_defined(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → bool

Get whether SVM list is provided by user.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm_list_defined() const –> bool

nmer_svm_pssm_feat(*args, **kwargs)

Overloaded function.

1. nmer_svm_pssm_feat(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

Get nmer_svm_pssm_feat_.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm_pssm_feat() const –> bool

2. nmer_svm_pssm_feat(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

Set nmer_svm_pssm_feat_.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm_pssm_feat(const bool) –> void

nmer_svm_rank(*args, **kwargs)

Overloaded function.

1. nmer_svm_rank(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> str

Get SVM rank file that was provided by the user.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm_rank() const –> const std::string &

2. nmer_svm_rank(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, filename: str) -> None

Set SVM rank file.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm_rank(const std::string &) –> void

nmer_svm_rank_defined(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → bool

Get whether an SVM rank file is provided by the user.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm_rank_defined() const –> bool

nmer_svm_rank_list(*args, **kwargs)

Overloaded function.

1. nmer_svm_rank_list(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> str

Get SVM rank list provided by the user.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm_rank_list() const –> const std::string &

2. nmer_svm_rank_list(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, filename: str) -> None

Set SVM rank list.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm_rank_list(const std::string &) –> void

nmer_svm_rank_list_defined(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → bool

Get whether SVM rank list is provided by the user.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm_rank_list_defined() const –> bool

nmer_svm_scorecut(*args, **kwargs)

Overloaded function.

1. nmer_svm_scorecut(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

Get the SVM scorecut.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm_scorecut() const –> const double &

2. nmer_svm_scorecut(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

Set the SVM scorecut.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm_scorecut(const double &) –> void

nmer_svm_scorecut_defined(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → bool

Get whether the SVM scorecut is defined.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm_scorecut_defined() const –> bool

nmer_svm_term_length(*args, **kwargs)

Overloaded function.

1. nmer_svm_term_length(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> int

Get SVM term length.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm_term_length() const –> unsigned long

2. nmer_svm_term_length(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: int) -> None

Set SVM term length.

Used by NMerSVMEnergy.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::methods::EnergyMethodOptions::nmer_svm_term_length(const unsigned long) –> void

ordered_pt_wat_penalty(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → float

C++: core::scoring::methods::EnergyMethodOptions::ordered_pt_wat_penalty() const –> double

ordered_wat_penalty(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → float

C++: core::scoring::methods::EnergyMethodOptions::ordered_wat_penalty() const –> double

pb_bound_tag(*args, **kwargs)

Overloaded function.

1. pb_bound_tag(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> str

C++: core::scoring::methods::EnergyMethodOptions::pb_bound_tag() –> std::string &

2. pb_bound_tag(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, tag: str) -> None

C++: core::scoring::methods::EnergyMethodOptions::pb_bound_tag(const std::string &) –> void

pb_unbound_tag(*args, **kwargs)

Overloaded function.

1. pb_unbound_tag(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> str

C++: core::scoring::methods::EnergyMethodOptions::pb_unbound_tag() –> std::string &

2. pb_unbound_tag(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, tag: str) -> None

C++: core::scoring::methods::EnergyMethodOptions::pb_unbound_tag(const std::string &) –> void

protein_dielectric(*args, **kwargs)

Overloaded function.

1. protein_dielectric(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

C++: core::scoring::methods::EnergyMethodOptions::protein_dielectric() const –> double

2. protein_dielectric(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

C++: core::scoring::methods::EnergyMethodOptions::protein_dielectric(double) –> void

put_intra_into_total(*args, **kwargs)

Overloaded function.

1. put_intra_into_total(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

C++: core::scoring::methods::EnergyMethodOptions::put_intra_into_total() const –> bool

2. put_intra_into_total(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

C++: core::scoring::methods::EnergyMethodOptions::put_intra_into_total(const bool) –> void

rna_options(*args, **kwargs)

Overloaded function.

1. rna_options(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> core::scoring::rna::RNA_EnergyMethodOptions

non-const access to the RNA options object

C++: core::scoring::methods::EnergyMethodOptions::rna_options() –> class core::scoring::rna::RNA_EnergyMethodOptions &

2. rna_options(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, opts: core::scoring::rna::RNA_EnergyMethodOptions) -> None

Set the FreeDOF options object – makes a deep copy

C++: core::scoring::methods::EnergyMethodOptions::rna_options(const class core::scoring::rna::RNA_EnergyMethodOptions &) –> void

secondary_structure_weights(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → pyrosetta.rosetta.core.scoring.SecondaryStructureWeights

C++: core::scoring::methods::EnergyMethodOptions::secondary_structure_weights() –> class core::scoring::SecondaryStructureWeights &

set_aa_composition_setup_files(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, input_filenames: pyrosetta.rosetta.utility.vector1_std_string) → None

Set the aa_composition setup file names.

Overrides existing.

C++: core::scoring::methods::EnergyMethodOptions::set_aa_composition_setup_files(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_cartesian_bonded_linear(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, lin_in: bool) → None

set the harmonic bond angle and bond-length spring constants

C++: core::scoring::methods::EnergyMethodOptions::set_cartesian_bonded_linear(bool) –> void

set_cartesian_bonded_parameters(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, len: float, ang: float, tors: float, proton: float, imp: float) → None

set the harmonic bond angle and bond-length spring constants

C++: core::scoring::methods::EnergyMethodOptions::set_cartesian_bonded_parameters(double, double, double, double, double) –> void

set_cartesian_bonded_skip_cutpoints(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) → None

set the harmonic bond angle and bond-length spring constants

C++: core::scoring::methods::EnergyMethodOptions::set_cartesian_bonded_skip_cutpoints(bool) –> void

set_density_sc_scale_byres(*args, **kwargs)

Overloaded function.

1. set_density_sc_scale_byres(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, newscscale: float) -> None

C++: core::scoring::methods::EnergyMethodOptions::set_density_sc_scale_byres(double) –> void

2. set_density_sc_scale_byres(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, aa: pyrosetta.rosetta.core.chemical.AA, newscscale: float) -> None

C++: core::scoring::methods::EnergyMethodOptions::set_density_sc_scale_byres(enum core::chemical::AA, double) –> void

set_elec_sigmoidal_die_params(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, D: float, D0: float, S: float) → None

C++: core::scoring::methods::EnergyMethodOptions::set_elec_sigmoidal_die_params(double, double, double) –> void

set_method_weights(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, type: pyrosetta.rosetta.core.scoring.ScoreType, wts: pyrosetta.rosetta.utility.vector1_double) → None

C++: core::scoring::methods::EnergyMethodOptions::set_method_weights(const enum core::scoring::ScoreType &, const class utility::vector1<double, class std::allocator<double> > &) –> void

set_mhc_epitope_setup_files(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, input_filenames: pyrosetta.rosetta.utility.vector1_std_string) → None

Set the mhc_epitope setup file names.

Overrides existing.

C++: core::scoring::methods::EnergyMethodOptions::set_mhc_epitope_setup_files(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_netcharge_setup_files(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, input_filenames: pyrosetta.rosetta.utility.vector1_std_string) → None

Set the netcharge setup file names.

Overrides existing.

C++: core::scoring::methods::EnergyMethodOptions::set_netcharge_setup_files(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_strand_strand_weights(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, ss_lowstrand: int, ss_cutoff: int) → None

C++: core::scoring::methods::EnergyMethodOptions::set_strand_strand_weights(int, int) –> void

show(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, out: pyrosetta.rosetta.std.ostream) → None

C++: core::scoring::methods::EnergyMethodOptions::show(std::ostream &) const –> void

smooth_fa_elec(*args, **kwargs)

Overloaded function.

1. smooth_fa_elec(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

C++: core::scoring::methods::EnergyMethodOptions::smooth_fa_elec() const –> bool

2. smooth_fa_elec(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

C++: core::scoring::methods::EnergyMethodOptions::smooth_fa_elec(bool) –> void

split_unfolded_label_type(*args, **kwargs)

Overloaded function.

1. split_unfolded_label_type(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> str

C++: core::scoring::methods::EnergyMethodOptions::split_unfolded_label_type() const –> const std::string &

2. split_unfolded_label_type(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, label_type: str) -> None

C++: core::scoring::methods::EnergyMethodOptions::split_unfolded_label_type(const std::string &) –> void

split_unfolded_value_type(*args, **kwargs)

Overloaded function.

1. split_unfolded_value_type(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> str

C++: core::scoring::methods::EnergyMethodOptions::split_unfolded_value_type() const –> const std::string &

2. split_unfolded_value_type(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, value_type: str) -> None

C++: core::scoring::methods::EnergyMethodOptions::split_unfolded_value_type(const std::string &) –> void

symmetric_gly_tables(*args, **kwargs)

Overloaded function.

1. symmetric_gly_tables(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

Should glyceine’s Ramachandran and P_AA_PP tables be symmetrized (e.g. for scoring in a mixed D/L context)?

Default false.

Vikram K. Mulligan (vmullig.edu)

C++: core::scoring::methods::EnergyMethodOptions::symmetric_gly_tables() const –> bool

2. symmetric_gly_tables(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

Set whether glyceine’s Ramachandran and P_AA_PP tables should be symmetrized (e.g. for scoring in a mixed D/L context).

Vikram K. Mulligan (vmullig.edu)

C++: core::scoring::methods::EnergyMethodOptions::symmetric_gly_tables(const bool) –> void

target_clash_pdb(*args, **kwargs)

Overloaded function.

1. target_clash_pdb(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: str) -> None

geter and setter for target clash energy

C++: core::scoring::methods::EnergyMethodOptions::target_clash_pdb(const std::string &) –> void

2. target_clash_pdb(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> str

C++: core::scoring::methods::EnergyMethodOptions::target_clash_pdb() const –> std::string

unfolded_energies_type(*args, **kwargs)

Overloaded function.

1. unfolded_energies_type(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> str

C++: core::scoring::methods::EnergyMethodOptions::unfolded_energies_type() const –> const std::string &

2. unfolded_energies_type(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, type: str) -> None

C++: core::scoring::methods::EnergyMethodOptions::unfolded_energies_type(const std::string &) –> void

use_gen_kirkwood(*args, **kwargs)

Overloaded function.

1. use_gen_kirkwood(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

C++: core::scoring::methods::EnergyMethodOptions::use_gen_kirkwood() const –> bool

2. use_gen_kirkwood(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

C++: core::scoring::methods::EnergyMethodOptions::use_gen_kirkwood(bool) –> void

use_polarization(*args, **kwargs)

Overloaded function.

1. use_polarization(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

C++: core::scoring::methods::EnergyMethodOptions::use_polarization() const –> bool

2. use_polarization(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

C++: core::scoring::methods::EnergyMethodOptions::use_polarization(bool) –> void

voids_penalty_energy_cone_distance_cutoff(*args, **kwargs)

Overloaded function.

1. voids_penalty_energy_cone_distance_cutoff(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

Get the cone distance cutoff for the voids penalty energy.

Vikram K. Mulligan (vmullig.edu)

C++: core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_cone_distance_cutoff() const –> double

2. voids_penalty_energy_cone_distance_cutoff(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

Set the cone distance cutoff for the voids penalty energy.

Vikram K. Mulligan (vmullig.edu)

C++: core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_cone_distance_cutoff(const double &) –> void

voids_penalty_energy_cone_dotproduct_cutoff(*args, **kwargs)

Overloaded function.

1. voids_penalty_energy_cone_dotproduct_cutoff(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

Get the cone dot product cutoff for the voids penalty energy.

Vikram K. Mulligan (vmullig.edu)

C++: core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_cone_dotproduct_cutoff() const –> double

2. voids_penalty_energy_cone_dotproduct_cutoff(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

Set the cone dot product cutoff for the voids penalty energy.

Vikram K. Mulligan (vmullig.edu)

C++: core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_cone_dotproduct_cutoff(const double &) –> void

voids_penalty_energy_containing_cones_cutoff(*args, **kwargs)

Overloaded function.

1. voids_penalty_energy_containing_cones_cutoff(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> int

Get the number of cones in which a voxel must lie in order for that voxel to be considered

to be “buried”.

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_containing_cones_cutoff() const –> unsigned long

2. voids_penalty_energy_containing_cones_cutoff(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: int) -> None

Set the number of cones in which a voxel must lie in order for that voxel to be considered

to be “buried”.

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_containing_cones_cutoff(const unsigned long) –> void

voids_penalty_energy_disabled_except_during_packing(*args, **kwargs)

Overloaded function.

1. voids_penalty_energy_disabled_except_during_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> bool

Get whether we’re prohibiting evaluation of the voids_penalty score term outside

of the context of the packer.

Vikram K. Mulligan (vmullig.edu)

C++: core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_disabled_except_during_packing() const –> bool

2. voids_penalty_energy_disabled_except_during_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: bool) -> None

Set whether we’re prohibiting evaluation of the voids_penalty score term outside

of the context of the packer.

Vikram K. Mulligan (vmullig.edu)

C++: core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_disabled_except_during_packing(const bool) –> void

voids_penalty_energy_voxel_grid_padding(*args, **kwargs)

Overloaded function.

1. voids_penalty_energy_voxel_grid_padding(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

Get the voxel grid padding for the voids penalty energy.

Vikram K. Mulligan (vmullig.edu)

C++: core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_voxel_grid_padding() const –> double

2. voids_penalty_energy_voxel_grid_padding(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

Set the voxel grid padding for the voids penalty energy.

Vikram K. Mulligan (vmullig.edu)

C++: core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_voxel_grid_padding(const double &) –> void

voids_penalty_energy_voxel_size(*args, **kwargs)

Overloaded function.

1. voids_penalty_energy_voxel_size(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

Get the voxel size for the voids penalty energy.

Vikram K. Mulligan (vmullig.edu)

C++: core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_voxel_size() const –> double

2. voids_penalty_energy_voxel_size(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

Set the voxel size for the voids penalty energy.

Vikram K. Mulligan (vmullig.edu)

C++: core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_voxel_size(const double &) –> void

water_dielectric(*args, **kwargs)

Overloaded function.

1. water_dielectric(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) -> float

C++: core::scoring::methods::EnergyMethodOptions::water_dielectric() const –> double

2. water_dielectric(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions, setting: float) -> None

C++: core::scoring::methods::EnergyMethodOptions::water_dielectric(double) –> void

static write_score_function_method_options_table_schema(db_session: pyrosetta.rosetta.utility.sql_database.session) → None

C++: core::scoring::methods::EnergyMethodOptions::write_score_function_method_options_table_schema(class std::shared_ptr<class utility::sql_database::session>) –> void

class pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

Bases: pybind11_object

Members:

ci_2b

cd_2b

ci_lr_2b

cd_lr_2b

ci_1b

cd_1b

ws

n_energy_method_types

cd_1b = <EnergyMethodType.cd_1b: 6>

cd_2b = <EnergyMethodType.cd_2b: 2>

cd_lr_2b = <EnergyMethodType.cd_lr_2b: 4>

ci_1b = <EnergyMethodType.ci_1b: 5>

ci_2b = <EnergyMethodType.ci_2b: 1>

ci_lr_2b = <EnergyMethodType.ci_lr_2b: 3>

n_energy_method_types = <EnergyMethodType.ws: 7>

property name

property value

ws = <EnergyMethodType.ws: 7>

class pyrosetta.rosetta.core.scoring.methods.EnergyMethods

Bases: pybind11_object

Members:

etable_method

dunbrack_method

hbond_method

elec_method

lkball_method

mm_lj_energy_inter_method

pair_e_method

reference_e_method

vdw_method

ramachandran_method

n_energy_methods

dunbrack_method = <EnergyMethods.dunbrack_method: 2>

elec_method = <EnergyMethods.elec_method: 4>

etable_method = <EnergyMethods.etable_method: 1>

hbond_method = <EnergyMethods.hbond_method: 3>

lkball_method = <EnergyMethods.lkball_method: 5>

mm_lj_energy_inter_method = <EnergyMethods.mm_lj_energy_inter_method: 6>

n_energy_methods = <EnergyMethods.ramachandran_method: 10>

property name

pair_e_method = <EnergyMethods.pair_e_method: 7>

ramachandran_method = <EnergyMethods.ramachandran_method: 10>

reference_e_method = <EnergyMethods.reference_e_method: 8>

property value

vdw_method = <EnergyMethods.vdw_method: 9>

class pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options, : pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options) → pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options

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

free_2HOprime_bonus(*args, **kwargs)

Overloaded function.

1. free_2HOprime_bonus(self: pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options) -> float

C++: core::scoring::methods::FreeDOF_Options::free_2HOprime_bonus() const –> double

2. free_2HOprime_bonus(self: pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options, setting: float) -> None

C++: core::scoring::methods::FreeDOF_Options::free_2HOprime_bonus(double) –> void

free_side_chain_bonus(*args, **kwargs)

Overloaded function.

1. free_side_chain_bonus(self: pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options) -> float

C++: core::scoring::methods::FreeDOF_Options::free_side_chain_bonus() const –> double

2. free_side_chain_bonus(self: pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options, setting: float) -> None

C++: core::scoring::methods::FreeDOF_Options::free_side_chain_bonus(double) –> void

free_sugar_bonus(*args, **kwargs)

Overloaded function.

1. free_sugar_bonus(self: pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options) -> float

C++: core::scoring::methods::FreeDOF_Options::free_sugar_bonus() const –> double

2. free_sugar_bonus(self: pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options, setting: float) -> None

C++: core::scoring::methods::FreeDOF_Options::free_sugar_bonus(double) –> void

free_suite_bonus(*args, **kwargs)

Overloaded function.

1. free_suite_bonus(self: pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options) -> float

C++: core::scoring::methods::FreeDOF_Options::free_suite_bonus() const –> double

2. free_suite_bonus(self: pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options, setting: float) -> None

C++: core::scoring::methods::FreeDOF_Options::free_suite_bonus(double) –> void

initialize_from_options(self: pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options) → None

C++: core::scoring::methods::FreeDOF_Options::initialize_from_options() –> void

pack_phosphate_penalty(*args, **kwargs)

Overloaded function.

1. pack_phosphate_penalty(self: pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options) -> float

C++: core::scoring::methods::FreeDOF_Options::pack_phosphate_penalty() const –> double

2. pack_phosphate_penalty(self: pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options, setting: float) -> None

C++: core::scoring::methods::FreeDOF_Options::pack_phosphate_penalty(double) –> void

show(self: pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options, out: pyrosetta.rosetta.std.ostream) → None

C++: core::scoring::methods::FreeDOF_Options::show(std::ostream &) const –> void

class pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType

Bases: pybind11_object

Members:

constraints_lr

gen_born_lr

multipole_elec_lr

vdw_tinker_lr

sasa_lr

epr_deer_lr

PB_elec_lr

cart_bonded_lr

dna_dihedral_lr

gen_bonded_lr

rama2b_lr

ramaprepro_lr

aspartimide_penalty_lr

rna_suite_lr

tna_suite_lr

rna_stub_coord_lr

DFIRE

sym_bonus_lr

elec_dens_energy

elec_dens_fast_energy

elec_dens_cen_energy

elec_dens_allatom_cen_energy

elec_dens_atomwise_energy

patterson_corr_energy

fa_disulfide_energy

disulfide_matching_energy

centroid_disulfide_energy

n_long_range_types

DFIRE = <LongRangeEnergyType.DFIRE: 17>

PB_elec_lr = <LongRangeEnergyType.PB_elec_lr: 7>

aspartimide_penalty_lr = <LongRangeEnergyType.aspartimide_penalty_lr: 13>

cart_bonded_lr = <LongRangeEnergyType.cart_bonded_lr: 8>

centroid_disulfide_energy = <LongRangeEnergyType.centroid_disulfide_energy: 27>

constraints_lr = <LongRangeEnergyType.constraints_lr: 1>

disulfide_matching_energy = <LongRangeEnergyType.disulfide_matching_energy: 26>

dna_dihedral_lr = <LongRangeEnergyType.dna_dihedral_lr: 9>

elec_dens_allatom_cen_energy = <LongRangeEnergyType.elec_dens_allatom_cen_energy: 22>

elec_dens_atomwise_energy = <LongRangeEnergyType.elec_dens_atomwise_energy: 23>

elec_dens_cen_energy = <LongRangeEnergyType.elec_dens_cen_energy: 21>

elec_dens_energy = <LongRangeEnergyType.elec_dens_energy: 19>

elec_dens_fast_energy = <LongRangeEnergyType.elec_dens_fast_energy: 20>

epr_deer_lr = <LongRangeEnergyType.epr_deer_lr: 6>

fa_disulfide_energy = <LongRangeEnergyType.fa_disulfide_energy: 25>

gen_bonded_lr = <LongRangeEnergyType.gen_bonded_lr: 10>

gen_born_lr = <LongRangeEnergyType.gen_born_lr: 2>

multipole_elec_lr = <LongRangeEnergyType.multipole_elec_lr: 3>

n_long_range_types = <LongRangeEnergyType.centroid_disulfide_energy: 27>

property name

patterson_corr_energy = <LongRangeEnergyType.patterson_corr_energy: 24>

rama2b_lr = <LongRangeEnergyType.rama2b_lr: 11>

ramaprepro_lr = <LongRangeEnergyType.ramaprepro_lr: 12>

rna_stub_coord_lr = <LongRangeEnergyType.rna_stub_coord_lr: 16>

rna_suite_lr = <LongRangeEnergyType.rna_suite_lr: 14>

sasa_lr = <LongRangeEnergyType.sasa_lr: 5>

sym_bonus_lr = <LongRangeEnergyType.sym_bonus_lr: 18>

tna_suite_lr = <LongRangeEnergyType.tna_suite_lr: 15>

property value

vdw_tinker_lr = <LongRangeEnergyType.vdw_tinker_lr: 4>

class pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy

Bases: TwoBodyEnergy

assign(self: pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy, : pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy

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

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.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers 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_pairwise_energies()

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

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

backbone of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the weighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

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

bump_energy_backbone(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None

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

bump_energy_full(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None

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

clone(self: pyrosetta.rosetta.core.scoring.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_residue_pair_energy(self: pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy, pose: core::pose::Pose, res1: int, res2: int) → bool

C++: core::scoring::methods::LongRangeTwoBodyEnergy::defines_residue_pair_energy(const class core::pose::Pose &, unsigned long, unsigned long) 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

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Evaluate the XYZ derivative for an atom in the pose.

Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom’s XYZ derivative

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) “Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations” Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

Evaluate the derivative for the intra-residue component of this energy method

for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd.

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

Evaluate the intra-residue energy for a given residue using the data held within the

ResSingleMinimizationData object. This function should be invoked only on derived instances of this class if they return “true” in a call to their use_extended_intrares_energy_interface method. This base class provides a noop implementation for classes that do not implement this interface, or that do not define intrares energies.

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

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

Evaluate the DOF derivative for a particular residue. The Pose merely serves as context,

and the input residue is not required to be a member of the Pose.

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

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

Evaluate the derivatives for all atoms on rsd1 and rsd2 with respect

to each other and increment the derivatives in atom-derivatives vector1s. The calling function must guarantee that the r1_atom_derivs vector1 holds at least as many entries as there are atoms in rsd1, and that the r2_atom_derivs vector1 holds at least as many entries as there are atoms in rsd2.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, residue: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector, energy_vector: pyrosetta.rosetta.utility.vector1_float) → None

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 rotamr

C++: core::scoring::methods::TwoBodyEnergy::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.TwoBodyEnergy, 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 rotamr

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

Batch computation of rotamer pair energies. Need not be overriden in

derived class – by default, iterates over all pairs of rotamers, and calls the derived class’s residue_pair_energy method.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, total_energy: core::scoring::EMapVector) → None

called by the ScoreFunction at the end of energy evaluation.

The derived class has the opportunity to accumulate a score into the pose’s total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

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

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.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

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

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, context_graphs_required: pyrosetta.rosetta.utility.vector1_bool) → None

Indicate in the context-graphs-required list which

context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed

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

long_range_type(self: pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType

C++: core::scoring::methods::LongRangeTwoBodyEnergy::long_range_type() const –> enum core::scoring::methods::LongRangeEnergyType

method_type(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

Return one of the 7 kinds of energy methods that exist:

e.g. context-dependent-one-body vs whole-structure.

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

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

Should this EnergyMethod have score and derivative evaluation

evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that’s serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return “true” will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction’s traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return “true” cannot be included in RTMin.

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

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Evaluate the interaction between a given residue pair

accumulating the unweighted energies in an EnergyMap

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResPairMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the two-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those two body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residues in a call to setup_for_minimizing_for_residue_pair before this function is invoked. This function should not be called unless the use_extended_residue_pair_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit().

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction) → None

Called immediately before atom- and DOF-derivatives are calculated

allowing the derived class a chance to prepare for future calls.

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

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

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

C++: core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &, class basic::datacache::BasicDataCache &) const –> void

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

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

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

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) → None

Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache, res_data_cache: core::scoring::ResSingleMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, res1_data_cache: core::scoring::ResSingleMinimizationData, res2_data_cache: core::scoring::ResSingleMinimizationData, data_cache: core::scoring::ResPairMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

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

before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None

if an energy method needs to cache something in the pose (e.g. in pose.energies()),

before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

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

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue (who is still guaranteed to be

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

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

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

Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

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

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

show additional information of the energy method

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

sidechain_sidechain_energy(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the sidechain of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, : core::pose::Pose, resid: int) → None

If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

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

Derived classes wishing to invoke the alternate, extended interface for eval_intrares_energy

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

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

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

Rely on the extended version of the residue_pair_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResPairMinimizationData in which the derived base class has (or should have) cached a piece of data that will make residue-pair energy evaluation faster than its absense (e.g. a neighbor list). Derived energy methods should return ‘true’ from this function to use the extended interface. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::TwoBodyEnergy::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.methods.MMBondAngleEnergy

Bases: ContextIndependentTwoBodyEnergy

assign(self: pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy, : 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 &

atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy) → float

MMBondAngleEnergy does not have an atomic interation threshold

C++: core::scoring::methods::MMBondAngleEnergy::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.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers 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_pairwise_energies()

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

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

backbone of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the weighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

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

bump_energy_backbone(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None

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

bump_energy_full(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None

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

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

clone

C++: core::scoring::methods::MMBondAngleEnergy::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.MMBondAngleEnergy, : pyrosetta.rosetta.core.scoring.EMapVector) → bool

C++: core::scoring::methods::MMBondAngleEnergy::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.methods.ShortRangeTwoBodyEnergy) → bool

A derived class should return true for this function if it implements its own

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

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::divides_backbone_and_sidechain_energetics() const –> bool

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy, id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: core::scoring::methods::MMBondAngleEnergy::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.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

Evaluate the derivative for the intra-residue component of this energy method

for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd.

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

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

Evaluate the intra-residue energy for a given residue using the data held within the

ResSingleMinimizationData object. This function should be invoked only on derived instances of this class if they return “true” in a call to their use_extended_intrares_energy_interface method. This base class provides a noop implementation for classes that do not implement this interface, or that do not define intrares energies.

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

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

Evaluate the DOF derivative for a particular residue. The Pose merely serves as context,

and the input residue is not required to be a member of the Pose.

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

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

Evaluate the derivatives for all atoms on rsd1 and rsd2 with respect

to each other and increment the derivatives in atom-derivatives vector1s. The calling function must guarantee that the r1_atom_derivs vector1 holds at least as many entries as there are atoms in rsd1, and that the r2_atom_derivs vector1 holds at least as many entries as there are atoms in rsd2.

C++: core::scoring::methods::TwoBodyEnergy::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.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, energy_vector: pyrosetta.rosetta.utility.vector1_float) → 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_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.methods.ShortRangeTwoBodyEnergy, set1: pyrosetta.rosetta.core.conformation.RotamerSetBase, set2: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector, energy_table: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) → None

Batch computation of rotamer pair energies. Need not be overriden in

derived class – by default, iterates over all pairs of rotamers, and calls derived class’s residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, total_energy: core::scoring::EMapVector) → None

called by the ScoreFunction at the end of energy evaluation.

The derived class has the opportunity to accumulate a score into the pose’s total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

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

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.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

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

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy, : pyrosetta.rosetta.utility.vector1_bool) → None

MMBondAngleEnergy is context independent; indicates that no

context graphs are required

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

method_type(self: pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

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

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

Should this EnergyMethod have score and derivative evaluation

evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that’s serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return “true” will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction’s traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return “true” cannot be included in RTMin.

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

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

residue_pair_energy(self: pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::methods::MMBondAngleEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResPairMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the two-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those two body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residues in a call to setup_for_minimizing_for_residue_pair before this function is invoked. This function should not be called unless the use_extended_residue_pair_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit().

C++: core::scoring::methods::TwoBodyEnergy::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

residue_type_param_set(*args, **kwargs)

Overloaded function.

1. residue_type_param_set(self: pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy, param_set: core::scoring::mm::MMBondAngleResidueTypeParamSet) -> None

set underlying MMBondAngleResidueTypeParamSet

C++: core::scoring::methods::MMBondAngleEnergy::residue_type_param_set(class std::shared_ptr<class core::scoring::mm::MMBondAngleResidueTypeParamSet>) –> void

2. residue_type_param_set(self: pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy) -> core::scoring::mm::MMBondAngleResidueTypeParamSet

get underlying MMBondAngleResidueTypeParamSet

C++: core::scoring::methods::MMBondAngleEnergy::residue_type_param_set() –> class std::shared_ptr<class core::scoring::mm::MMBondAngleResidueTypeParamSet>

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.methods.MMBondAngleEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

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

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

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

C++: core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &, class basic::datacache::BasicDataCache &) const –> void

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

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

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

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) → None

Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache, res_data_cache: core::scoring::ResSingleMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, res1_data_cache: core::scoring::ResSingleMinimizationData, res2_data_cache: core::scoring::ResSingleMinimizationData, data_cache: core::scoring::ResPairMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.MMBondAngleEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

C++: core::scoring::methods::MMBondAngleEnergy::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.methods.MMBondAngleEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

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

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue (who is still guaranteed to be

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

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

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

Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

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

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

show additional information of the energy method

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

sidechain_sidechain_energy(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the sidechain of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, : core::pose::Pose, resid: int) → None

If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

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

Derived classes wishing to invoke the alternate, extended interface for eval_intrares_energy

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

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

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

Rely on the extended version of the residue_pair_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResPairMinimizationData in which the derived base class has (or should have) cached a piece of data that will make residue-pair energy evaluation faster than its absense (e.g. a neighbor list). Derived energy methods should return ‘true’ from this function to use the extended interface. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::TwoBodyEnergy::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.methods.MMBondAngleEnergyCreator

Bases: EnergyMethodCreator

assign(self: pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergyCreator) → pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergyCreator

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

create_energy_method(self: pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

Instantiate a new MMBondAngleEnergy

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

class pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy

Bases: ContextIndependentTwoBodyEnergy

assign(self: pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy, : 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 &

atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy) → float

MMBondLengthEnergy does not have an atomic interation threshold

C++: core::scoring::methods::MMBondLengthEnergy::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.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers 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_pairwise_energies()

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

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

backbone of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the weighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

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

bump_energy_backbone(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None

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

bump_energy_full(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None

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

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

clone

C++: core::scoring::methods::MMBondLengthEnergy::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.MMBondLengthEnergy, : pyrosetta.rosetta.core.scoring.EMapVector) → bool

C++: core::scoring::methods::MMBondLengthEnergy::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.methods.ShortRangeTwoBodyEnergy) → bool

A derived class should return true for this function if it implements its own

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

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::divides_backbone_and_sidechain_energetics() const –> bool

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy, id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: core::scoring::methods::MMBondLengthEnergy::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.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

Evaluate the derivative for the intra-residue component of this energy method

for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd.

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

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

Evaluate the intra-residue energy for a given residue using the data held within the

ResSingleMinimizationData object. This function should be invoked only on derived instances of this class if they return “true” in a call to their use_extended_intrares_energy_interface method. This base class provides a noop implementation for classes that do not implement this interface, or that do not define intrares energies.

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

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

Evaluate the DOF derivative for a particular residue. The Pose merely serves as context,

and the input residue is not required to be a member of the Pose.

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

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

Evaluate the derivatives for all atoms on rsd1 and rsd2 with respect

to each other and increment the derivatives in atom-derivatives vector1s. The calling function must guarantee that the r1_atom_derivs vector1 holds at least as many entries as there are atoms in rsd1, and that the r2_atom_derivs vector1 holds at least as many entries as there are atoms in rsd2.

C++: core::scoring::methods::TwoBodyEnergy::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.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, energy_vector: pyrosetta.rosetta.utility.vector1_float) → 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_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.methods.ShortRangeTwoBodyEnergy, set1: pyrosetta.rosetta.core.conformation.RotamerSetBase, set2: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector, energy_table: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) → None

Batch computation of rotamer pair energies. Need not be overriden in

derived class – by default, iterates over all pairs of rotamers, and calls derived class’s residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, total_energy: core::scoring::EMapVector) → None

called by the ScoreFunction at the end of energy evaluation.

The derived class has the opportunity to accumulate a score into the pose’s total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

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

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.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

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

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy, : pyrosetta.rosetta.utility.vector1_bool) → None

MMBondLengthEnergy is context independent; indicates that no

context graphs are required

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

method_type(self: pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

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

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

Should this EnergyMethod have score and derivative evaluation

evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that’s serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return “true” will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction’s traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return “true” cannot be included in RTMin.

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

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

residue_pair_energy(self: pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::methods::MMBondLengthEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResPairMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the two-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those two body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residues in a call to setup_for_minimizing_for_residue_pair before this function is invoked. This function should not be called unless the use_extended_residue_pair_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit().

C++: core::scoring::methods::TwoBodyEnergy::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.methods.MMBondLengthEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

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

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

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

C++: core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &, class basic::datacache::BasicDataCache &) const –> void

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

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

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

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) → None

Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache, res_data_cache: core::scoring::ResSingleMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, res1_data_cache: core::scoring::ResSingleMinimizationData, res2_data_cache: core::scoring::ResSingleMinimizationData, data_cache: core::scoring::ResPairMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.MMBondLengthEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

C++: core::scoring::methods::MMBondLengthEnergy::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.methods.MMBondLengthEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

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

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue (who is still guaranteed to be

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

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

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

Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

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

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

show additional information of the energy method

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

sidechain_sidechain_energy(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the sidechain of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, : core::pose::Pose, resid: int) → None

If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

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

Derived classes wishing to invoke the alternate, extended interface for eval_intrares_energy

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

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

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

Rely on the extended version of the residue_pair_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResPairMinimizationData in which the derived base class has (or should have) cached a piece of data that will make residue-pair energy evaluation faster than its absense (e.g. a neighbor list). Derived energy methods should return ‘true’ from this function to use the extended interface. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::TwoBodyEnergy::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.methods.MMBondLengthEnergyCreator

Bases: EnergyMethodCreator

assign(self: pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergyCreator) → pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergyCreator

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

create_energy_method(self: pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

Instantiate a new MMBondLengthEnergy

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

class pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter

Bases: ContextIndependentTwoBodyEnergy

assign(self: pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy, : 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 &

atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter) → float

MMLJEnergyInter does not have an atomic interation threshold

C++: core::scoring::methods::MMLJEnergyInter::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.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers 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_pairwise_energies()

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

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

backbone of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the weighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

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

bump_energy_backbone(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter, 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::methods::MMLJEnergyInter::bump_energy_backbone(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

bump_energy_full(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter, 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::methods::MMLJEnergyInter::bump_energy_full(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

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

clone

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

create_rotamer_trie(*args, **kwargs)

Overloaded function.

1. create_rotamer_trie(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter, rotset: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.trie.RotamerTrieBase

C++: core::scoring::methods::MMLJEnergyInter::create_rotamer_trie(const class core::conformation::RotamerSetBase &, const class core::pose::Pose &) const –> class std::shared_ptr<class core::scoring::trie::RotamerTrieBase>

2. create_rotamer_trie(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter, res: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.trie.RotamerTrieBase

C++: core::scoring::methods::MMLJEnergyInter::create_rotamer_trie(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::shared_ptr<class core::scoring::trie::RotamerTrieBase>

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.MMLJEnergyInter, : pyrosetta.rosetta.core.scoring.EMapVector) → bool

C++: core::scoring::methods::MMLJEnergyInter::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.methods.ShortRangeTwoBodyEnergy) → bool

A derived class should return true for this function if it implements its own

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

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::divides_backbone_and_sidechain_energetics() const –> bool

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter, id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, : 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::methods::MMLJEnergyInter::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.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

Evaluate the derivative for the intra-residue component of this energy method

for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd.

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

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

Evaluate the intra-residue energy for a given residue using the data held within the

ResSingleMinimizationData object. This function should be invoked only on derived instances of this class if they return “true” in a call to their use_extended_intrares_energy_interface method. This base class provides a noop implementation for classes that do not implement this interface, or that do not define intrares energies.

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

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

Evaluate the DOF derivative for a particular residue. The Pose merely serves as context,

and the input residue is not required to be a member of the Pose.

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

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

Evaluate the derivatives for all atoms on rsd1 and rsd2 with respect

to each other and increment the derivatives in atom-derivatives vector1s. The calling function must guarantee that the r1_atom_derivs vector1 holds at least as many entries as there are atoms in rsd1, and that the r2_atom_derivs vector1 holds at least as many entries as there are atoms in rsd2.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.MMLJEnergyInter, 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::methods::MMLJEnergyInter::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.methods.MMLJEnergyInter, 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::methods::MMLJEnergyInter::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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, total_energy: core::scoring::EMapVector) → None

called by the ScoreFunction at the end of energy evaluation.

The derived class has the opportunity to accumulate a score into the pose’s total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

C++: core::scoring::methods::EnergyMethod::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.methods.MMLJEnergyInter, res1: int, res2: int, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction

required for neighbor list and to be more lke the ETable

C++: core::scoring::methods::MMLJEnergyInter::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>

2. get_count_pair_function(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter, 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

required for neighbor list and to be more lke the ETable

C++: core::scoring::methods::MMLJEnergyInter::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_count_pair_function_trie(*args, **kwargs)

Overloaded function.

1. get_count_pair_function_trie(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, trie1: pyrosetta.rosetta.core.scoring.trie.RotamerTrieBase, trie2: pyrosetta.rosetta.core.scoring.trie.RotamerTrieBase, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> pyrosetta.rosetta.core.scoring.trie.TrieCountPairBase

C++: core::scoring::methods::MMLJEnergyInter::get_count_pair_function_trie(const class core::conformation::Residue &, const class core::conformation::Residue &, class std::shared_ptr<const class core::scoring::trie::RotamerTrieBase>, class std::shared_ptr<const class core::scoring::trie::RotamerTrieBase>, const class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> class std::shared_ptr<class core::scoring::trie::TrieCountPairBase>

2. get_count_pair_function_trie(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter, set1: pyrosetta.rosetta.core.conformation.RotamerSetBase, set2: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> pyrosetta.rosetta.core.scoring.trie.TrieCountPairBase

C++: core::scoring::methods::MMLJEnergyInter::get_count_pair_function_trie(const class core::conformation::RotamerSetBase &, const class core::conformation::RotamerSetBase &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> class std::shared_ptr<class core::scoring::trie::TrieCountPairBase>

get_intrares_countpair(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter, 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

required for neighbor list and to be more lke the ETable

C++: core::scoring::methods::MMLJEnergyInter::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.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

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

heavyatom_heavyatom_energy(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter, at1: pyrosetta.rosetta.core.scoring.mm.mmtrie.MMEnergyTableAtom, at2: pyrosetta.rosetta.core.scoring.mm.mmtrie.MMEnergyTableAtom, d2: float, path_dist: int) → float

C++: core::scoring::methods::MMLJEnergyInter::heavyatom_heavyatom_energy(const class core::scoring::mm::mmtrie::MMEnergyTableAtom &, const class core::scoring::mm::mmtrie::MMEnergyTableAtom &, double &, unsigned long &) const –> double

heavyatom_hydrogenatom_energy(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter, at1: pyrosetta.rosetta.core.scoring.mm.mmtrie.MMEnergyTableAtom, at2: pyrosetta.rosetta.core.scoring.mm.mmtrie.MMEnergyTableAtom, path_dist: int, : pyrosetta.rosetta.core.scoring.trie.TrieVsTrieCachedDataContainerBase) → float

C++: core::scoring::methods::MMLJEnergyInter::heavyatom_hydrogenatom_energy(const class core::scoring::mm::mmtrie::MMEnergyTableAtom &, const class core::scoring::mm::mmtrie::MMEnergyTableAtom &, unsigned long &, const class core::scoring::trie::TrieVsTrieCachedDataContainerBase *const) const –> double

hydrogen_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter) → float

C++: core::scoring::methods::MMLJEnergyInter::hydrogen_interaction_cutoff() const –> double

hydrogen_interaction_cutoff2(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter) → float

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

max heavy-to-hydrogen distance ( MAGIC NUMBER!!!! FIX IT ) + atom-pair interaction distance.

C++: core::scoring::methods::MMLJEnergyInter::hydrogen_interaction_cutoff2() const –> double

hydrogenatom_heavyatom_energy(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter, at1: pyrosetta.rosetta.core.scoring.mm.mmtrie.MMEnergyTableAtom, at2: pyrosetta.rosetta.core.scoring.mm.mmtrie.MMEnergyTableAtom, path_dist: int, : pyrosetta.rosetta.core.scoring.trie.TrieVsTrieCachedDataContainerBase) → float

C++: core::scoring::methods::MMLJEnergyInter::hydrogenatom_heavyatom_energy(const class core::scoring::mm::mmtrie::MMEnergyTableAtom &, const class core::scoring::mm::mmtrie::MMEnergyTableAtom &, unsigned long &, const class core::scoring::trie::TrieVsTrieCachedDataContainerBase *const) const –> double

hydrogenatom_hydrogenatom_energy(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter, at1: pyrosetta.rosetta.core.scoring.mm.mmtrie.MMEnergyTableAtom, at2: pyrosetta.rosetta.core.scoring.mm.mmtrie.MMEnergyTableAtom, path_dist: int, : pyrosetta.rosetta.core.scoring.trie.TrieVsTrieCachedDataContainerBase) → float

C++: core::scoring::methods::MMLJEnergyInter::hydrogenatom_hydrogenatom_energy(const class core::scoring::mm::mmtrie::MMEnergyTableAtom &, const class core::scoring::mm::mmtrie::MMEnergyTableAtom &, unsigned long &, const class core::scoring::trie::TrieVsTrieCachedDataContainerBase *const) const –> double

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter, : pyrosetta.rosetta.utility.vector1_bool) → None

MMLJEnergyInter is context independent; indicates that no context graphs are required

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

method_type(self: pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

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

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

Should this EnergyMethod have score and derivative evaluation

evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that’s serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return “true” will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction’s traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return “true” cannot be included in RTMin.

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

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter, pose: pyrosetta.rosetta.core.pose.Pose, set: pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

C++: core::scoring::methods::MMLJEnergyInter::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.methods.TwoBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

residue_pair_energy(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::methods::MMLJEnergyInter::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResPairMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the two-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those two body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residues in a call to setup_for_minimizing_for_residue_pair before this function is invoked. This function should not be called unless the use_extended_residue_pair_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit().

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction) → None

Called immediately before atom- and DOF-derivatives are calculated

allowing the derived class a chance to prepare for future calls.

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

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

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

C++: core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &, class basic::datacache::BasicDataCache &) const –> void

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

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

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

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

C++: core::scoring::methods::MMLJEnergyInter::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.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache, res_data_cache: core::scoring::ResSingleMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, res1_data_cache: core::scoring::ResSingleMinimizationData, res2_data_cache: core::scoring::ResSingleMinimizationData, data_cache: core::scoring::ResPairMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.MMLJEnergyInter, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

C++: core::scoring::methods::MMLJEnergyInter::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.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None

if an energy method needs to cache something in the pose (e.g. in pose.energies()),

before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

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

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue (who is still guaranteed to be

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

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

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

Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

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

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

show additional information of the energy method

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

sidechain_sidechain_energy(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the sidechain of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.MMLJEnergyInter, pose: pyrosetta.rosetta.core.pose.Pose, resid: int) → None

C++: core::scoring::methods::MMLJEnergyInter::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

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

Derived classes wishing to invoke the alternate, extended interface for eval_intrares_energy

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

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

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

Rely on the extended version of the residue_pair_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResPairMinimizationData in which the derived base class has (or should have) cached a piece of data that will make residue-pair energy evaluation faster than its absense (e.g. a neighbor list). Derived energy methods should return ‘true’ from this function to use the extended interface. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::TwoBodyEnergy::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.methods.MMLJEnergyInterCreator

Bases: EnergyMethodCreator

assign(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInterCreator, : pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInterCreator) → pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInterCreator

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

create_energy_method(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInterCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

Instantiate a new MMTorsionEnergy

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

class pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra

Bases: ContextIndependentTwoBodyEnergy

assign(self: pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy, : 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 &

atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra) → float

MMLJEnergy does not have an atomic interation threshold

C++: core::scoring::methods::MMLJEnergyIntra::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.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers 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_pairwise_energies()

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

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

backbone of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the weighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

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

bump_energy_backbone(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None

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

bump_energy_full(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None

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

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

clone

C++: core::scoring::methods::MMLJEnergyIntra::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.MMLJEnergyIntra, : pyrosetta.rosetta.core.scoring.EMapVector) → bool

C++: core::scoring::methods::MMLJEnergyIntra::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.methods.ShortRangeTwoBodyEnergy) → bool

A derived class should return true for this function if it implements its own

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

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::divides_backbone_and_sidechain_energetics() const –> bool

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Evaluate the XYZ derivative for an atom in the pose.

Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom’s XYZ derivative

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) “Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations” Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

C++: core::scoring::methods::EnergyMethod::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.methods.MMLJEnergyIntra, rsd: pyrosetta.rosetta.core.conformation.Residue, res_data_cache: 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::methods::MMLJEnergyIntra::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.MMLJEnergyIntra, 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::methods::MMLJEnergyIntra::eval_intrares_energy(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

eval_intrares_energy_ext(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra, rsd: pyrosetta.rosetta.core.conformation.Residue, res_data_cache: 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::methods::MMLJEnergyIntra::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, : core::scoring::ResSingleMinimizationData, : core::scoring::ResSingleMinimizationData, min_data: core::scoring::ResPairMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, r1_atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair, r2_atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

Evaluate the derivatives for all atoms on rsd1 and rsd2 with respect

to each other and increment the derivatives in atom-derivatives vector1s. The calling function must guarantee that the r1_atom_derivs vector1 holds at least as many entries as there are atoms in rsd1, and that the r2_atom_derivs vector1 holds at least as many entries as there are atoms in rsd2.

C++: core::scoring::methods::TwoBodyEnergy::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.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, energy_vector: pyrosetta.rosetta.utility.vector1_float) → 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_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.methods.ShortRangeTwoBodyEnergy, set1: pyrosetta.rosetta.core.conformation.RotamerSetBase, set2: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector, energy_table: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) → None

Batch computation of rotamer pair energies. Need not be overriden in

derived class – by default, iterates over all pairs of rotamers, and calls derived class’s residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, total_energy: core::scoring::EMapVector) → None

called by the ScoreFunction at the end of energy evaluation.

The derived class has the opportunity to accumulate a score into the pose’s total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

C++: core::scoring::methods::EnergyMethod::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.methods.MMLJEnergyIntra, res1: int, res2: int, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction

required for neighbor list and to be more lke the ETable

C++: core::scoring::methods::MMLJEnergyIntra::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>

2. get_count_pair_function(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra, 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

required for neighbor list and to be more lke the ETable

C++: core::scoring::methods::MMLJEnergyIntra::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.methods.MMLJEnergyIntra, 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

required for neighbor list and to be more lke the ETable

C++: core::scoring::methods::MMLJEnergyIntra::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.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

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

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra, : pyrosetta.rosetta.utility.vector1_bool) → None

MMLJEnergy is context independent; indicates that no context graphs are required

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

method_type(self: pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

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

minimize_in_whole_structure_context(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra, : pyrosetta.rosetta.core.pose.Pose) → bool

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

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

residue_pair_energy(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::methods::MMLJEnergyIntra::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResPairMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the two-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those two body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residues in a call to setup_for_minimizing_for_residue_pair before this function is invoked. This function should not be called unless the use_extended_residue_pair_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit().

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction) → None

Called immediately before atom- and DOF-derivatives are calculated

allowing the derived class a chance to prepare for future calls.

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

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

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

C++: core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &, class basic::datacache::BasicDataCache &) const –> void

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

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

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

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) → None

Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

C++: core::scoring::methods::EnergyMethod::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.methods.MMLJEnergyIntra, 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, res_data_cache: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData) → None

C++: core::scoring::methods::MMLJEnergyIntra::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, res1_data_cache: core::scoring::ResSingleMinimizationData, res2_data_cache: core::scoring::ResSingleMinimizationData, data_cache: core::scoring::ResPairMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

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

before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None

if an energy method needs to cache something in the pose (e.g. in pose.energies()),

before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

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

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue (who is still guaranteed to be

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

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

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

Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

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

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

show additional information of the energy method

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

sidechain_sidechain_energy(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the sidechain of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, : core::pose::Pose, resid: int) → None

If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

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

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

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

Rely on the extended version of the residue_pair_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResPairMinimizationData in which the derived base class has (or should have) cached a piece of data that will make residue-pair energy evaluation faster than its absense (e.g. a neighbor list). Derived energy methods should return ‘true’ from this function to use the extended interface. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::TwoBodyEnergy::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.methods.MMLJEnergyIntraCreator

Bases: EnergyMethodCreator

assign(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntraCreator, : pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntraCreator) → pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntraCreator

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

create_energy_method(self: pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntraCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

Instantiate a new MMTorsionEnergy

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

class pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy

Bases: ContextIndependentTwoBodyEnergy

assign(self: pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy, : 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 &

atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy) → float

MMTorsionEnergy does not have an atomic interation threshold

C++: core::scoring::methods::MMTorsionEnergy::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.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers 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_pairwise_energies()

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

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

backbone of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the weighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

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

bump_energy_backbone(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None

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

bump_energy_full(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None

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

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

clone

C++: core::scoring::methods::MMTorsionEnergy::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.MMTorsionEnergy, : pyrosetta.rosetta.core.scoring.EMapVector) → bool

C++: core::scoring::methods::MMTorsionEnergy::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.methods.ShortRangeTwoBodyEnergy) → bool

A derived class should return true for this function if it implements its own

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

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::divides_backbone_and_sidechain_energetics() const –> bool

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy, id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

evaluate xyz derivatives (and not DOF derivatives)

for a particular atom.

C++: core::scoring::methods::MMTorsionEnergy::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.methods.MMTorsionEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, : pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

C++: core::scoring::methods::MMTorsionEnergy::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.MMTorsionEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None

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

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

Evaluate the intra-residue energy for a given residue using the data held within the

ResSingleMinimizationData object. This function should be invoked only on derived instances of this class if they return “true” in a call to their use_extended_intrares_energy_interface method. This base class provides a noop implementation for classes that do not implement this interface, or that do not define intrares energies.

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

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

Evaluate the DOF derivative for a particular residue. The Pose merely serves as context,

and the input residue is not required to be a member of the Pose.

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

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

Evaluate the derivatives for all atoms on rsd1 and rsd2 with respect

to each other and increment the derivatives in atom-derivatives vector1s. The calling function must guarantee that the r1_atom_derivs vector1 holds at least as many entries as there are atoms in rsd1, and that the r2_atom_derivs vector1 holds at least as many entries as there are atoms in rsd2.

C++: core::scoring::methods::TwoBodyEnergy::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.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, energy_vector: pyrosetta.rosetta.utility.vector1_float) → 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_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.methods.ShortRangeTwoBodyEnergy, set1: pyrosetta.rosetta.core.conformation.RotamerSetBase, set2: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector, energy_table: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) → None

Batch computation of rotamer pair energies. Need not be overriden in

derived class – by default, iterates over all pairs of rotamers, and calls derived class’s residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, total_energy: core::scoring::EMapVector) → None

called by the ScoreFunction at the end of energy evaluation.

The derived class has the opportunity to accumulate a score into the pose’s total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

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

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.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

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

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy, : pyrosetta.rosetta.utility.vector1_bool) → None

MMTorsionEnergy is context independent; indicates that no

context graphs are required

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

method_type(self: pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

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

minimize_in_whole_structure_context(self: pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy, : pyrosetta.rosetta.core.pose.Pose) → bool

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

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

residue_pair_energy(self: pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::methods::MMTorsionEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResPairMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the two-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those two body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residues in a call to setup_for_minimizing_for_residue_pair before this function is invoked. This function should not be called unless the use_extended_residue_pair_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit().

C++: core::scoring::methods::TwoBodyEnergy::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.methods.MMTorsionEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

setup for derivatives

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

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

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

C++: core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &, class basic::datacache::BasicDataCache &) const –> void

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

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

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

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) → None

Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache, res_data_cache: core::scoring::ResSingleMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, res1_data_cache: core::scoring::ResSingleMinimizationData, res2_data_cache: core::scoring::ResSingleMinimizationData, data_cache: core::scoring::ResPairMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.MMTorsionEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

setup for packing

C++: core::scoring::methods::MMTorsionEnergy::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.methods.MMTorsionEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

setup for scoring

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

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue (who is still guaranteed to be

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

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

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

Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

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

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

show additional information of the energy method

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

sidechain_sidechain_energy(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the sidechain of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, : core::pose::Pose, resid: int) → None

If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

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

Derived classes wishing to invoke the alternate, extended interface for eval_intrares_energy

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

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

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

Rely on the extended version of the residue_pair_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResPairMinimizationData in which the derived base class has (or should have) cached a piece of data that will make residue-pair energy evaluation faster than its absense (e.g. a neighbor list). Derived energy methods should return ‘true’ from this function to use the extended interface. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::TwoBodyEnergy::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.methods.MMTorsionEnergyCreator

Bases: EnergyMethodCreator

assign(self: pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergyCreator) → pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergyCreator

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

create_energy_method(self: pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

Instantiate a new MMTorsionEnergy

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

class pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy

Bases: ContextIndependentOneBodyEnergy

assign(self: pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy, : pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy) → pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy

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

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.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers 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_pairwise_energies()

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

C++: core::scoring::methods::EnergyMethod::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

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

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

defines_dof_derivatives(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, 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::OneBodyEnergy::defines_dof_derivatives(const class core::pose::Pose &) const –> bool

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_score_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue) → bool

During minimization, energy methods are allowed to decide that they say nothing

about a particular residue (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default behavior is to return “true” for all residues.

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

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Evaluate the XYZ derivative for an atom in the pose.

Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom’s XYZ derivative

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) “Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations” Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

C++: core::scoring::methods::EnergyMethod::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_dof_derivative(self: pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy, dof_id: pyrosetta.rosetta.core.id.DOF_ID, tor_id: pyrosetta.rosetta.core.id.TorsionID, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector) → float

C++: core::scoring::methods::NMerPSSMEnergy::eval_dof_derivative(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_derivatives(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

Evaluate the derivatives for all atoms on this residue and increment them

into the input atom_derivs vector1. The calling function must guarantee that setup for derivatives is called before this function is, and that the atom_derivs vector contains at least as many entries as there are atoms in the input Residue. This base class provides a default noop implementation of this function.

C++: core::scoring::methods::OneBodyEnergy::eval_residue_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_residue_dof_derivative(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, 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::OneBodyEnergy::eval_residue_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

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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, total_energy: core::scoring::EMapVector) → None

called by the ScoreFunction at the end of energy evaluation.

The derived class has the opportunity to accumulate a score into the pose’s total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

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

gate_pssm_scores(self: pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy, : bool) → None

set minimum value for low scoring nmers?

C++: core::scoring::methods::NMerPSSMEnergy::gate_pssm_scores(const bool) –> void

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.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

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

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy, : pyrosetta.rosetta.utility.vector1_bool) → None

DunbrackEnergy is context independent; indicates that no

context graphs are required

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

method_type(self: pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

Returns the ci_1b element of the EnergyMethodType enumeration; this

method should NOT be overridden by derived classes.

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

minimize_in_whole_structure_context(self: pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy, : pyrosetta.rosetta.core.pose.Pose) → bool

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

n_pssms(self: pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy) → int

return the number of total pssms loaded

C++: core::scoring::methods::NMerPSSMEnergy::n_pssms() const –> unsigned long

nmer_length(self: pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy, : int) → None

define length N of NMer polymer subsequence to calculate (must match pssm)

C++: core::scoring::methods::NMerPSSMEnergy::nmer_length(const unsigned long) –> void

nmer_pssm_scorecut(self: pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy, : float) → None

nmer pssm scorecut gate for ignoring low scoring nmers

C++: core::scoring::methods::NMerPSSMEnergy::nmer_pssm_scorecut(const double) –> void

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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

pssm_energy_at_frame_seqpos(self: pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy, : int, : pyrosetta.rosetta.core.chemical.AA, : int) → float

return the pssm energy of a single pssm for one entry in the pssm matrix

C++: core::scoring::methods::NMerPSSMEnergy::pssm_energy_at_frame_seqpos(const unsigned long, const enum core::chemical::AA, const unsigned long) const –> double

read_nmer_pssm(self: pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy, : str) → None

read a pssm file and load it

C++: core::scoring::methods::NMerPSSMEnergy::read_nmer_pssm(std::string) –> void

read_nmer_pssm_fname_vector(self: pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy, : pyrosetta.rosetta.utility.vector1_std_string) → None

accept a vector of pssm filenames and load them

C++: core::scoring::methods::NMerPSSMEnergy::read_nmer_pssm_fname_vector(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

read_nmer_pssm_list(self: pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy, : str) → None

read a file containing a list of pssm filenames and load them

C++: core::scoring::methods::NMerPSSMEnergy::read_nmer_pssm_list(std::string) –> void

requires_a_setup_for_derivatives_for_residue_opportunity(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

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

requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

C++: core::scoring::methods::OneBodyEnergy::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

residue_energy(self: pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::methods::NMerPSSMEnergy::residue_energy(const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

residue_energy_ext(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, emap: core::scoring::EMapVector) → None

Evaluate the one-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those one body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to setup_for_minimizing_for_residue before this function is invoked. This function should not be called unless the use_extended_residue_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit(). The Pose merely serves as context, and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::OneBodyEnergy::residue_energy_ext(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, 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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction) → None

Called immediately before atom- and DOF-derivatives are calculated

allowing the derived class a chance to prepare for future calls.

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

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

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

C++: core::scoring::methods::OneBodyEnergy::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_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) → None

Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

C++: core::scoring::methods::EnergyMethod::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.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase, : pyrosetta.rosetta.basic.datacache.BasicDataCache, : core::scoring::ResSingleMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResSingleMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. The Pose merely serves as context, and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::OneBodyEnergy::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_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

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

before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None

if an energy method needs to cache something in the pose (e.g. in pose.energies()),

before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

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

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue, who is still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

C++: core::scoring::methods::OneBodyEnergy::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

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

update_residue_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, resid: int) → None

If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

use_extended_residue_energy_interface(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy) → bool

Rely on the extended version of the residue_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResSingleMinimizationData. Return ‘true’ for the extended version. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::OneBodyEnergy::use_extended_residue_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.methods.NMerPSSMEnergyCreator

Bases: EnergyMethodCreator

assign(self: pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergyCreator) → pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergyCreator

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

create_energy_method(self: pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

Instantiate a new NMerPSSMEnergy

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

class pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy

Bases: ContextIndependentOneBodyEnergy

assign(self: pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy, : pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy) → pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy

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

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.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers 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_pairwise_energies()

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

C++: core::scoring::methods::EnergyMethod::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

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

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

defines_dof_derivatives(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, 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::OneBodyEnergy::defines_dof_derivatives(const class core::pose::Pose &) const –> bool

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_score_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue) → bool

During minimization, energy methods are allowed to decide that they say nothing

about a particular residue (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default behavior is to return “true” for all residues.

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

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Evaluate the XYZ derivative for an atom in the pose.

Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom’s XYZ derivative

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) “Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations” Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

C++: core::scoring::methods::EnergyMethod::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_dof_derivative(self: pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy, dof_id: pyrosetta.rosetta.core.id.DOF_ID, tor_id: pyrosetta.rosetta.core.id.TorsionID, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector) → float

C++: core::scoring::methods::NMerRefEnergy::eval_dof_derivative(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_derivatives(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

Evaluate the derivatives for all atoms on this residue and increment them

into the input atom_derivs vector1. The calling function must guarantee that setup for derivatives is called before this function is, and that the atom_derivs vector contains at least as many entries as there are atoms in the input Residue. This base class provides a default noop implementation of this function.

C++: core::scoring::methods::OneBodyEnergy::eval_residue_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_residue_dof_derivative(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, 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::OneBodyEnergy::eval_residue_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

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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, total_energy: core::scoring::EMapVector) → None

called by the ScoreFunction at the end of energy evaluation.

The derived class has the opportunity to accumulate a score into the pose’s total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

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

get_residue_energy_by_table(self: pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy, : pyrosetta.rosetta.core.pose.Pose, : int, : float, : pyrosetta.rosetta.utility.vector1_double) → None

return the reference energy for a given reference list at a nmer frame sequence position

C++: core::scoring::methods::NMerRefEnergy::get_residue_energy_by_table(const class core::pose::Pose &, const unsigned long, double &, class utility::vector1<double, class std::allocator<double> > &) const –> void

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.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

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

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy, : pyrosetta.rosetta.utility.vector1_bool) → None

DunbrackEnergy is context independent; indicates that no

context graphs are required

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

initialize_from_options(self: pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy) → None

init all options from option flags

C++: core::scoring::methods::NMerRefEnergy::initialize_from_options() –> void

method_type(self: pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

Returns the ci_1b element of the EnergyMethodType enumeration; this

method should NOT be overridden by derived classes.

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

minimize_in_whole_structure_context(self: pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy, : pyrosetta.rosetta.core.pose.Pose) → bool

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

n_tables(self: pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy) → int

return number of tables currently loaded in memory

C++: core::scoring::methods::NMerRefEnergy::n_tables() const –> unsigned long

nmer_length(self: pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy, nmer_length: int) → None

C++: core::scoring::methods::NMerRefEnergy::nmer_length(const unsigned long) –> void

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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

read_nmer_fname_vector(self: pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy, : pyrosetta.rosetta.utility.vector1_std_string) → None

read reference energy lists from a vector of filenames

C++: core::scoring::methods::NMerRefEnergy::read_nmer_fname_vector(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

requires_a_setup_for_derivatives_for_residue_opportunity(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

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

requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

C++: core::scoring::methods::OneBodyEnergy::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

residue_energy(self: pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::methods::NMerRefEnergy::residue_energy(const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

residue_energy_ext(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, emap: core::scoring::EMapVector) → None

Evaluate the one-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those one body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to setup_for_minimizing_for_residue before this function is invoked. This function should not be called unless the use_extended_residue_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit(). The Pose merely serves as context, and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::OneBodyEnergy::residue_energy_ext(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, 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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction) → None

Called immediately before atom- and DOF-derivatives are calculated

allowing the derived class a chance to prepare for future calls.

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

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

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

C++: core::scoring::methods::OneBodyEnergy::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_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) → None

Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

C++: core::scoring::methods::EnergyMethod::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.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase, : pyrosetta.rosetta.basic.datacache.BasicDataCache, : core::scoring::ResSingleMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResSingleMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. The Pose merely serves as context, and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::OneBodyEnergy::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_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

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

before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None

if an energy method needs to cache something in the pose (e.g. in pose.energies()),

before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

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

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue, who is still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

C++: core::scoring::methods::OneBodyEnergy::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

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

update_residue_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, resid: int) → None

If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

use_extended_residue_energy_interface(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy) → bool

Rely on the extended version of the residue_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResSingleMinimizationData. Return ‘true’ for the extended version. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::OneBodyEnergy::use_extended_residue_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.methods.NMerRefEnergyCreator

Bases: EnergyMethodCreator

assign(self: pyrosetta.rosetta.core.scoring.methods.NMerRefEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.NMerRefEnergyCreator) → pyrosetta.rosetta.core.scoring.methods.NMerRefEnergyCreator

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

create_energy_method(self: pyrosetta.rosetta.core.scoring.methods.NMerRefEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

Instantiate a new NMerRefEnergy

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

class pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy

Bases: ContextIndependentOneBodyEnergy

add_encoded_termini(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : str, : int, : pyrosetta.rosetta.utility.vector1_double) → None

C++: core::scoring::methods::NMerSVMEnergy::add_encoded_termini(const std::string &, const unsigned long, class utility::vector1<double, class std::allocator<double> > &) const –> void

add_pssm_features(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : str, : int, : pyrosetta.rosetta.utility.vector1_double) → None

C++: core::scoring::methods::NMerSVMEnergy::add_pssm_features(const std::string &, const unsigned long, class utility::vector1<double, class std::allocator<double> > &) const –> void

assign(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy) → pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy

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

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.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers 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_pairwise_energies()

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

C++: core::scoring::methods::EnergyMethod::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

avg_rank_as_energy(*args, **kwargs)

Overloaded function.

1. avg_rank_as_energy(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : bool) -> None

C++: core::scoring::methods::NMerSVMEnergy::avg_rank_as_energy(const bool) –> void

2. avg_rank_as_energy(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy) -> bool

C++: core::scoring::methods::NMerSVMEnergy::avg_rank_as_energy() const –> bool

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

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

defines_dof_derivatives(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, 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::OneBodyEnergy::defines_dof_derivatives(const class core::pose::Pose &) const –> bool

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_score_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue) → bool

During minimization, energy methods are allowed to decide that they say nothing

about a particular residue (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default behavior is to return “true” for all residues.

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

encode_aa_string(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : str) → pyrosetta.rosetta.utility.vector1_double

C++: core::scoring::methods::NMerSVMEnergy::encode_aa_string(const std::string &) const –> class utility::vector1<double, class std::allocator<double> >

encode_nmer(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : str, : int, : int) → pyrosetta.rosetta.utility.vector1_double

C++: core::scoring::methods::NMerSVMEnergy::encode_nmer(const std::string &, const unsigned long, const unsigned long) const –> class utility::vector1<double, class std::allocator<double> >

encode_wtd_avg_aa_string(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : str, : pyrosetta.rosetta.utility.vector1_double) → pyrosetta.rosetta.utility.vector1_double

C++: core::scoring::methods::NMerSVMEnergy::encode_wtd_avg_aa_string(const std::string &, const class utility::vector1<double, class std::allocator<double> > &) const –> class utility::vector1<double, class std::allocator<double> >

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Evaluate the XYZ derivative for an atom in the pose.

Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom’s XYZ derivative

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) “Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations” Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

C++: core::scoring::methods::EnergyMethod::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_dof_derivative(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, dof_id: pyrosetta.rosetta.core.id.DOF_ID, tor_id: pyrosetta.rosetta.core.id.TorsionID, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector) → float

C++: core::scoring::methods::NMerSVMEnergy::eval_dof_derivative(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_derivatives(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

Evaluate the derivatives for all atoms on this residue and increment them

into the input atom_derivs vector1. The calling function must guarantee that setup for derivatives is called before this function is, and that the atom_derivs vector contains at least as many entries as there are atoms in the input Residue. This base class provides a default noop implementation of this function.

C++: core::scoring::methods::OneBodyEnergy::eval_residue_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_residue_dof_derivative(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, 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::OneBodyEnergy::eval_residue_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

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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, total_energy: core::scoring::EMapVector) → None

called by the ScoreFunction at the end of energy evaluation.

The derived class has the opportunity to accumulate a score into the pose’s total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

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

gate_svm_scores(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : bool) → None

C++: core::scoring::methods::NMerSVMEnergy::gate_svm_scores(const bool) –> void

get_residue_energy_by_svm(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : pyrosetta.rosetta.core.pose.Pose, : int, : float, : float, : pyrosetta.rosetta.utility.vector1_double, : pyrosetta.rosetta.utility.vector1_double) → None

C++: core::scoring::methods::NMerSVMEnergy::get_residue_energy_by_svm(const class core::pose::Pose &, const unsigned long &, double &, double &, class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void

get_residue_energy_from_sequence(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : str, : int, : float, : float, : pyrosetta.rosetta.utility.vector1_double, : pyrosetta.rosetta.utility.vector1_double) → None

C++: core::scoring::methods::NMerSVMEnergy::get_residue_energy_from_sequence(const std::string &, const unsigned long &, double &, double &, class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void

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.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

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

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : pyrosetta.rosetta.utility.vector1_bool) → None

context independent; indicates that no

context graphs are required

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

method_type(self: pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

Returns the ci_1b element of the EnergyMethodType enumeration; this

method should NOT be overridden by derived classes.

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

minimize_in_whole_structure_context(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : pyrosetta.rosetta.core.pose.Pose) → bool

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

n_svms(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy) → int

C++: core::scoring::methods::NMerSVMEnergy::n_svms() const –> unsigned long

nmer_length(*args, **kwargs)

Overloaded function.

1. nmer_length(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : int) -> None

C++: core::scoring::methods::NMerSVMEnergy::nmer_length(const unsigned long) –> void

2. nmer_length(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy) -> int

C++: core::scoring::methods::NMerSVMEnergy::nmer_length() const –> unsigned long

nmer_svm_scorecut(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : float) → None

C++: core::scoring::methods::NMerSVMEnergy::nmer_svm_scorecut(const double) –> void

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::prepare_rotamers_for_packing(const class core::pose::Pose &, class core::conformation::RotamerSetBase &) const –> void

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

Provide the citation for this EnergyMethod

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

read_aa_encoding_matrix(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : str) → None

C++: core::scoring::methods::NMerSVMEnergy::read_aa_encoding_matrix(const std::string &) –> void

read_nmer_svm(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : str) → None

C++: core::scoring::methods::NMerSVMEnergy::read_nmer_svm(const std::string &) –> void

read_nmer_svm_fname_vector(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::scoring::methods::NMerSVMEnergy::read_nmer_svm_fname_vector(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

read_nmer_svm_list(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : str) → None

C++: core::scoring::methods::NMerSVMEnergy::read_nmer_svm_list(const std::string &) –> void

read_nmer_svm_rank(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : str) → None

C++: core::scoring::methods::NMerSVMEnergy::read_nmer_svm_rank(const std::string &) –> void

read_nmer_svm_rank_fname_vector(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::scoring::methods::NMerSVMEnergy::read_nmer_svm_rank_fname_vector(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

read_nmer_svm_rank_list(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : str) → None

C++: core::scoring::methods::NMerSVMEnergy::read_nmer_svm_rank_list(const std::string &) –> void

read_pssm_features(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : str) → None

C++: core::scoring::methods::NMerSVMEnergy::read_pssm_features(const std::string) –> void

requires_a_setup_for_derivatives_for_residue_opportunity(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

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

requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

C++: core::scoring::methods::OneBodyEnergy::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

residue_energy(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::methods::NMerSVMEnergy::residue_energy(const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

residue_energy_ext(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, emap: core::scoring::EMapVector) → None

Evaluate the one-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those one body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to setup_for_minimizing_for_residue before this function is invoked. This function should not be called unless the use_extended_residue_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit(). The Pose merely serves as context, and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::OneBodyEnergy::residue_energy_ext(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, 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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction) → None

Called immediately before atom- and DOF-derivatives are calculated

allowing the derived class a chance to prepare for future calls.

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

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

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

C++: core::scoring::methods::OneBodyEnergy::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_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) → None

Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

C++: core::scoring::methods::EnergyMethod::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.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase, : pyrosetta.rosetta.basic.datacache.BasicDataCache, : core::scoring::ResSingleMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResSingleMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. The Pose merely serves as context, and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::OneBodyEnergy::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_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

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

before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None

if an energy method needs to cache something in the pose (e.g. in pose.energies()),

before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

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

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue, who is still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

C++: core::scoring::methods::OneBodyEnergy::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

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

term_length(*args, **kwargs)

Overloaded function.

1. term_length(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : int) -> None

C++: core::scoring::methods::NMerSVMEnergy::term_length(const unsigned long) –> void

2. term_length(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy) -> int

C++: core::scoring::methods::NMerSVMEnergy::term_length() const –> unsigned long

update_residue_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, resid: int) → None

If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

use_extended_residue_energy_interface(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy) → bool

Rely on the extended version of the residue_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResSingleMinimizationData. Return ‘true’ for the extended version. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::OneBodyEnergy::use_extended_residue_energy_interface() const –> bool

use_pssm_features(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy, : bool) → None

C++: core::scoring::methods::NMerSVMEnergy::use_pssm_features(const bool) –> void

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.methods.NMerSVMEnergyCreator

Bases: EnergyMethodCreator

assign(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergyCreator) → pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergyCreator

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

create_energy_method(self: pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

Instantiate a new NMerSVMEnergy

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

class pyrosetta.rosetta.core.scoring.methods.NeighborListData

Bases: CacheableData

assign(self: pyrosetta.rosetta.core.scoring.methods.NeighborListData, : pyrosetta.rosetta.core.scoring.methods.NeighborListData) → pyrosetta.rosetta.core.scoring.methods.NeighborListData

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

clone(self: pyrosetta.rosetta.core.scoring.methods.NeighborListData) → pyrosetta.rosetta.basic.datacache.CacheableData

C++: core::scoring::methods::NeighborListData::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.basic.datacache.CacheableData

C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t

C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

nblist(*args, **kwargs)

Overloaded function.

1. nblist(self: pyrosetta.rosetta.core.scoring.methods.NeighborListData) -> pyrosetta.rosetta.core.scoring.NeighborList

C++: core::scoring::methods::NeighborListData::nblist() const –> class std::shared_ptr<class core::scoring::NeighborList>

2. nblist(self: pyrosetta.rosetta.core.scoring.methods.NeighborListData, nblist: pyrosetta.rosetta.core.scoring.NeighborList) -> None

C++: core::scoring::methods::NeighborListData::nblist(class std::shared_ptr<class core::scoring::NeighborList>) –> void

class pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy

Bases: EnergyMethod

assign(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, : pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy

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

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.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers 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_pairwise_energies()

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

C++: core::scoring::methods::EnergyMethod::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

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_dof_derivatives(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, 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::OneBodyEnergy::defines_dof_derivatives(const class core::pose::Pose &) const –> bool

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_score_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue) → bool

During minimization, energy methods are allowed to decide that they say nothing

about a particular residue (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default behavior is to return “true” for all residues.

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

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Evaluate the XYZ derivative for an atom in the pose.

Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom’s XYZ derivative

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) “Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations” Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

C++: core::scoring::methods::EnergyMethod::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_residue_derivatives(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

Evaluate the derivatives for all atoms on this residue and increment them

into the input atom_derivs vector1. The calling function must guarantee that setup for derivatives is called before this function is, and that the atom_derivs vector contains at least as many entries as there are atoms in the input Residue. This base class provides a default noop implementation of this function.

C++: core::scoring::methods::OneBodyEnergy::eval_residue_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_residue_dof_derivative(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, 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::OneBodyEnergy::eval_residue_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

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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, total_energy: core::scoring::EMapVector) → None

called by the ScoreFunction at the end of energy evaluation.

The derived class has the opportunity to accumulate a score into the pose’s total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

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

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.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

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

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, context_graphs_required: pyrosetta.rosetta.utility.vector1_bool) → None

Indicate in the context-graphs-required list which

context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed

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

method_type(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

Return one of the 7 kinds of energy methods that exist:

e.g. context-dependent-one-body vs whole-structure.

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

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

Should this EnergyMethod have score and derivative evaluation

evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that’s serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return “true” will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction’s traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return “true” cannot be included in RTMin.

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

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.OneBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

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

requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

C++: core::scoring::methods::OneBodyEnergy::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

residue_energy(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, emap: core::scoring::EMapVector) → None

Evaluate the one-body energies for a particular residue, in the context of a

given Pose, and increment those energies in the input Emap (do not overwrite them).

C++: core::scoring::methods::OneBodyEnergy::residue_energy(const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

residue_energy_ext(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, emap: core::scoring::EMapVector) → None

Evaluate the one-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those one body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to setup_for_minimizing_for_residue before this function is invoked. This function should not be called unless the use_extended_residue_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit(). The Pose merely serves as context, and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::OneBodyEnergy::residue_energy_ext(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, 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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction) → None

Called immediately before atom- and DOF-derivatives are calculated

allowing the derived class a chance to prepare for future calls.

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

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

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

C++: core::scoring::methods::OneBodyEnergy::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_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) → None

Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

C++: core::scoring::methods::EnergyMethod::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.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase, : pyrosetta.rosetta.basic.datacache.BasicDataCache, : core::scoring::ResSingleMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResSingleMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. The Pose merely serves as context, and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::OneBodyEnergy::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_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

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

before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None

if an energy method needs to cache something in the pose (e.g. in pose.energies()),

before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

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

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue, who is still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

C++: core::scoring::methods::OneBodyEnergy::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

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

update_residue_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, resid: int) → None

If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

use_extended_residue_energy_interface(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy) → bool

Rely on the extended version of the residue_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResSingleMinimizationData. Return ‘true’ for the extended version. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::OneBodyEnergy::use_extended_residue_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.methods.PyEnergyMethodRegistrator

Bases: pybind11_object

This class will register an instance of an EnergyMethodCreator (class T) with the ScoringManager. It will ensure that no energy method creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place

class pyrosetta.rosetta.core.scoring.methods.ResidueAtomOverlaps

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.scoring.methods.ResidueAtomOverlaps, : pyrosetta.rosetta.core.scoring.methods.ResidueAtomOverlaps) → pyrosetta.rosetta.core.scoring.methods.ResidueAtomOverlaps

C++: core::scoring::methods::ResidueAtomOverlaps::operator=(const struct core::scoring::methods::ResidueAtomOverlaps &) –> struct core::scoring::methods::ResidueAtomOverlaps &

property res1

property res1_ovl1_overlaps

property res1_ovl2_overlaps

property res2

property res2_ovu1_overlaps

class pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy

Bases: TwoBodyEnergy

assign(self: pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy, : pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy

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

atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy) → float

how far apart must two heavy atoms be to have a zero interaction energy?

If hydrogen atoms interact at the same range as heavy atoms, then this distance should build-in a 2 * max-bound-h-distance-cutoff buffer. There is an improper mixing here between run-time aquired chemical knowledge (max-bound-h-distance-cutoff) and compile time aquired scoring knowledge (max atom cutoff); this could be resolved by adding a boolean uses_hydrogen_interaction_distance() to the SRTBEnergy class along with a method of the ChemicalManager max_bound_h_distance_cutoff().

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::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.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers 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_pairwise_energies()

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

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

backbone of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the weighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

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

bump_energy_backbone(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None

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

bump_energy_full(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None

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

clone(self: pyrosetta.rosetta.core.scoring.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.methods.ShortRangeTwoBodyEnergy) → bool

A derived class should return true for this function if it implements its own

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

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::divides_backbone_and_sidechain_energetics() const –> bool

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Evaluate the XYZ derivative for an atom in the pose.

Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom’s XYZ derivative

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) “Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations” Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

Evaluate the derivative for the intra-residue component of this energy method

for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd.

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

Evaluate the intra-residue energy for a given residue using the data held within the

ResSingleMinimizationData object. This function should be invoked only on derived instances of this class if they return “true” in a call to their use_extended_intrares_energy_interface method. This base class provides a noop implementation for classes that do not implement this interface, or that do not define intrares energies.

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

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

Evaluate the DOF derivative for a particular residue. The Pose merely serves as context,

and the input residue is not required to be a member of the Pose.

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

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

Evaluate the derivatives for all atoms on rsd1 and rsd2 with respect

to each other and increment the derivatives in atom-derivatives vector1s. The calling function must guarantee that the r1_atom_derivs vector1 holds at least as many entries as there are atoms in rsd1, and that the r2_atom_derivs vector1 holds at least as many entries as there are atoms in rsd2.

C++: core::scoring::methods::TwoBodyEnergy::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.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, energy_vector: pyrosetta.rosetta.utility.vector1_float) → 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_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.methods.ShortRangeTwoBodyEnergy, set1: pyrosetta.rosetta.core.conformation.RotamerSetBase, set2: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector, energy_table: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) → None

Batch computation of rotamer pair energies. Need not be overriden in

derived class – by default, iterates over all pairs of rotamers, and calls derived class’s residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, total_energy: core::scoring::EMapVector) → None

called by the ScoreFunction at the end of energy evaluation.

The derived class has the opportunity to accumulate a score into the pose’s total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

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

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.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

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

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, context_graphs_required: pyrosetta.rosetta.utility.vector1_bool) → None

Indicate in the context-graphs-required list which

context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed

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

method_type(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

Return one of the 7 kinds of energy methods that exist:

e.g. context-dependent-one-body vs whole-structure.

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

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

Should this EnergyMethod have score and derivative evaluation

evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that’s serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return “true” will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction’s traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return “true” cannot be included in RTMin.

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

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Evaluate the interaction between a given residue pair

accumulating the unweighted energies in an EnergyMap

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResPairMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the two-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those two body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residues in a call to setup_for_minimizing_for_residue_pair before this function is invoked. This function should not be called unless the use_extended_residue_pair_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit().

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction) → None

Called immediately before atom- and DOF-derivatives are calculated

allowing the derived class a chance to prepare for future calls.

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

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

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

C++: core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &, class basic::datacache::BasicDataCache &) const –> void

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

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

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

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) → None

Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache, res_data_cache: core::scoring::ResSingleMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, res1_data_cache: core::scoring::ResSingleMinimizationData, res2_data_cache: core::scoring::ResSingleMinimizationData, data_cache: core::scoring::ResPairMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

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

before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None

if an energy method needs to cache something in the pose (e.g. in pose.energies()),

before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

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

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue (who is still guaranteed to be

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

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

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

Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

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

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

show additional information of the energy method

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

sidechain_sidechain_energy(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the sidechain of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, : core::pose::Pose, resid: int) → None

If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

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

Derived classes wishing to invoke the alternate, extended interface for eval_intrares_energy

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

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

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

Rely on the extended version of the residue_pair_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResPairMinimizationData in which the derived base class has (or should have) cached a piece of data that will make residue-pair energy evaluation faster than its absense (e.g. a neighbor list). Derived energy methods should return ‘true’ from this function to use the extended interface. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy

Bases: EnergyMethod

assign(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy

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

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.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers 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_pairwise_energies()

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

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

backbone of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the weighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

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

bump_energy_backbone(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None

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

bump_energy_full(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) → None

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

clone(self: pyrosetta.rosetta.core.scoring.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

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Evaluate the XYZ derivative for an atom in the pose.

Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom’s XYZ derivative

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) “Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations” Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

Evaluate the derivative for the intra-residue component of this energy method

for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd.

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

Evaluate the intra-residue energy for a given residue using the data held within the

ResSingleMinimizationData object. This function should be invoked only on derived instances of this class if they return “true” in a call to their use_extended_intrares_energy_interface method. This base class provides a noop implementation for classes that do not implement this interface, or that do not define intrares energies.

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

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

Evaluate the DOF derivative for a particular residue. The Pose merely serves as context,

and the input residue is not required to be a member of the Pose.

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

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

Evaluate the derivatives for all atoms on rsd1 and rsd2 with respect

to each other and increment the derivatives in atom-derivatives vector1s. The calling function must guarantee that the r1_atom_derivs vector1 holds at least as many entries as there are atoms in rsd1, and that the r2_atom_derivs vector1 holds at least as many entries as there are atoms in rsd2.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, residue: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector, energy_vector: pyrosetta.rosetta.utility.vector1_float) → None

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 rotamr

C++: core::scoring::methods::TwoBodyEnergy::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.TwoBodyEnergy, 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 rotamr

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

Batch computation of rotamer pair energies. Need not be overriden in

derived class – by default, iterates over all pairs of rotamers, and calls the derived class’s residue_pair_energy method.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, total_energy: core::scoring::EMapVector) → None

called by the ScoreFunction at the end of energy evaluation.

The derived class has the opportunity to accumulate a score into the pose’s total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

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

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.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

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

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, context_graphs_required: pyrosetta.rosetta.utility.vector1_bool) → None

Indicate in the context-graphs-required list which

context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed

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

method_type(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

Return one of the 7 kinds of energy methods that exist:

e.g. context-dependent-one-body vs whole-structure.

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

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

Should this EnergyMethod have score and derivative evaluation

evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that’s serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return “true” will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction’s traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return “true” cannot be included in RTMin.

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

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

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

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

Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false

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

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

Does this EnergyMethod require the opportunity to examine each residue pair before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

Evaluate the interaction between a given residue pair

accumulating the unweighted energies in an EnergyMap

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResPairMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the two-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those two body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residues in a call to setup_for_minimizing_for_residue_pair before this function is invoked. This function should not be called unless the use_extended_residue_pair_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit().

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction) → None

Called immediately before atom- and DOF-derivatives are calculated

allowing the derived class a chance to prepare for future calls.

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

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

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

C++: core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &, class basic::datacache::BasicDataCache &) const –> void

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

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

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

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) → None

Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

C++: core::scoring::methods::EnergyMethod::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.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache, res_data_cache: core::scoring::ResSingleMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, res1_data_cache: core::scoring::ResSingleMinimizationData, res2_data_cache: core::scoring::ResSingleMinimizationData, data_cache: core::scoring::ResPairMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

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

before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None

if an energy method needs to cache something in the pose (e.g. in pose.energies()),

before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

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

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue (who is still guaranteed to be

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

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

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

Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

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

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

show additional information of the energy method

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

sidechain_sidechain_energy(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the interaction between the sidechain of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::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.methods.EnergyMethod, : core::pose::Pose, resid: int) → None

If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

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

Derived classes wishing to invoke the alternate, extended interface for eval_intrares_energy

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

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

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

Rely on the extended version of the residue_pair_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResPairMinimizationData in which the derived base class has (or should have) cached a piece of data that will make residue-pair energy evaluation faster than its absense (e.g. a neighbor list). Derived energy methods should return ‘true’ from this function to use the extended interface. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::TwoBodyEnergy::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.methods.WholeStructureEnergy

Bases: EnergyMethod

Base class for EnergyMethods which are meaningful only on entire structures, for example, the Radius of Gyration. These EnergyMethods do all of their work in the “finalize_total_energy” section of score function evaluation.

assign(self: pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy, : pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy) → pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy

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

atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy) → float

how far apart must two heavy atoms be to have a zero interaction energy?

If hydrogen atoms interact at the same range as heavy atoms, then this distance should build-in a 2 * max-bound-h-distance-cutoff buffer. There is an improper mixing here between run-time aquired chemical knowledge (max-bound-h-distance-cutoff) and compile time aquired scoring knowledge (max atom cutoff); this could be resolved by adding a boolean uses_hydrogen_interaction_distance() to the SRTBEnergy class along with a method of the ChemicalManager max_bound_h_distance_cutoff().

This method allows the WholeStructureEnergy class to define which edges should be included in the EnergyGraph so that during the finalize() method the Energy class can iterate across the EnergyGraph. This iteration occurrs in the SecondaryStructureEnergy class, where the edges must span 12 angstroms between the centroids. Arguably, the SecondaryStructureEnergy class could use the TwelveANeighborGraph (a context graph) and not require that the EnergyGraph span such long distances.

C++: core::scoring::methods::WholeStructureEnergy::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.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers 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_pairwise_energies()

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

C++: core::scoring::methods::EnergyMethod::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

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

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Evaluate the XYZ derivative for an atom in the pose.

Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom’s XYZ derivative

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) “Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations” Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

C++: core::scoring::methods::EnergyMethod::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

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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, total_energy: core::scoring::EMapVector) → None

called by the ScoreFunction at the end of energy evaluation.

The derived class has the opportunity to accumulate a score into the pose’s total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

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

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.methods.EnergyMethod) → bool

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

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

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, context_graphs_required: pyrosetta.rosetta.utility.vector1_bool) → None

Indicate in the context-graphs-required list which

context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed

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

method_type(self: pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

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

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

Should this EnergyMethod have score and derivative evaluation

evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that’s serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return “true” will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction’s traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return “true” cannot be included in RTMin.

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

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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_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

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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction) → None

Called immediately before atom- and DOF-derivatives are calculated

allowing the derived class a chance to prepare for future calls.

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

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) → None

Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

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

setup_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

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

before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None

if an energy method needs to cache something in the pose (e.g. in pose.energies()),

before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

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

setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

Do any setup work before scoring, caching any slow-to-compute data that will be used during

energy evaluation inside of the input Residue object’s data cache. (The Residue on the whole is given as a constant reference, but non-constant access to its data cache is granted.)

C++: core::scoring::methods::EnergyMethod::setup_for_scoring_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class basic::datacache::BasicDataCache &) 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

update_residue_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, resid: int) → None

If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

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

pyrosetta.rosetta.core.scoring.methods.atoms_interact(rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, id1: pyrosetta.rosetta.core.id.AtomID, id2: pyrosetta.rosetta.core.id.AtomID, interaction_cutoff: float) → bool

C++: core::scoring::methods::atoms_interact(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::id::AtomID &, const class core::id::AtomID &, const double) –> bool

pyrosetta.rosetta.core.scoring.methods.create_long_range_energy_container(pose: pyrosetta.rosetta.core.pose.Pose, scoretype: pyrosetta.rosetta.core.scoring.ScoreType, lr_type: pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType) → None

Determines whether a long-range energies container exists in the pose energies object. If not,

creates a new one and appends the score type to it, if necessary.

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::methods::create_long_range_energy_container(class core::pose::Pose &, const enum core::scoring::ScoreType, const enum core::scoring::methods::LongRangeEnergyType) –> void

pyrosetta.rosetta.core.scoring.methods.determine_lo_and_hi_residues(pose: pyrosetta.rosetta.core.pose.Pose, rsd1: int, rsd2: int, res1_is_lo: bool, res2_is_lo: bool) → None

Given two residues that may or may not be connected, determine which of the two, if any,

is the lower one and which is the upper.

Inputs are rsd1 and rsd2; outputs are rsd1_is_lo and rsd2_is_lo. Both will be false if the residues aren’t connected (s.t. the C of one connected to some connection of the other).

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::methods::determine_lo_and_hi_residues(const class core::pose::Pose &, const unsigned long, const unsigned long, bool &, bool &) –> void

pyrosetta.rosetta.core.scoring.methods.find_cutpoint_variants(pose: pyrosetta.rosetta.core.pose.Pose, tree: pyrosetta.rosetta.core.kinematics.FoldTree, cutpoints: pyrosetta.rosetta.utility.vector1_int) → None

C++: core::scoring::methods::find_cutpoint_variants(const class core::pose::Pose &, const class core::kinematics::FoldTree &, class utility::vector1<int, class std::allocator<int> > &) –> void

pyrosetta.rosetta.core.scoring.methods.find_relevant_connections_onersd(pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, branch_connection: pyrosetta.rosetta.core.scoring.methods.ResidueAtomOverlaps) → None

C++: core::scoring::methods::find_relevant_connections_onersd(const class core::pose::Pose &, const unsigned long, struct core::scoring::methods::ResidueAtomOverlaps &) –> void

pyrosetta.rosetta.core.scoring.methods.get_lower_cutpoint_partner_for_upper(pose: pyrosetta.rosetta.core.pose.Pose, upper_res: int) → int

Instead of assuming cutpoint partner is simply res-1, find which residue connects via lower/upper.

C++: core::scoring::methods::get_lower_cutpoint_partner_for_upper(const class core::pose::Pose &, const unsigned long) –> unsigned long

pyrosetta.rosetta.core.scoring.methods.get_residue_weight_by_ss(ss: str) → float

C++: core::scoring::methods::get_residue_weight_by_ss(char) –> double

pyrosetta.rosetta.core.scoring.methods.get_upper_cutpoint_partner_for_lower(pose: pyrosetta.rosetta.core.pose.Pose, lower_res: int) → int

Instead of assuming cutpoint partner is simply cutpoint+1, find which residue connects via lower/upper.

C++: core::scoring::methods::get_upper_cutpoint_partner_for_lower(const class core::pose::Pose &, const unsigned long) –> unsigned long

pyrosetta.rosetta.core.scoring.methods.is_lower_cutpoint(residue: int, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: core::scoring::methods::is_lower_cutpoint(unsigned long, const class core::pose::Pose &) –> bool

pyrosetta.rosetta.core.scoring.methods.is_upper_cutpoint(residue: int, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: core::scoring::methods::is_upper_cutpoint(unsigned long, const class core::pose::Pose &) –> bool

pyrosetta.rosetta.core.scoring.methods.lower_upper_connected_across_cutpoint(lower_rsd: pyrosetta.rosetta.core.conformation.Residue, upper_rsd: pyrosetta.rosetta.core.conformation.Residue) → bool

helper function for looking at residue connections to get lower/upper partners

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

pyrosetta.rosetta.core.scoring.methods.residues_interact(rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, interaction_cutoff: float) → bool

C++: core::scoring::methods::residues_interact(const class core::conformation::Residue &, const class core::conformation::Residue &, const double) –> bool