custom_pair_distance

Bindings for core::scoring::custom_pair_distance namespace

class pyrosetta.rosetta.core.scoring.custom_pair_distance.AtomPairFuncList

Bases: pybind11_object

add_interaction(self: pyrosetta.rosetta.core.scoring.custom_pair_distance.AtomPairFuncList, interacting_pair: pyrosetta.rosetta.core.scoring.custom_pair_distance.atoms_and_func_struct) → None

C++: core::scoring::custom_pair_distance::AtomPairFuncList::add_interaction(const struct core::scoring::custom_pair_distance::atoms_and_func_struct &) –> void

assign(self: pyrosetta.rosetta.core.scoring.custom_pair_distance.AtomPairFuncList, : pyrosetta.rosetta.core.scoring.custom_pair_distance.AtomPairFuncList) → pyrosetta.rosetta.core.scoring.custom_pair_distance.AtomPairFuncList

C++: core::scoring::custom_pair_distance::AtomPairFuncList::operator=(const class core::scoring::custom_pair_distance::AtomPairFuncList &) –> class core::scoring::custom_pair_distance::AtomPairFuncList &

ats_n_func_list(self: pyrosetta.rosetta.core.scoring.custom_pair_distance.AtomPairFuncList) → pyrosetta.rosetta.std.list_core_scoring_custom_pair_distance_atoms_and_func_struct_t

C++: core::scoring::custom_pair_distance::AtomPairFuncList::ats_n_func_list() const –> const class std::list<struct core::scoring::custom_pair_distance::atoms_and_func_struct, class std::allocator<struct core::scoring::custom_pair_distance::atoms_and_func_struct> > &

class pyrosetta.rosetta.core.scoring.custom_pair_distance.DistanceFunc

Bases: Func

assign(self: pyrosetta.rosetta.core.scoring.custom_pair_distance.DistanceFunc, : pyrosetta.rosetta.core.scoring.custom_pair_distance.DistanceFunc) → pyrosetta.rosetta.core.scoring.custom_pair_distance.DistanceFunc

C++: core::scoring::custom_pair_distance::DistanceFunc::operator=(const class core::scoring::custom_pair_distance::DistanceFunc &) –> class core::scoring::custom_pair_distance::DistanceFunc &

clone(self: pyrosetta.rosetta.core.scoring.custom_pair_distance.DistanceFunc) → pyrosetta.rosetta.core.scoring.func.Func

C++: core::scoring::custom_pair_distance::DistanceFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.custom_pair_distance.DistanceFunc, : float) → float

C++: core::scoring::custom_pair_distance::DistanceFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)

Overloaded function.

1. estimate_dfunc(self: pyrosetta.rosetta.core.scoring.func.Func, r: float) -> float

Estimates the derivative of this function at a given radius by

calculating the slope of the secant line from func(r) and func(r+1e-05).

C++: core::scoring::func::Func::estimate_dfunc(const double) const –> double

2. estimate_dfunc(self: pyrosetta.rosetta.core.scoring.func.Func, r: float, h: float) -> float

Estimates the derivative of this function at a given radius by

calculating the slope of the secant line from func(r) and func(r+h).

C++: core::scoring::func::Func::estimate_dfunc(const double, const double) const –> double

func(self: pyrosetta.rosetta.core.scoring.custom_pair_distance.DistanceFunc, : float) → float

C++: core::scoring::custom_pair_distance::DistanceFunc::func(const double) const –> double

max_dis(self: pyrosetta.rosetta.core.scoring.custom_pair_distance.DistanceFunc) → float

C++: core::scoring::custom_pair_distance::DistanceFunc::max_dis() const –> double

min_dis(self: pyrosetta.rosetta.core.scoring.custom_pair_distance.DistanceFunc) → float

C++: core::scoring::custom_pair_distance::DistanceFunc::min_dis() const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.Func, : pyrosetta.rosetta.std.istream) → None

initialize this Func from the given std::istream.

C++: core::scoring::func::Func::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.custom_pair_distance.DistanceFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool

C++: core::scoring::custom_pair_distance::DistanceFunc::same_type_as_me(const class core::scoring::func::Func &) const –> bool

show(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream) → None

Prints out space-delimited columns for r, func, dfunc and

dfunc_est. The values for func, dfunc and dfunc_est are plotted as a function of r, which is varied from 2-20 in steps of 0.5. The value for dfunc_est is the estimated by the method estimate_dfunc( r ).

C++: core::scoring::func::Func::show(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream) → None

shows the definition of this function, usually the string type of

function and the parameters passed in to the constructor.

C++: core::scoring::func::Func::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

1. show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int

2. show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int, threshold: float) -> int

show some sort of stringified representation of the violations for

this constraint.

C++: core::scoring::func::Func::show_violations(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy

Bases: ContextIndependentTwoBodyEnergy

assign(self: pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy, : pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy) → pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy

C++: core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::operator=(const class core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy &) –> class core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy &

atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy) → float

C++: core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::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.custom_pair_distance.FullatomCustomPairDistanceEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

clone

C++: core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::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.custom_pair_distance.FullatomCustomPairDistanceEnergy, : pyrosetta.rosetta.core.scoring.EMapVector) → bool

C++: core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::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.custom_pair_distance.FullatomCustomPairDistanceEnergy, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, res_moving_wrt_eachother: bool) → bool

Returns true if there are atoms on residue 1 & 2 that have interactions defined between them,

and false otherwise. This avoids unnecessary calls to residue_pair_energy_ext during minimization between pairs of atoms that have no interactons

C++: core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::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.custom_pair_distance.FullatomCustomPairDistanceEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, : pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::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.custom_pair_distance.FullatomCustomPairDistanceEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, : pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, min_data: pyrosetta.rosetta.core.scoring.ResPairMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector, r1_atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair, r2_atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

Evaluate all f1/f2 derivative vector pairs for all interacting atoms

on the input residue pair.

C++: core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::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.custom_pair_distance.FullatomCustomPairDistanceEnergy, : pyrosetta.rosetta.utility.vector1_bool) → None

C++: core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::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.custom_pair_distance.FullatomCustomPairDistanceEnergy, : pyrosetta.rosetta.core.pose.Pose) → bool

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

Extract the cached std::list< atoms_and_func_struct > object from the ResPairMinimizationData

object that was stored for this particular residue pair in setup_for_minimizing_for_residue_pair, and use this cached list to evaluate the atom-pair interactions.

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

Find the list of atom-pair interactions from the pair_and_func_map_ for the given

residue-type pair and cache that list in the input ResPairMinimizationData object.

C++: core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::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.custom_pair_distance.FullatomCustomPairDistanceEnergy) → bool

Returns true. This class takes advantage of the opportunity to store sequence-specific data

in a ResiduePairMinimiazationObject listing the atom-pair interactions for a particular residue pair and to extract that data from cache for easy use inside residue_pair_energy_ext.

C++: core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::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.custom_pair_distance.FullatomCustomPairDistanceEnergyCreator

Bases: EnergyMethodCreator

assign(self: pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergyCreator, : pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergyCreator) → pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergyCreator

C++: core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergyCreator::operator=(const class core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergyCreator &) –> class core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergyCreator &

create_energy_method(self: pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

Instantiate a new NVscore

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

class pyrosetta.rosetta.core.scoring.custom_pair_distance.PairFuncMap

Bases: pybind11_object

get_atom_pair_func_list(*args, **kwargs)

Overloaded function.

1. get_atom_pair_func_list(self: pyrosetta.rosetta.core.scoring.custom_pair_distance.PairFuncMap, rsdtype1: pyrosetta.rosetta.core.chemical.ResidueType, rsdtype2: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.core.scoring.custom_pair_distance.AtomPairFuncList

C++: core::scoring::custom_pair_distance::PairFuncMap::get_atom_pair_func_list(const class core::chemical::ResidueType &, const class core::chemical::ResidueType &) const –> class std::shared_ptr<class core::scoring::custom_pair_distance::AtomPairFuncList>

2. get_atom_pair_func_list(self: pyrosetta.rosetta.core.scoring.custom_pair_distance.PairFuncMap, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) -> pyrosetta.rosetta.core.scoring.custom_pair_distance.AtomPairFuncList

C++: core::scoring::custom_pair_distance::PairFuncMap::get_atom_pair_func_list(const class core::conformation::Residue &, const class core::conformation::Residue &) const –> class std::shared_ptr<const class core::scoring::custom_pair_distance::AtomPairFuncList>

restype_destruction_observer(self: pyrosetta.rosetta.core.scoring.custom_pair_distance.PairFuncMap, event: pyrosetta.rosetta.core.chemical.RestypeDestructionEvent) → None

C++: core::scoring::custom_pair_distance::PairFuncMap::restype_destruction_observer(const struct core::chemical::RestypeDestructionEvent &) –> void

set_atom_pair_func(self: pyrosetta.rosetta.core.scoring.custom_pair_distance.PairFuncMap, rsdtype1: pyrosetta.rosetta.core.chemical.ResidueType, rsdtype2: pyrosetta.rosetta.core.chemical.ResidueType, func_list: pyrosetta.rosetta.core.scoring.custom_pair_distance.AtomPairFuncList) → None

C++: core::scoring::custom_pair_distance::PairFuncMap::set_atom_pair_func(const class core::chemical::ResidueType &, const class core::chemical::ResidueType &, class std::shared_ptr<class core::scoring::custom_pair_distance::AtomPairFuncList>) –> void

size(self: pyrosetta.rosetta.core.scoring.custom_pair_distance.PairFuncMap) → int

C++: core::scoring::custom_pair_distance::PairFuncMap::size() const –> unsigned long

class pyrosetta.rosetta.core.scoring.custom_pair_distance.atoms_and_func_struct

Bases: pybind11_object

property func_

property resA_atom_index_

property resB_atom_index_

class pyrosetta.rosetta.core.scoring.custom_pair_distance.resatom_and_func_struct

Bases: pybind11_object

property atom_index_

property func_

property res_index_