vdwaals¶
Bindings for core::scoring::vdwaals namespace
- class pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom¶
Bases:
pybind11_object
- atom_type(*args, **kwargs)¶
Overloaded function.
atom_type(self: pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom) -> int
C++: core::scoring::vdwaals::VDWAtom::atom_type() const –> int
atom_type(self: pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom, setting: int) -> None
C++: core::scoring::vdwaals::VDWAtom::atom_type(int) –> void
- is_hydrogen(*args, **kwargs)¶
Overloaded function.
is_hydrogen(self: pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom) -> bool
method required for the trie
C++: core::scoring::vdwaals::VDWAtom::is_hydrogen() const –> bool
is_hydrogen(self: pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom, setting: bool) -> None
setter
C++: core::scoring::vdwaals::VDWAtom::is_hydrogen(bool) –> void
- is_wat(*args, **kwargs)¶
Overloaded function.
is_wat(self: pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom) -> bool
hydrate/SPaDES protocol
C++: core::scoring::vdwaals::VDWAtom::is_wat() const –> bool
is_wat(self: pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom, setting: bool) -> None
hydrate/SPaDES protocol
C++: core::scoring::vdwaals::VDWAtom::is_wat(bool) –> void
- print(*args, **kwargs)¶
Overloaded function.
print(self: pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom) -> None
send a description of the atom to standard out
C++: core::scoring::vdwaals::VDWAtom::print() const –> void
print(self: pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom, os: pyrosetta.rosetta.std.ostream) -> None
send a description of the atom to an output stream
C++: core::scoring::vdwaals::VDWAtom::print(std::ostream &) const –> void
- xyz(*args, **kwargs)¶
Overloaded function.
xyz(self: pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom) -> pyrosetta.rosetta.numeric.xyzVector_double_t
C++: core::scoring::vdwaals::VDWAtom::xyz() const –> const class numeric::xyzVector<double> &
xyz(self: pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom, setting: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None
C++: core::scoring::vdwaals::VDWAtom::xyz(const class numeric::xyzVector<double> &) –> void
- class pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieCountPair1B¶
Bases:
TrieCountPairBase
- assign(self: pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieCountPair1B, : pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieCountPair1B) pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieCountPair1B ¶
C++: core::scoring::vdwaals::VDWTrieCountPair1B::operator=(const class core::scoring::vdwaals::VDWTrieCountPair1B &) –> class core::scoring::vdwaals::VDWTrieCountPair1B &
- class pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieEvaluator¶
Bases:
pybind11_object
- atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieEvaluator) float ¶
C++: core::scoring::vdwaals::VDWTrieEvaluator::atomic_interaction_cutoff() const –> double
- heavyatom_heavyatom_energy(self: pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieEvaluator, at1: pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom, at2: pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom, d2: float, : int) float ¶
C++: core::scoring::vdwaals::VDWTrieEvaluator::heavyatom_heavyatom_energy(const class core::scoring::vdwaals::VDWAtom &, const class core::scoring::vdwaals::VDWAtom &, double &, unsigned long &) const –> double
- heavyatom_hydrogenatom_energy(self: pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieEvaluator, at1: pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom, at2: pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom, : int, : pyrosetta.rosetta.core.scoring.trie.TrieVsTrieCachedDataContainerBase) float ¶
C++: core::scoring::vdwaals::VDWTrieEvaluator::heavyatom_hydrogenatom_energy(const class core::scoring::vdwaals::VDWAtom &, const class core::scoring::vdwaals::VDWAtom &, unsigned long &, const class core::scoring::trie::TrieVsTrieCachedDataContainerBase *const) const –> double
- hydrogen_interaction_cutoff2(self: pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieEvaluator) float ¶
C++: core::scoring::vdwaals::VDWTrieEvaluator::hydrogen_interaction_cutoff2() const –> double
- hydrogenatom_heavyatom_energy(self: pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieEvaluator, at1: pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom, at2: pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom, : int, : pyrosetta.rosetta.core.scoring.trie.TrieVsTrieCachedDataContainerBase) float ¶
C++: core::scoring::vdwaals::VDWTrieEvaluator::hydrogenatom_heavyatom_energy(const class core::scoring::vdwaals::VDWAtom &, const class core::scoring::vdwaals::VDWAtom &, unsigned long &, const class core::scoring::trie::TrieVsTrieCachedDataContainerBase *const) const –> double
- hydrogenatom_hydrogenatom_energy(self: pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieEvaluator, at1: pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom, at2: pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom, : int, : pyrosetta.rosetta.core.scoring.trie.TrieVsTrieCachedDataContainerBase) float ¶
C++: core::scoring::vdwaals::VDWTrieEvaluator::hydrogenatom_hydrogenatom_energy(const class core::scoring::vdwaals::VDWAtom &, const class core::scoring::vdwaals::VDWAtom &, unsigned long &, const class core::scoring::trie::TrieVsTrieCachedDataContainerBase *const) const –> double
- vdw_weight(self: pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieEvaluator) float ¶
C++: core::scoring::vdwaals::VDWTrieEvaluator::vdw_weight() const –> double
- weighted_atom_pair_energy(self: pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieEvaluator, at1: pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom, at2: pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom, d2: float) float ¶
C++: core::scoring::vdwaals::VDWTrieEvaluator::weighted_atom_pair_energy(const class core::scoring::vdwaals::VDWAtom &, const class core::scoring::vdwaals::VDWAtom &, double &) const –> double
- class pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy¶
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 &
- atom_pair_energy(self: pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy, at1: pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom, at2: pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom, d2: float) float ¶
inlined version of the atom-pair energy evaluation for use in the trie
C++: core::scoring::vdwaals::VDW_Energy::atom_pair_energy(const class core::scoring::vdwaals::VDWAtom &, const class core::scoring::vdwaals::VDWAtom &, double &) const –> double
- atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy) float ¶
C++: core::scoring::vdwaals::VDW_Energy::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.vdwaals.VDW_Energy) pyrosetta.rosetta.core.scoring.methods.EnergyMethod ¶
clone
C++: core::scoring::vdwaals::VDW_Energy::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.vdwaals.VDW_Energy, : pyrosetta.rosetta.core.scoring.EMapVector) bool ¶
C++: core::scoring::vdwaals::VDW_Energy::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.vdwaals.VDW_Energy, atom_id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, scorefxn: 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::vdwaals::VDW_Energy::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.vdwaals.VDW_Energy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, : pyrosetta.rosetta.core.scoring.EMapVector) None ¶
C++: core::scoring::vdwaals::VDW_Energy::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.vdwaals.VDW_Energy, 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 ¶
Trie related functions
C++: core::scoring::vdwaals::VDW_Energy::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.vdwaals.VDW_Energy, context_graphs_required: pyrosetta.rosetta.utility.vector1_bool) None ¶
C++: core::scoring::vdwaals::VDW_Energy::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.vdwaals.VDW_Energy, pose: pyrosetta.rosetta.core.pose.Pose, set: pyrosetta.rosetta.core.conformation.RotamerSetBase) None ¶
C++: core::scoring::vdwaals::VDW_Energy::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.vdwaals.VDW_Energy, 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::vdwaals::VDW_Energy::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.vdwaals.VDW_Energy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: core::scoring::vdwaals::VDW_Energy::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:
setup_for_packing() is called for all energy methods
rotamers are built
setup_for_packing_with_rotsets() is called for all energy methods
prepare_rotamers_for_packing() is called for all energy methods
The energy methods are asked to score all rotamers and rotamer pairs
Annealing
The pose is specifically non-const here so that energy methods can store data in it
: Used in ApproximateBuriedUnsatPenalty to pre-compute compatible rotamers
C++: core::scoring::methods::EnergyMethod::setup_for_packing_with_rotsets(class core::pose::Pose &, const class std::shared_ptr<class core::pack_basic::RotamerSetsBase> &, const class core::scoring::ScoreFunction &) const –> void
- setup_for_scoring(self: pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: core::scoring::vdwaals::VDW_Energy::setup_for_scoring(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void
- setup_for_scoring_for_residue(*args, **kwargs)¶
Overloaded function.
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
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.vdwaals.VDW_Energy) int ¶
C++: core::scoring::vdwaals::VDW_Energy::version() const –> unsigned long
- class pyrosetta.rosetta.core.scoring.vdwaals.VDW_EnergyCreator¶
Bases:
EnergyMethodCreator
- assign(self: pyrosetta.rosetta.core.scoring.vdwaals.VDW_EnergyCreator, : pyrosetta.rosetta.core.scoring.vdwaals.VDW_EnergyCreator) pyrosetta.rosetta.core.scoring.vdwaals.VDW_EnergyCreator ¶
C++: core::scoring::vdwaals::VDW_EnergyCreator::operator=(const class core::scoring::vdwaals::VDW_EnergyCreator &) –> class core::scoring::vdwaals::VDW_EnergyCreator &
- create_energy_method(self: pyrosetta.rosetta.core.scoring.vdwaals.VDW_EnergyCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) pyrosetta.rosetta.core.scoring.methods.EnergyMethod ¶
Instantiate a new VDW_Energy
C++: core::scoring::vdwaals::VDW_EnergyCreator::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.vdwaals.VDW_EnergyCreator) 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::vdwaals::VDW_EnergyCreator::score_types_for_method() const –> class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> >