scoring¶
Bindings for protocols::membrane::scoring namespace
- class pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy¶
Bases:
ContextDependentOneBodyEnergy
Fullatom Membrane Environment Energy
- assign(self: pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy, : pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy) pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy ¶
C++: protocols::membrane::scoring::FaWaterToBilayerEnergy::operator=(const class protocols::membrane::scoring::FaWaterToBilayerEnergy &) –> class protocols::membrane::scoring::FaWaterToBilayerEnergy &
- atomistic_energy(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, atmno: int, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) None ¶
- Evaluate the (one body) energy associated with a particular atom
This may be a “self” energy, or it may be the single atom contribution from a whole structure term. NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_energies()
This is return-by-reference in the EnergyMap - Implementations should accumulate, not replace.
C++: core::scoring::methods::EnergyMethod::atomistic_energy(unsigned long, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void
- atomistic_pair_energy(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) None ¶
- Evaluate the energy for a particular pair of atoms
This function may be fed the same residue with different atom numbers NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_pairwise_energies()
This is return-by-reference in the EnergyMap - Implementations should accumulate, not replace.
C++: core::scoring::methods::EnergyMethod::atomistic_pair_energy(unsigned long, const class core::conformation::Residue &, unsigned long, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void
- clone(self: pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy) pyrosetta.rosetta.core.scoring.methods.EnergyMethod ¶
Clone Energy Method
C++: protocols::membrane::scoring::FaWaterToBilayerEnergy::clone() const –> class std::shared_ptr<class core::scoring::methods::EnergyMethod>
- defines_dof_derivatives(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, p: core::pose::Pose) bool ¶
- Use the dof_derivative interface for this energy method when
calculating derivatives? It is possible to define both dof_derivatives and atom-derivatives; they are not mutually exclusive.
C++: core::scoring::methods::OneBodyEnergy::defines_dof_derivatives(const class core::pose::Pose &) const –> bool
- defines_high_order_terms(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose) bool ¶
- Should this EnergyMethod have score and derivative evaluation
evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta’s get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns “false”.
C++: core::scoring::methods::EnergyMethod::defines_high_order_terms(const class core::pose::Pose &) const –> bool
- defines_score_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue) bool ¶
- During minimization, energy methods are allowed to decide that they say nothing
about a particular residue (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default behavior is to return “true” for all residues.
C++: core::scoring::methods::OneBodyEnergy::defines_score_for_residue(const class core::conformation::Residue &) const –> bool
- eval_atom_derivative(self: pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy, id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) None ¶
Evaluate Per-Atom Derivatives
C++: protocols::membrane::scoring::FaWaterToBilayerEnergy::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_fa_wtbe(self: pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy, p: protocols::membrane::scoring::MEnvAtomParams) float ¶
Evaluate Per-Atom Env term
C++: protocols::membrane::scoring::FaWaterToBilayerEnergy::eval_fa_wtbe(const class protocols::membrane::scoring::MEnvAtomParams &) const –> double
- eval_residue_derivatives(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) None ¶
- Evaluate the derivatives for all atoms on this residue and increment them
into the input atom_derivs vector1. The calling function must guarantee that setup for derivatives is called before this function is, and that the atom_derivs vector contains at least as many entries as there are atoms in the input Residue. This base class provides a default noop implementation of this function.
C++: core::scoring::methods::OneBodyEnergy::eval_residue_derivatives(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, const class core::scoring::EMapVector &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &) const –> void
- eval_residue_dof_derivative(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, dof_id: pyrosetta.rosetta.core.id.DOF_ID, torsion_id: core::id::TorsionID, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector) float ¶
- Evaluate the DOF derivative for a particular residue. The Pose merely serves as context,
and the input residue is not required to be a member of the Pose.
C++: core::scoring::methods::OneBodyEnergy::eval_residue_dof_derivative(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::id::DOF_ID &, const class core::id::TorsionID &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &) const –> double
- finalize_after_derivatives(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) None ¶
called at the end of derivatives evaluation
C++: core::scoring::methods::EnergyMethod::finalize_after_derivatives(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void
- finalize_after_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose) None ¶
- Called after minimization, allowing a derived class to do some
teardown steps.
Base class function does nothing. Derived classes may override.
Vikram K. Mulligan (vmullig.edu).
C++: core::scoring::methods::EnergyMethod::finalize_after_minimizing(class core::pose::Pose &) const –> void
- finalize_total_energy(self: pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None ¶
Fianlzie Total Per-Residue Energies
C++: protocols::membrane::scoring::FaWaterToBilayerEnergy::finalize_total_energy(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void
- get_menv_params_for_residue(self: pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy, pose: pyrosetta.rosetta.core.pose.Pose, rsd: pyrosetta.rosetta.core.conformation.Residue, atomno: int) protocols::membrane::scoring::MEnvAtomParams ¶
C++: protocols::membrane::scoring::FaWaterToBilayerEnergy::get_menv_params_for_residue(const class core::pose::Pose &, const class core::conformation::Residue &, unsigned long) const –> class std::shared_ptr<const class protocols::membrane::scoring::MEnvAtomParams>
- 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.protocols.membrane.scoring.FaWaterToBilayerEnergy, : pyrosetta.rosetta.utility.vector1_bool) None ¶
Fa_MbenvEnergy is context independent
C++: protocols::membrane::scoring::FaWaterToBilayerEnergy::indicate_required_context_graphs(class utility::vector1<bool, class std::allocator<bool> > &) const –> void
- method_type(self: pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy) pyrosetta.rosetta.core.scoring.methods.EnergyMethodType ¶
- Returns the cd_1b element of the EnergyMethodType enumeration; this method
should NOT be overridden by derived classes.
C++: core::scoring::methods::ContextDependentOneBodyEnergy::method_type() const –> enum core::scoring::methods::EnergyMethodType
- minimize_in_whole_structure_context(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose) bool ¶
- Should this EnergyMethod have score and derivative evaluation
evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that’s serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return “true” will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction’s traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return “true” cannot be included in RTMin.
C++: core::scoring::methods::EnergyMethod::minimize_in_whole_structure_context(const class core::pose::Pose &) const –> bool
- prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) None ¶
- If an energy method needs to cache data in a packing::RotamerSet object before
rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.
C++: core::scoring::methods::EnergyMethod::prepare_rotamers_for_packing(const class core::pose::Pose &, class core::conformation::RotamerSetBase &) const –> void
- provide_citation_info(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by energy methods wishing to provide citation information.
C++: core::scoring::methods::EnergyMethod::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- requires_a_setup_for_derivatives_for_residue_opportunity(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, pose: core::pose::Pose) bool ¶
- Does this EnergyMethod require the opportunity to examine the residue before derivative evaluation begins? Not
all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.
C++: core::scoring::methods::OneBodyEnergy::requires_a_setup_for_derivatives_for_residue_opportunity(const class core::pose::Pose &) const –> bool
- requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, pose: core::pose::Pose) bool ¶
- Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not
all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.
C++: core::scoring::methods::OneBodyEnergy::requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(const class core::pose::Pose &) const –> bool
- requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose) bool ¶
- Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not
all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false
C++: core::scoring::methods::EnergyMethod::requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(const class core::pose::Pose &) const –> bool
- residue_energy(self: pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.core.scoring.EMapVector) None ¶
Compute Per-Residue Energies
C++: protocols::membrane::scoring::FaWaterToBilayerEnergy::residue_energy(const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void
- residue_energy_ext(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, emap: core::scoring::EMapVector) None ¶
- Evaluate the one-body energies for a particular residue, in the context of a
given Pose, and with the help of a piece of cached data for minimization, increment those one body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to setup_for_minimizing_for_residue before this function is invoked. This function should not be called unless the use_extended_residue_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit(). The Pose merely serves as context, and the input residue is not required to be a member of the Pose.
C++: core::scoring::methods::OneBodyEnergy::residue_energy_ext(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void
- score_types(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType ¶
Returns the score types that this energy method computes.
C++: core::scoring::methods::EnergyMethod::score_types() const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &
- setup_for_derivatives(self: pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
Setup for Computing Derivatives
C++: protocols::membrane::scoring::FaWaterToBilayerEnergy::setup_for_derivatives(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void
- setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) None ¶
Do any setup work necessary before evaluating the derivatives for this residue
C++: core::scoring::methods::OneBodyEnergy::setup_for_derivatives_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &, class basic::datacache::BasicDataCache &) const –> void
- setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) None ¶
- Called at the beginning of atom tree minimization, this method
allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.
C++: core::scoring::methods::EnergyMethod::setup_for_minimizing(class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &) const –> void
- setup_for_minimizing_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase, : pyrosetta.rosetta.basic.datacache.BasicDataCache, : core::scoring::ResSingleMinimizationData) None ¶
- Called at the beginning of minimization, allowing this energy method to cache data
pertinent for a single residue in the the ResSingleMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. The Pose merely serves as context, and the input residue is not required to be a member of the Pose.
C++: core::scoring::methods::OneBodyEnergy::setup_for_minimizing_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &, class basic::datacache::BasicDataCache &, class core::scoring::ResSingleMinimizationData &) const –> void
- setup_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) None ¶
- if an energy method needs to cache data in the Energies object,
before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.
C++: core::scoring::methods::EnergyMethod::setup_for_packing(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> void
- setup_for_packing_with_rotsets(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose, rotsets: core::pack_basic::RotamerSetsBase, sfxn: core::scoring::ScoreFunction) None ¶
- if an energy method needs to cache data in the Energies object,
before packing begins and requires access to the RotamerSets object, then it does so during this function. The default behavior is to do nothing.
- The exact order of events when setting up for packing are as follows:
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.protocols.membrane.scoring.FaWaterToBilayerEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
Setup Method for initial scoring
C++: protocols::membrane::scoring::FaWaterToBilayerEnergy::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.OneBodyEnergy, 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.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None
- Do any setup work should the coordinates of this residue, who is still guaranteed to be
of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed
C++: core::scoring::methods::OneBodyEnergy::setup_for_scoring_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &) const –> void
- show_additional_info(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.std.ostream, : core::pose::Pose, : bool) None ¶
show additional information of the energy method
C++: core::scoring::methods::EnergyMethod::show_additional_info(std::ostream &, class core::pose::Pose &, bool) const –> void
- update_residue_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, resid: int) None ¶
- If the pose changes in the middle of a packing (as happens in rotamer trials) and if
an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.
C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void
- use_extended_residue_energy_interface(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy) bool ¶
- Rely on the extended version of the residue_energy function during score-function
evaluation in minimization? The extended version (below) takes a ResSingleMinimizationData. Return ‘true’ for the extended version. The default method implemented in this class returns ‘false’
C++: core::scoring::methods::OneBodyEnergy::use_extended_residue_energy_interface() const –> bool
- version(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) int ¶
Return the version of the energy method
C++: core::scoring::methods::EnergyMethod::version() const –> unsigned long
- class pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergyCreator¶
Bases:
EnergyMethodCreator
Creator Class for Membrane CBeta Energy Method
- assign(self: pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergyCreator, : pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergyCreator) pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergyCreator ¶
C++: protocols::membrane::scoring::FaWaterToBilayerEnergyCreator::operator=(const class protocols::membrane::scoring::FaWaterToBilayerEnergyCreator &) –> class protocols::membrane::scoring::FaWaterToBilayerEnergyCreator &
- create_energy_method(self: pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) pyrosetta.rosetta.core.scoring.methods.EnergyMethod ¶
Instantiate a new MPEnvEnergy
C++: protocols::membrane::scoring::FaWaterToBilayerEnergyCreator::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.protocols.membrane.scoring.FaWaterToBilayerEnergyCreator) pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType ¶
Return MPEnv Score Type Claimed by this energy method
C++: protocols::membrane::scoring::FaWaterToBilayerEnergyCreator::score_types_for_method() const –> class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> >
- class pyrosetta.rosetta.protocols.membrane.scoring.MEnvAtomParams¶
Bases:
pybind11_object
A container for storing memrbane environemnt parameters and derivatives
- assign(self: pyrosetta.rosetta.protocols.membrane.scoring.MEnvAtomParams, : pyrosetta.rosetta.protocols.membrane.scoring.MEnvAtomParams) pyrosetta.rosetta.protocols.membrane.scoring.MEnvAtomParams ¶
C++: protocols::membrane::scoring::MEnvAtomParams::operator=(const class protocols::membrane::scoring::MEnvAtomParams &) –> class protocols::membrane::scoring::MEnvAtomParams &
- atom_type_name(self: pyrosetta.rosetta.protocols.membrane.scoring.MEnvAtomParams) str ¶
C++: protocols::membrane::scoring::MEnvAtomParams::atom_type_name() const –> std::string
- clone(self: pyrosetta.rosetta.protocols.membrane.scoring.MEnvAtomParams) pyrosetta.rosetta.protocols.membrane.scoring.MEnvAtomParams ¶
C++: protocols::membrane::scoring::MEnvAtomParams::clone() const –> class std::shared_ptr<class protocols::membrane::scoring::MEnvAtomParams>
- dGfreeB(self: pyrosetta.rosetta.protocols.membrane.scoring.MEnvAtomParams) float ¶
C++: protocols::membrane::scoring::MEnvAtomParams::dGfreeB() const –> double
- dGfreeW(self: pyrosetta.rosetta.protocols.membrane.scoring.MEnvAtomParams) float ¶
C++: protocols::membrane::scoring::MEnvAtomParams::dGfreeW() const –> double
- f1(self: pyrosetta.rosetta.protocols.membrane.scoring.MEnvAtomParams) pyrosetta.rosetta.numeric.xyzVector_double_t ¶
C++: protocols::membrane::scoring::MEnvAtomParams::f1() const –> class numeric::xyzVector<double>
- f2(self: pyrosetta.rosetta.protocols.membrane.scoring.MEnvAtomParams) pyrosetta.rosetta.numeric.xyzVector_double_t ¶
C++: protocols::membrane::scoring::MEnvAtomParams::f2() const –> class numeric::xyzVector<double>
- hydration(self: pyrosetta.rosetta.protocols.membrane.scoring.MEnvAtomParams) float ¶
C++: protocols::membrane::scoring::MEnvAtomParams::hydration() const –> double
- set_hydration(self: pyrosetta.rosetta.protocols.membrane.scoring.MEnvAtomParams, hyd: float) None ¶
C++: protocols::membrane::scoring::MEnvAtomParams::set_hydration(double) –> void