potentials

• sspot

Bindings for protocols::fldsgn::potentials namespace

class pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy) -> None
2. __init__(self: pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy, comp_constraint_aas: pyrosetta.rosetta.std.map_core_chemical_AA_std_pair_double_double_t) -> None
3. __init__(self: pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy, arg0: pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

assign(self: pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy, : pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy) → pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy

C++: protocols::fldsgn::potentials::AACompositionEnergy::operator=(const class protocols::fldsgn::potentials::AACompositionEnergy &) –> class protocols::fldsgn::potentials::AACompositionEnergy &

clone(self: pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

clone

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

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

Should this EnergyMethod have score and derivative evaluation

evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta’s get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns “false”.

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

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

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

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

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

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, domain_map: ObjexxFCL::FArray1D<int>, 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 the XYZ derivative for an atom in the pose.

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

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

C++: core::scoring::methods::EnergyMethod::eval_atom_derivative(const class core::id::AtomID &, const class core::pose::Pose &, const class ObjexxFCL::FArray1D<int> &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> void

eval_residue_derivatives(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.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: pyrosetta.rosetta.core.id.TorsionID, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.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, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.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_total_energy(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, total_energy: pyrosetta.rosetta.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

indicate_required_context_graphs(self: pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy, : pyrosetta.rosetta.utility.vector1_bool) → None

DunbrackEnergy is context independent; indicates that no

context graphs are required

C++: protocols::fldsgn::potentials::AACompositionEnergy::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, : pyrosetta.rosetta.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, : pyrosetta.rosetta.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

requires_a_setup_for_derivatives_for_residue_opportunity(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, pose: pyrosetta.rosetta.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: pyrosetta.rosetta.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: pyrosetta.rosetta.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.fldsgn.potentials.AACompositionEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: protocols::fldsgn::potentials::AACompositionEnergy::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: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.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> > &

set_comp_constraint_aa(self: pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy, comp_constraint_aas: pyrosetta.rosetta.std.map_core_chemical_AA_std_pair_double_double_t) → None

C++: protocols::fldsgn::potentials::AACompositionEnergy::set_comp_constraint_aa(const class std::map<enum core::chemical::AA, struct std::pair<double, double>, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, struct std::pair<double, double> > > > &) –> void

setup_for_derivatives(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

Called immediately before atom- and DOF-derivatives are calculated

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

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

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.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, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, : pyrosetta.rosetta.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, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, : pyrosetta.rosetta.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, : pyrosetta.rosetta.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_scoring(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

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

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

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

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

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

show additional information of the energy method

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

update_residue_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.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.protocols.fldsgn.potentials.AACompositionEnergy) → int

C++: protocols::fldsgn::potentials::AACompositionEnergy::version() const –> unsigned long