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- builtins.object
-
- NVlookup
- rosetta.core.scoring.methods.ContextDependentOneBodyEnergy(rosetta.core.scoring.methods.OneBodyEnergy)
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- NVscore
- rosetta.core.scoring.methods.EnergyMethodCreator(builtins.object)
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- NVscoreCreator
class NVscore(rosetta.core.scoring.methods.ContextDependentOneBodyEnergy) |
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- Method resolution order:
- NVscore
- rosetta.core.scoring.methods.ContextDependentOneBodyEnergy
- rosetta.core.scoring.methods.OneBodyEnergy
- rosetta.core.scoring.methods.EnergyMethod
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.scoring.nv.NVscore) -> rosetta.core.scoring.methods.EnergyMethod
clone
- indicate_required_context_graphs(...) from builtins.PyCapsule
- indicate_required_context_graphs(self : rosetta.core.scoring.nv.NVscore, context_graphs_required : rosetta.utility.vector1_bool) -> NoneType
- neighbor_weight(...) from builtins.PyCapsule
- neighbor_weight(self : rosetta.core.scoring.nv.NVscore, distance : float) -> float
- residue_energy(...) from builtins.PyCapsule
- residue_energy(self : rosetta.core.scoring.nv.NVscore, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType
- setup_for_derivatives(...) from builtins.PyCapsule
- setup_for_derivatives(self : rosetta.core.scoring.nv.NVscore, pose : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction) -> NoneType
- setup_for_minimizing(...) from builtins.PyCapsule
- setup_for_minimizing(self : rosetta.core.scoring.nv.NVscore, pose : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction, : rosetta.core.kinematics.MinimizerMapBase) -> NoneType
- setup_for_packing(...) from builtins.PyCapsule
- setup_for_packing(self : rosetta.core.scoring.nv.NVscore, pose : rosetta.core.pose.Pose, : rosetta.utility.vector1_bool, : rosetta.utility.vector1_bool) -> NoneType
- setup_for_scoring(...) from builtins.PyCapsule
- setup_for_scoring(self : rosetta.core.scoring.nv.NVscore, pose : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction) -> NoneType
Methods inherited from rosetta.core.scoring.methods.ContextDependentOneBodyEnergy:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.scoring.methods.ContextDependentOneBodyEnergy, : rosetta.core.scoring.methods.ContextDependentOneBodyEnergy) -> rosetta.core.scoring.methods.ContextDependentOneBodyEnergy
- method_type(...) from builtins.PyCapsule
- method_type(rosetta.core.scoring.methods.ContextDependentOneBodyEnergy) -> rosetta.core.scoring.methods.EnergyMethodType
Returns the cd_1b element of the EnergyMethodType enumeration; this method
should NOT be overridden by derived classes.
Methods inherited from rosetta.core.scoring.methods.OneBodyEnergy:
- defines_dof_derivatives(...) from builtins.PyCapsule
- defines_dof_derivatives(self : rosetta.core.scoring.methods.OneBodyEnergy, p : 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.
- defines_score_for_residue(...) from builtins.PyCapsule
- defines_score_for_residue(self : rosetta.core.scoring.methods.OneBodyEnergy, : 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.
- eval_residue_derivatives(...) from builtins.PyCapsule
- eval_residue_derivatives(self : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue, min_data : core::scoring::ResSingleMinimizationData, pose : rosetta.core.pose.Pose, weights : rosetta.core.scoring.EMapVector, atom_derivs : rosetta.utility.vector1_core_scoring_DerivVectorPair) -> NoneType
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.
- eval_residue_dof_derivative(...) from builtins.PyCapsule
- eval_residue_dof_derivative(self : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue, min_data : core::scoring::ResSingleMinimizationData, dof_id : rosetta.core.id.DOF_ID, torsion_id : rosetta.core.id.TorsionID, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, weights : 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.
- requires_a_setup_for_derivatives_for_residue_opportunity(...) from builtins.PyCapsule
- requires_a_setup_for_derivatives_for_residue_opportunity(self : rosetta.core.scoring.methods.OneBodyEnergy, pose : 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.
- requires_a_setup_for_scoring_for_residue_opportunity(...) from builtins.PyCapsule
- requires_a_setup_for_scoring_for_residue_opportunity(self : rosetta.core.scoring.methods.OneBodyEnergy, pose : 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.
- residue_energy_ext(...) from builtins.PyCapsule
- residue_energy_ext(self : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue, min_data : core::scoring::ResSingleMinimizationData, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType
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.
- setup_for_derivatives_for_residue(...) from builtins.PyCapsule
- setup_for_derivatives_for_residue(self : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, min_data : core::scoring::ResSingleMinimizationData) -> NoneType
Do any setup work necessary before evaluating the derivatives for this residue
- setup_for_minimizing_for_residue(...) from builtins.PyCapsule
- setup_for_minimizing_for_residue(self : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue, : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction, : rosetta.core.kinematics.MinimizerMapBase, : core::scoring::ResSingleMinimizationData) -> NoneType
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.
- setup_for_scoring_for_residue(...) from builtins.PyCapsule
- setup_for_scoring_for_residue(self : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, min_data : core::scoring::ResSingleMinimizationData) -> NoneType
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
- use_extended_residue_energy_interface(...) from builtins.PyCapsule
- use_extended_residue_energy_interface(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'
Methods inherited from rosetta.core.scoring.methods.EnergyMethod:
- defines_high_order_terms(...) from builtins.PyCapsule
- defines_high_order_terms(self : rosetta.core.scoring.methods.EnergyMethod, : 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".
- eval_atom_derivative(...) from builtins.PyCapsule
- eval_atom_derivative(self : rosetta.core.scoring.methods.EnergyMethod, id : rosetta.core.id.AtomID, pose : rosetta.core.pose.Pose, domain_map : ObjexxFCL::FArray1D<int>, sfxn : rosetta.core.scoring.ScoreFunction, emap : rosetta.core.scoring.EMapVector, F1 : rosetta.numeric.xyzVector_double_t, F2 : rosetta.numeric.xyzVector_double_t) -> NoneType
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.
- finalize_after_derivatives(...) from builtins.PyCapsule
- finalize_after_derivatives(self : rosetta.core.scoring.methods.EnergyMethod, : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction) -> NoneType
called at the end of derivatives evaluation
- finalize_total_energy(...) from builtins.PyCapsule
- finalize_total_energy(self : rosetta.core.scoring.methods.EnergyMethod, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, total_energy : rosetta.core.scoring.EMapVector) -> NoneType
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.
- minimize_in_whole_structure_context(...) from builtins.PyCapsule
- minimize_in_whole_structure_context(self : rosetta.core.scoring.methods.EnergyMethod, : 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.
- prepare_rotamers_for_packing(...) from builtins.PyCapsule
- prepare_rotamers_for_packing(self : rosetta.core.scoring.methods.EnergyMethod, : rosetta.core.pose.Pose, : rosetta.core.conformation.RotamerSetBase) -> NoneType
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.
- score_types(...) from builtins.PyCapsule
- score_types(rosetta.core.scoring.methods.EnergyMethod) -> rosetta.utility.vector1_core_scoring_ScoreType
Returns the score types that this energy method computes.
- update_residue_for_packing(...) from builtins.PyCapsule
- update_residue_for_packing(self : rosetta.core.scoring.methods.EnergyMethod, : rosetta.core.pose.Pose, resid : int) -> NoneType
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.
- version(...) from builtins.PyCapsule
- version(rosetta.core.scoring.methods.EnergyMethod) -> int
Return the version of the energy method
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