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- rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy(rosetta.core.scoring.methods.OneBodyEnergy)
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- SugarBackboneEnergy
- rosetta.core.scoring.methods.EnergyMethodCreator(builtins.object)
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- SugarBackboneEnergyCreator
class SugarBackboneEnergy(rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy) |
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This class makes use of the "CarboHydrate Intrinsic" (CHI) energy function developed by Woods Lab.
Carbohydrate phi angles are scored based on whether they are at alpha or beta linkages.
Psi angles are scored based on whether they are at ->2-axial, ->3-equatorial, or ->4-axial OR ->2-equatorial,
->3-axial, or ->4-equatorial linkages.
->6 linkages (with omega angles) are not scored.
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- Method resolution order:
- SugarBackboneEnergy
- rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy
- 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.methods.carbohydrates.SugarBackboneEnergy) -> rosetta.core.scoring.methods.EnergyMethod
- defines_dof_derivatives(...) from builtins.PyCapsule
- defines_dof_derivatives(self : rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy, : rosetta.core.pose.Pose) -> bool
Should the dof_derivative interface be used for this EnergyMethod when calculating derivatives?
true
- eval_residue_dof_derivative(...) from builtins.PyCapsule
- eval_residue_dof_derivative(self : rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy, rsd : rosetta.core.conformation.Residue, min_data : rosetta.core.scoring.ResSingleMinimizationData, dof_id : rosetta.core.id.DOF_ID, torsion_id : rosetta.core.id.TorsionID, pose : rosetta.core.pose.Pose, sf : rosetta.core.scoring.ScoreFunction, weights : rosetta.core.scoring.EMapVector) -> float
Evaluate the DoF derivative for a particular residue.
- indicate_required_context_graphs(...) from builtins.PyCapsule
- indicate_required_context_graphs(self : rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy, : rosetta.utility.vector1_bool) -> NoneType
Indicate in the context-graphs-required list which context-graphs this energy method requires that the
Pose maintains when doing neighbor evaluation.
not implemented for SugarBackboneEnergy
- minimize_in_whole_structure_context(...) from builtins.PyCapsule
- minimize_in_whole_structure_context(self : rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy, : rosetta.core.pose.Pose) -> bool
Should this EnergyMethod have score and derivative evaluation evaluated ONLY in the context of a whole
Pose?
false
- residue_energy(...) from builtins.PyCapsule
- residue_energy(self : rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType
Evaluate the one-body carbohydrate backbone energies for a particular residue, in the context of the
given Pose, and increment those energies in the input Emap.
Methods inherited from rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy, : rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy) -> rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy
- method_type(...) from builtins.PyCapsule
- method_type(rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy) -> rosetta.core.scoring.methods.EnergyMethodType
Returns the ci_1b element of the EnergyMethodType enumeration; this
method should NOT be overridden by derived classes.
Methods inherited from rosetta.core.scoring.methods.OneBodyEnergy:
- 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.
- 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.
- 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.
- setup_for_derivatives(...) from builtins.PyCapsule
- setup_for_derivatives(self : rosetta.core.scoring.methods.EnergyMethod, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
Called immediately before atom- and DOF-derivatives are calculated
allowing the derived class a chance to prepare for future calls.
- setup_for_minimizing(...) from builtins.PyCapsule
- setup_for_minimizing(self : rosetta.core.scoring.methods.EnergyMethod, : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction, : rosetta.core.kinematics.MinimizerMapBase) -> NoneType
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.
- setup_for_packing(...) from builtins.PyCapsule
- setup_for_packing(self : rosetta.core.scoring.methods.EnergyMethod, : rosetta.core.pose.Pose, : rosetta.utility.vector1_bool, : rosetta.utility.vector1_bool) -> NoneType
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.
- setup_for_scoring(...) from builtins.PyCapsule
- setup_for_scoring(self : rosetta.core.scoring.methods.EnergyMethod, : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction) -> NoneType
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.
- 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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