Rosetta 3.4
Public Types | Public Member Functions
core::scoring::methods::OneBodyEnergy Class Reference

#include <OneBodyEnergy.hh>

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List of all members.

Public Types

typedef EnergyMethod parent

Public Member Functions

 OneBodyEnergy (EnergyMethodCreatorOP)
 Constructor with an EnergyMethodCreator to inform the EnergyMethod parent which ScoreTypes this EnergyMethod is responsible for computing.
virtual ~OneBodyEnergy ()
virtual void residue_energy (conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const =0
 Evaluate the one-body energies for a particular residue, in the context of a given Pose, and increment those energies in the input Emap (do not overwrite them).
virtual bool defines_score_for_residue (conformation::Residue const &) const
 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.
virtual bool use_extended_residue_energy_interface () const
 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'.
virtual void residue_energy_ext (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap &emap) const
 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.
virtual void setup_for_minimizing_for_residue (conformation::Residue const &rsd, pose::Pose const &, ScoreFunction const &, kinematics::MinimizerMapBase const &, ResSingleMinimizationData &) const
 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.
virtual bool requires_a_setup_for_scoring_for_residue_opportunity (pose::Pose const &pose) const
 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.
virtual void setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data) const
 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.
virtual bool requires_a_setup_for_derivatives_for_residue_opportunity (pose::Pose const &pose) const
 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.
virtual void setup_for_derivatives_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data) const
 Do any setup work necessary before evaluating the derivatives for this residue.
virtual void eval_residue_derivatives (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &atom_derivs) const
 Evaluate the derivative for an atom in a residue in the context of a particular pose, and increment the F1 and F2 vectors. 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 Pose merely serves as context, and the input residue is not required to be a member of the Pose. DEPRECATED -- too slow.
virtual bool defines_dof_derivatives (pose::Pose const &p) const
 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.
virtual Real eval_residue_dof_derivative (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights) const
 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.

Member Typedef Documentation


Constructor & Destructor Documentation

core::scoring::methods::OneBodyEnergy::OneBodyEnergy ( EnergyMethodCreatorOP  creator)

Constructor with an EnergyMethodCreator to inform the EnergyMethod parent which ScoreTypes this EnergyMethod is responsible for computing.

core::scoring::methods::OneBodyEnergy::~OneBodyEnergy ( ) [virtual]

Member Function Documentation

bool core::scoring::methods::OneBodyEnergy::defines_dof_derivatives ( pose::Pose const &  p) const [virtual]

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.

Reimplemented in core::pack::dunbrack::DunbrackEnergy, core::scoring::methods::OmegaTetherEnergy, core::scoring::methods::P_AA_pp_Energy, core::scoring::methods::RamachandranEnergy, and core::scoring::methods::YHHPlanarityEnergy.

bool core::scoring::methods::OneBodyEnergy::defines_score_for_residue ( conformation::Residue const &  ) const [virtual]

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.

void core::scoring::methods::OneBodyEnergy::eval_residue_derivatives ( conformation::Residue const &  rsd,
ResSingleMinimizationData const &  min_data,
pose::Pose const &  pose,
EnergyMap const &  weights,
utility::vector1< DerivVectorPair > &  atom_derivs 
) const [virtual]

Evaluate the derivative for an atom in a residue in the context of a particular pose, and increment the F1 and F2 vectors. 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 Pose merely serves as context, and the input residue is not required to be a member of the Pose. DEPRECATED -- too slow.

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.

Reimplemented in core::scoring::methods::SmoothEnvEnergy.

Real core::scoring::methods::OneBodyEnergy::eval_residue_dof_derivative ( conformation::Residue const &  rsd,
ResSingleMinimizationData const &  min_data,
id::DOF_ID const &  dof_id,
id::TorsionID const &  torsion_id,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap const &  weights 
) const [virtual]

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.

Reimplemented in core::pack::dunbrack::DunbrackEnergy, core::scoring::methods::OmegaTetherEnergy, core::scoring::methods::P_AA_pp_Energy, core::scoring::methods::RamachandranEnergy, and core::scoring::methods::YHHPlanarityEnergy.

bool core::scoring::methods::OneBodyEnergy::requires_a_setup_for_derivatives_for_residue_opportunity ( pose::Pose const &  pose) const [virtual]

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.

bool core::scoring::methods::OneBodyEnergy::requires_a_setup_for_scoring_for_residue_opportunity ( pose::Pose const &  pose) const [virtual]

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.

virtual void core::scoring::methods::OneBodyEnergy::residue_energy ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
EnergyMap emap 
) const [pure virtual]

Evaluate the one-body energies for a particular residue, in the context of a given Pose, and increment those energies in the input Emap (do not overwrite them).

Implemented in core::pack::dunbrack::DunbrackEnergy, core::pack::interaction_graph::HPatchEnergy, core::pack::interaction_graph::SurfaceEnergy, core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy, core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody, core::scoring::methods::BurialEnergy, core::scoring::methods::ContextDependentOneBodyEnergy, core::scoring::methods::ContextIndependentOneBodyEnergy, core::scoring::methods::EnvEnergy, core::scoring::methods::EnvSmoothEnergy, core::scoring::methods::Fa_MbenvEnergy, core::scoring::methods::MembraneCbetaEnergy, core::scoring::methods::MembraneEnvEnergy, core::scoring::methods::MembraneEnvSmoothEnergy, core::scoring::methods::OmegaTetherEnergy, core::scoring::methods::P_AA_Energy, core::scoring::methods::P_AA_pp_Energy, core::scoring::methods::pHEnergy, core::scoring::methods::PyContextIndependentOneBodyEnergy, core::scoring::methods::RamachandranEnergy, core::scoring::methods::ReferenceEnergy, core::scoring::methods::SequenceDependentRefEnergy, core::scoring::methods::SmoothEnvEnergy, core::scoring::methods::SymmetricLigandEnergy, core::scoring::methods::UnfoldedStateEnergy, core::scoring::methods::WaterAdductIntraEnergy, core::scoring::methods::YHHPlanarityEnergy, core::scoring::nv::NVscore, core::scoring::rna::RNA_BulgeEnergy, core::scoring::rna::RNA_FullAtomVDW_BasePhosphate, core::scoring::rna::RNA_SugarCloseEnergy, protocols::fldsgn::potentials::AACompositionEnergy, protocols::scoring::methods::InterchainEnvEnergy, and protocols::scoring::methods::SpecialRotamerEnergy.

void core::scoring::methods::OneBodyEnergy::residue_energy_ext ( conformation::Residue const &  rsd,
ResSingleMinimizationData const &  min_data,
pose::Pose const &  pose,
EnergyMap emap 
) const [virtual]

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.

void core::scoring::methods::OneBodyEnergy::setup_for_derivatives_for_residue ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
ResSingleMinimizationData min_data 
) const [virtual]

Do any setup work necessary before evaluating the derivatives for this residue.

void core::scoring::methods::OneBodyEnergy::setup_for_minimizing_for_residue ( conformation::Residue const &  rsd,
pose::Pose const &  ,
ScoreFunction const &  ,
kinematics::MinimizerMapBase const &  ,
ResSingleMinimizationData  
) const [virtual]

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.

void core::scoring::methods::OneBodyEnergy::setup_for_scoring_for_residue ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
ResSingleMinimizationData min_data 
) const [virtual]

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.

bool core::scoring::methods::OneBodyEnergy::use_extended_residue_energy_interface ( ) const [virtual]

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'.


The documentation for this class was generated from the following files:
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