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Rosetta 3.4
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Rosetta 3.4
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#include <SmoothEnvEnergy.hh>
Public Types | |
| typedef ContextDependentOneBodyEnergy | parent |
Public Member Functions | |
| SmoothEnvEnergy () | |
| c-tor | |
| virtual EnergyMethodOP | clone () const |
| clone | |
| virtual void | setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const |
| virtual void | residue_energy (conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const |
| 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 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 void | finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &) const |
| 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. | |
| virtual void | indicate_required_context_graphs (utility::vector1< bool > &) const |
| Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed. | |
Reimplemented from core::scoring::methods::ContextDependentOneBodyEnergy.
| core::scoring::methods::SmoothEnvEnergy::SmoothEnvEnergy | ( | ) |
c-tor
Referenced by clone().
| EnergyMethodOP core::scoring::methods::SmoothEnvEnergy::clone | ( | ) | const [virtual] |
| void core::scoring::methods::SmoothEnvEnergy::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 from core::scoring::methods::OneBodyEnergy.
References core::conformation::Residue::aa(), core::conformation::Residue::atom(), core::scoring::cen_pair_smooth, core::scoring::cenpack_smooth, core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::nbr_atom(), core::chemical::num_canonical_aas, and protocols::kinmatch::xyz().
| void core::scoring::methods::SmoothEnvEnergy::finalize_total_energy | ( | pose::Pose & | pose, |
| ScoreFunction const & | sfxn, | ||
| EnergyMap & | total_energy | ||
| ) | const [virtual] |
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.
called at the end of energy evaluation
Reimplemented from core::scoring::methods::EnergyMethod.
References core::scoring::SmoothEnvPairPotential::finalize().
| virtual void core::scoring::methods::SmoothEnvEnergy::indicate_required_context_graphs | ( | utility::vector1< bool > & | context_graphs_required | ) | const [inline, virtual] |
Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.
Implements core::scoring::methods::EnergyMethod.
| void core::scoring::methods::SmoothEnvEnergy::residue_energy | ( | conformation::Residue const & | rsd, |
| 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 increment those energies in the input Emap (do not overwrite them).
Implements core::scoring::methods::ContextDependentOneBodyEnergy.
References core::conformation::Residue::aa(), core::scoring::cbeta_smooth, core::scoring::cen_env_smooth, core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_scores(), core::conformation::Residue::has_variant_type(), and core::chemical::num_canonical_aas.
| void core::scoring::methods::SmoothEnvEnergy::setup_for_scoring | ( | pose::Pose & | pose, |
| ScoreFunction const & | |||
| ) | const [virtual] |
Reimplemented from core::scoring::methods::EnergyMethod.
References core::scoring::SmoothEnvPairPotential::compute_centroid_environment(), and core::pose::Pose::update_residue_neighbors().
1.7.4
