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

#include <SmoothCenPairEnergy.hh>

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List of all members.

Public Types

typedef
ContextIndependentTwoBodyEnergy 
parent

Public Member Functions

 SmoothCenPairEnergy ()
 c-tor
virtual EnergyMethodOP clone () const
 clone
virtual void setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const
virtual void residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &, ScoreFunction const &, EnergyMap &emap) const
 Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap.
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 eval_residue_pair_derivatives (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &, ResSingleMinimizationData const &, ResPairMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const
 Evaluate the derivative for an atom in rsd1 with respect to rsd2 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 ResPairMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. DEPRECATED. Too slow. Too much overhead for each atom; slowed fast-relax runs by ~40%.
virtual bool defines_intrares_energy (EnergyMap const &) const
 This method *should* admit to defining intraresidue energies.
void eval_intrares_energy (conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const
 Evaluate the intra-residue energy for a given residue.
virtual Distance atomic_interaction_cutoff () const
 SmoothCenPairEnergy distance cutoff.
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.

Member Typedef Documentation


Constructor & Destructor Documentation

core::scoring::methods::SmoothCenPairEnergy::SmoothCenPairEnergy ( )

c-tor

Referenced by clone().


Member Function Documentation

Distance core::scoring::methods::SmoothCenPairEnergy::atomic_interaction_cutoff ( ) const [virtual]
EnergyMethodOP core::scoring::methods::SmoothCenPairEnergy::clone ( ) const [virtual]
virtual bool core::scoring::methods::SmoothCenPairEnergy::defines_intrares_energy ( EnergyMap const &  ) const [inline, virtual]

This method *should* admit to defining intraresidue energies.

Implements core::scoring::methods::TwoBodyEnergy.

void core::scoring::methods::SmoothCenPairEnergy::eval_intrares_energy ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [inline, virtual]

Evaluate the intra-residue energy for a given residue.

Implements core::scoring::methods::TwoBodyEnergy.

void core::scoring::methods::SmoothCenPairEnergy::eval_residue_pair_derivatives ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
ResSingleMinimizationData const &  ,
ResSingleMinimizationData const &  ,
ResPairMinimizationData const &  min_data,
pose::Pose const &  pose,
EnergyMap const &  weights,
utility::vector1< DerivVectorPair > &  r1_atom_derivs,
utility::vector1< DerivVectorPair > &  r2_atom_derivs 
) const [virtual]

Evaluate the derivative for an atom in rsd1 with respect to rsd2 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 ResPairMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. DEPRECATED. Too slow. Too much overhead for each atom; slowed fast-relax runs by ~40%.

Evaluate the derivatives for all atoms on rsd1 and rsd2 with respect to each other and increment the derivatives in atom-derivatives vector1s. The calling function must guarantee that the r1_atom_derivs vector1 holds at least as many entries as there are atoms in rsd1, and that the r2_atom_derivs vector1 holds at least as many entries as there are atoms in rsd2.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

References core::conformation::Residue::aa(), core::conformation::Residue::atom(), core::scoring::cen_pair_smooth, core::scoring::cenpack_smooth, core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::nbr_atom(), core::chemical::num_canonical_aas, protocols::kinmatch::xyz(), and core::conformation::Atom::xyz().

void core::scoring::methods::SmoothCenPairEnergy::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::SmoothCenPairEnergy::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::SmoothCenPairEnergy::residue_pair_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]
void core::scoring::methods::SmoothCenPairEnergy::setup_for_scoring ( pose::Pose pose,
ScoreFunction const &   
) const [virtual]

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