Rosetta 3.4
Public Member Functions | Public Attributes
core::scoring::geometric_solvation::GeometricSolEnergy Class Reference

#include <GeometricSolEnergy.hh>

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List of all members.

Public Member Functions

 GeometricSolEnergy (methods::EnergyMethodOptions const &options)
 copy c-tor
 GeometricSolEnergy (GeometricSolEnergy const &src)
 copy c-tor
virtual methods::EnergyMethodOP clone () const
 clone
virtual void setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const
virtual void setup_for_derivatives (pose::Pose &pose, ScoreFunction const &) const
 Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls.
virtual void residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &, EnergyMap &emap) const
 Everything in here.
void eval_atom_derivative_intra_RNA (id::AtomID const &atom_id, pose::Pose const &pose, EnergyMap const &weights, Vector &F1, Vector &F2) const
virtual void eval_atom_derivative (id::AtomID const &atom_id, pose::Pose const &pose, kinematics::DomainMap const &, ScoreFunction const &, EnergyMap const &weights, Vector &F1, Vector &F2) const
 f1 and f2 are zeroed
Real eval_atom_energy (id::AtomID const &atom_id, pose::Pose const &pose) const
virtual bool defines_intrares_energy (EnergyMap const &weights) const
 Two body energies are able to define intra-residue energies, and to do so only in the presence of certain non-zero weights. The ScoreFunction will hand over its weight set as it asks whether the energy method defines an intraresidue energy or not.
virtual void eval_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &, EnergyMap &emap) const
 Evaluate the intra-residue energy for a given residue.
virtual Distance atomic_interaction_cutoff () const
 HACK! MAX_R defines the maximum donorH to acceptor distance.
virtual void indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const
 GeometricSolEnergy is context sensitive.

Public Attributes

 __pad0__:ContextDependentTwoBodyEnergy parent

Constructor & Destructor Documentation

core::scoring::geometric_solvation::GeometricSolEnergy::GeometricSolEnergy ( methods::EnergyMethodOptions const &  options)

copy c-tor

Referenced by clone().

core::scoring::geometric_solvation::GeometricSolEnergy::GeometricSolEnergy ( GeometricSolEnergy const &  src)

copy c-tor

copy ctor


Member Function Documentation

Distance core::scoring::geometric_solvation::GeometricSolEnergy::atomic_interaction_cutoff ( ) const [virtual]

HACK! MAX_R defines the maximum donorH to acceptor distance.

Note -- this is used in HBonds to add up backbone/backbone energies, while the residue_pair_energy does the sidechain stuff. For now make this an empty function, although it will come back into the game if we decide to speed up the packer.

Implements core::scoring::methods::ShortRangeTwoBodyEnergy.

References core::scoring::hbonds::MAX_R.

methods::EnergyMethodOP core::scoring::geometric_solvation::GeometricSolEnergy::clone ( ) const [virtual]
bool core::scoring::geometric_solvation::GeometricSolEnergy::defines_intrares_energy ( EnergyMap const &  weights) const [virtual]

Two body energies are able to define intra-residue energies, and to do so only in the presence of certain non-zero weights. The ScoreFunction will hand over its weight set as it asks whether the energy method defines an intraresidue energy or not.

For example, the Etable method defines intra-residue energies only when one or more of the fa_intra_{atr,rep,sol} weights are non-zero.

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

References core::scoring::geom_sol_intra_RNA.

void core::scoring::geometric_solvation::GeometricSolEnergy::eval_atom_derivative ( id::AtomID const &  atom_id,
pose::Pose const &  pose,
kinematics::DomainMap const &  ,
ScoreFunction const &  ,
EnergyMap const &  weights,
Vector F1,
Vector F2 
) const [virtual]
void core::scoring::geometric_solvation::GeometricSolEnergy::eval_atom_derivative_intra_RNA ( id::AtomID const &  atom_id,
pose::Pose const &  pose,
EnergyMap const &  weights,
Vector F1,
Vector F2 
) const
Real core::scoring::geometric_solvation::GeometricSolEnergy::eval_atom_energy ( id::AtomID const &  atom_id,
pose::Pose const &  pose 
) const
void core::scoring::geometric_solvation::GeometricSolEnergy::eval_intrares_energy ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]

Evaluate the intra-residue energy for a given residue.

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

References core::scoring::geom_sol_intra_RNA, and core::conformation::Residue::is_RNA().

void core::scoring::geometric_solvation::GeometricSolEnergy::indicate_required_context_graphs ( utility::vector1< bool > &  context_graphs_required) const [virtual]
void core::scoring::geometric_solvation::GeometricSolEnergy::residue_pair_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  ,
EnergyMap emap 
) const [virtual]

Everything in here.

This evaluates everything for now, but eventually may want to split this based on backbone/backbone vs. others, as is carried out in HBondEnergy.cc

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

References core::scoring::geom_sol, and core::conformation::Residue::seqpos().

void core::scoring::geometric_solvation::GeometricSolEnergy::setup_for_derivatives ( pose::Pose pose,
ScoreFunction const &  sfxn 
) const [virtual]

Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls.

default implementation noop

Reimplemented from core::scoring::methods::EnergyMethod.

References core::scoring::Energies::data(), core::pose::Pose::energies(), core::scoring::hbonds::fill_hbond_set(), core::scoring::EnergiesCacheableDataType::HBOND_SET, core::pose::Pose::total_residue(), and core::pose::Pose::update_residue_neighbors().

void core::scoring::geometric_solvation::GeometricSolEnergy::setup_for_scoring ( pose::Pose pose,
ScoreFunction const &   
) const [virtual]

Member Data Documentation


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