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

#include <RG_Energy_Fast.hh>

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List of all members.

Public Types

typedef WholeStructureEnergy parent

Public Member Functions

 RG_Energy_Fast ()
 Defines a center of mass based RG calculation that is O(n) rather than O(n^2).
virtual EnergyMethodOP clone () const
 clone
void finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) 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.
core::Real calculate_rg_score (pose::Pose const &pose) const
core::Real calculate_rg_score (pose::Pose const &pose, utility::vector1< bool > const &relevant_residues) const
virtual void setup_for_derivatives (pose::Pose &pose, ScoreFunction const &sf) const
 Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls.
virtual void eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &sfxn, EnergyMap const &weights, Vector &F1, Vector &F2) const
 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.
virtual core::Size version () const
 Return the version of the energy method.
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::RG_Energy_Fast::RG_Energy_Fast ( )

Defines a center of mass based RG calculation that is O(n) rather than O(n^2).

c-tor

Referenced by clone().


Member Function Documentation

core::Real core::scoring::methods::RG_Energy_Fast::calculate_rg_score ( pose::Pose const &  pose) const
core::Real core::scoring::methods::RG_Energy_Fast::calculate_rg_score ( pose::Pose const &  pose,
utility::vector1< bool > const &  relevant_residues 
) const
EnergyMethodOP core::scoring::methods::RG_Energy_Fast::clone ( ) const [virtual]
void core::scoring::methods::RG_Energy_Fast::eval_atom_derivative ( id::AtomID const &  id,
pose::Pose const &  pose,
kinematics::DomainMap const &  domain_map,
ScoreFunction const &  sfxn,
EnergyMap const &  emap,
Vector F1,
Vector F2 
) const [virtual]

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.

default implementation does not alter either the F1 or F2 vectors.

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

References core::scoring::methods::RG_MinData::com, core::conformation::Residue::nbr_atom(), core::scoring::methods::RG_MinData::nres_scored, core::pose::Pose::residue(), core::scoring::rg, core::scoring::methods::RG_MinData::rg, core::scoring::rna::X, and core::pose::Pose::xyz().

void core::scoring::methods::RG_Energy_Fast::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 calculate_rg_score(), core::scoring::rg, and RG().

void core::scoring::methods::RG_Energy_Fast::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::RG_Energy_Fast::setup_for_derivatives ( pose::Pose pose,
ScoreFunction const &  sfxn 
) const [virtual]
core::Size core::scoring::methods::RG_Energy_Fast::version ( ) const [virtual]

Return the version of the energy method.

Implements core::scoring::methods::EnergyMethod.


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