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

Base class for EnergyMethods which are meaningful only on entire structures, for example, the Radius of Gyration. These EnergyMethods do all of their work in the "finalize_total_energy" section of score function evaluation. More...

#include <WholeStructureEnergy.hh>

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List of all members.

Public Types

typedef EnergyMethod parent

Public Member Functions

 WholeStructureEnergy (EnergyMethodCreatorOP)
 Constructor with EnergyMethodCreator to list the ScoreTypes computed by this WholeStructureEnergy.
virtual ~WholeStructureEnergy ()
EnergyMethodType method_type () const
 Return one of the 7 kinds of energy methods that exist: e.g. context-dependent-one-body vs whole-structure.
virtual Distance atomic_interaction_cutoff () const
 how far apart must two heavy atoms be to have a zero interaction energy?

Detailed Description

Base class for EnergyMethods which are meaningful only on entire structures, for example, the Radius of Gyration. These EnergyMethods do all of their work in the "finalize_total_energy" section of score function evaluation.


Member Typedef Documentation


Constructor & Destructor Documentation

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

Constructor with EnergyMethodCreator to list the ScoreTypes computed by this WholeStructureEnergy.

virtual core::scoring::methods::WholeStructureEnergy::~WholeStructureEnergy ( ) [inline, virtual]

Member Function Documentation

virtual Distance core::scoring::methods::WholeStructureEnergy::atomic_interaction_cutoff ( ) const [inline, virtual]

how far apart must two heavy atoms be to have a zero interaction energy?

If hydrogen atoms interact at the same range as heavy atoms, then this distance should build-in a 2 * max-bound-h-distance-cutoff buffer. There is an improper mixing here between run-time aquired chemical knowledge (max-bound-h-distance-cutoff) and compile time aquired scoring knowledge (max atom cutoff); this could be resolved by adding a boolean uses_hydrogen_interaction_distance() to the SRTBEnergy class along with a method of the ChemicalManager max_bound_h_distance_cutoff().

This method allows the WholeStructureEnergy class to define which edges should be included in the EnergyGraph so that during the finalize() method the Energy class can iterate across the EnergyGraph. This iteration occurrs in the SecondaryStructureEnergy class, where the edges must span 12 angstroms between the centroids. Arguably, the SecondaryStructureEnergy class could use the TwelveANeighborGraph (a context graph) and not require that the EnergyGraph span such long distances.

Reimplemented in core::scoring::methods::SecondaryStructureEnergy, core::scoring::rna::RNA_BaseBaseEnergy, and protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy.

EnergyMethodType core::scoring::methods::WholeStructureEnergy::method_type ( ) const [virtual]

Return one of the 7 kinds of energy methods that exist: e.g. context-dependent-one-body vs whole-structure.

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

References core::scoring::methods::ws.


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