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

#include <SequenceDependentRefEnergy.hh>

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List of all members.

Public Types

typedef
ContextIndependentOneBodyEnergy 
parent

Public Member Functions

 SequenceDependentRefEnergy ()
 SequenceDependentRefEnergy (utility::vector1< utility::vector1< Real > > const &aa_seq_weights_in)
virtual ~SequenceDependentRefEnergy ()
virtual EnergyMethodOP clone () 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).
bool minimize_in_whole_structure_context (pose::Pose const &) const
 Should this EnergyMethod have score and derivative evaluation evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that's serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return "true" will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction's traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return "true" cannot be included in RTMin.
virtual Real eval_dof_derivative (id::DOF_ID const &dof_id, id::TorsionID const &tor_id, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights) const
virtual void indicate_required_context_graphs (utility::vector1< bool > &) const
 DunbrackEnergy is context independent; indicates that no context graphs are required.

Member Typedef Documentation


Constructor & Destructor Documentation

core::scoring::methods::SequenceDependentRefEnergy::SequenceDependentRefEnergy ( )

Referenced by clone().

core::scoring::methods::SequenceDependentRefEnergy::SequenceDependentRefEnergy ( utility::vector1< utility::vector1< Real > > const &  aa_seq_weights_in)
core::scoring::methods::SequenceDependentRefEnergy::~SequenceDependentRefEnergy ( ) [virtual]

Member Function Documentation

EnergyMethodOP core::scoring::methods::SequenceDependentRefEnergy::clone ( ) const [virtual]
Real core::scoring::methods::SequenceDependentRefEnergy::eval_dof_derivative ( id::DOF_ID const &  dof_id,
id::TorsionID const &  tor_id,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap const &  weights 
) const [virtual]
void core::scoring::methods::SequenceDependentRefEnergy::indicate_required_context_graphs ( utility::vector1< bool > &  ) const [virtual]

DunbrackEnergy is context independent; indicates that no context graphs are required.

SequenceDependentRefEnergy is context independent; indicates that no context graphs are required.

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

bool core::scoring::methods::SequenceDependentRefEnergy::minimize_in_whole_structure_context ( pose::Pose const &  ) const [inline, virtual]

Should this EnergyMethod have score and derivative evaluation evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that's serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return "true" will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction's traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return "true" cannot be included in RTMin.

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

void core::scoring::methods::SequenceDependentRefEnergy::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::ContextIndependentOneBodyEnergy.

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


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