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

#include <Fa_MbenvEnergy.hh>

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List of all members.

Public Types

typedef
ContextDependentOneBodyEnergy 
parent

Public Member Functions

 Fa_MbenvEnergy (etable::MembEtable const &memb_etable_in)
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).
virtual void finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &emap) 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 setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) 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 &emap, 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 void indicate_required_context_graphs (utility::vector1< bool > &) const
 Fa_MbenvEnergy is context independent; indicates that no context graphs are required.
MembraneTopology const & MembraneTopology_from_pose (pose::Pose const &) const
Membrane_FAEmbed const & Membrane_FAEmbed_from_pose (pose::Pose const &) const
MembraneEmbed const & MembraneEmbed_from_pose (pose::Pose const &) const
void setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const

Member Typedef Documentation


Constructor & Destructor Documentation

core::scoring::methods::Fa_MbenvEnergy::Fa_MbenvEnergy ( etable::MembEtable const &  memb_etable_in)

Referenced by clone().


Member Function Documentation

EnergyMethodOP core::scoring::methods::Fa_MbenvEnergy::clone ( ) const [virtual]
void core::scoring::methods::Fa_MbenvEnergy::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::id::AtomID::atomno(), core::scoring::Membrane_FAEmbed::fa_proj_coord(), core::scoring::Membrane_FAEmbed::fa_proj_deriv(), Membrane_FAEmbed_from_pose(), MembraneEmbed_from_pose(), core::pose::Pose::residue(), and core::id::AtomID::rsd().

void core::scoring::methods::Fa_MbenvEnergy::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::fa_mbenv.

void core::scoring::methods::Fa_MbenvEnergy::indicate_required_context_graphs ( utility::vector1< bool > &  ) const [virtual]

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

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

Membrane_FAEmbed const & core::scoring::methods::Fa_MbenvEnergy::Membrane_FAEmbed_from_pose ( pose::Pose const &  pose) const

Pose must already contain a cenlist object or this method will fail.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_FAEMBED.

Referenced by eval_atom_derivative(), and residue_energy().

MembraneEmbed const & core::scoring::methods::Fa_MbenvEnergy::MembraneEmbed_from_pose ( pose::Pose const &  pose) const
MembraneTopology const & core::scoring::methods::Fa_MbenvEnergy::MembraneTopology_from_pose ( pose::Pose const &  pose) const
void core::scoring::methods::Fa_MbenvEnergy::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::ContextDependentOneBodyEnergy.

References core::conformation::Residue::atom(), core::scoring::fa_mbenv, core::scoring::Membrane_FAEmbed::fa_proj(), Membrane_FAEmbed_from_pose(), core::conformation::Residue::nheavyatoms(), and core::conformation::Residue::seqpos().

void core::scoring::methods::Fa_MbenvEnergy::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::fa_mbenv, and core::scoring::ScoreFunction::weights().

void core::scoring::methods::Fa_MbenvEnergy::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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