core::scoring::methods::MembraneEnvSmoothEnergy Class Reference

#include <MembraneEnvSmoothEnergy.hh>

Inheritance diagram for core::scoring::methods::MembraneEnvSmoothEnergy:

Collaboration diagram for core::scoring::methods::MembraneEnvSmoothEnergy:

List of all members.

Public Types
typedef ContextDependentOneBodyEnergy	parent
Public Member Functions
	MembraneEnvSmoothEnergy ()
virtual EnergyMethodOP	clone () const
	clone
virtual void	setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const
	computes dScore/dNumNeighbors for all residues for rapid use in later atom derivate calculations
virtual void	setup_for_derivatives (pose::Pose &pose, ScoreFunction const &sf) const
	causes a neighbor graph update
virtual void	residue_energy (conformation::Residue const &rsd, pose::Pose const &, EnergyMap &) const
	evaluates the one-body energy for a residue
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
	increments the F1 and F2 derivative vectors for an atom
Distance	atomic_interaction_cutoff () const
	unused by the MembraneEnvSmoothEnergy class, returns 0
virtual void	indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const
	Tells the scoring function to maintain the TwelveANeighborGraph.

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Member Typedef Documentation

typedef ContextDependentOneBodyEnergy core::scoring::methods::MembraneEnvSmoothEnergy::parent

Reimplemented from core::scoring::methods::ContextDependentOneBodyEnergy.

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Constructor & Destructor Documentation

core::scoring::methods::MembraneEnvSmoothEnergy::MembraneEnvSmoothEnergy

(

)

Referenced by clone().

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Member Function Documentation

Distance core::scoring::methods::MembraneEnvSmoothEnergy::atomic_interaction_cutoff

(

)

const

unused by the MembraneEnvSmoothEnergy class, returns 0

MembraneEnvSmoothEnergy distance cutoff.

EnergyMethodOP core::scoring::methods::MembraneEnvSmoothEnergy::clone

(

)

const [virtual]

clone

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

References MembraneEnvSmoothEnergy().

void core::scoring::methods::MembraneEnvSmoothEnergy::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]

increments the F1 and F2 derivative vectors for an atom

Special cases handled for when an atom is both the representative atom for an amino acid, and its nbr_atom.

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

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), core::id::AtomID::atomno(), core::pose::Pose::energies(), core::conformation::Residue::is_protein(), core::scoring::Menv_smooth, core::chemical::ResidueType::nbr_atom(), core::pose::Pose::residue(), core::id::AtomID::rsd(), core::conformation::Residue::seqpos(), core::scoring::Energies::twelveA_neighbor_graph(), and core::conformation::Residue::type().

void core::scoring::methods::MembraneEnvSmoothEnergy::indicate_required_context_graphs

(

utility::vector1< bool > &

context_graphs_required

)

const [virtual]

Tells the scoring function to maintain the TwelveANeighborGraph.

MembraneEnvSmoothEnergy.

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

References core::scoring::twelve_A_neighbor_graph.

void core::scoring::methods::MembraneEnvSmoothEnergy::residue_energy	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		EnergyMap &	emap
	)		const [virtual]

evaluates the one-body energy for a residue

counts the number of nbr atoms within a given radius of the for the input residue. Because the representative atom on the input residue may be in a different location than the representative atom on the same residue when scoring_begin() is called, these neighbor counts cannot be reused; therefore, scoring_begin does not keep neighbor counts.

Implements core::scoring::methods::ContextDependentOneBodyEnergy.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), core::pose::Pose::energies(), core::conformation::Residue::is_protein(), core::scoring::Menv_smooth, core::pose::Pose::residue(), core::conformation::Residue::seqpos(), core::scoring::Energies::twelveA_neighbor_graph(), and core::conformation::Atom::xyz().

void core::scoring::methods::MembraneEnvSmoothEnergy::setup_for_derivatives	(	pose::Pose &	pose,
		ScoreFunction const &	sf
	)		const [virtual]

causes a neighbor graph update

stores dScore/dNumNeighbors so that when neighbor atoms on adjacent residues move, their influence on the score of the surrounding residues is rapidly computed.

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

References core::pose::Pose::aa(), core::conformation::Residue::atom_index(), core::pose::Pose::energies(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::pose::Pose::update_residue_neighbors(), and core::conformation::Atom::xyz().

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

computes dScore/dNumNeighbors for all residues for rapid use in later atom derivate calculations

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

References core::pose::Pose::update_residue_neighbors().

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

• src/core/scoring/methods/MembraneEnvSmoothEnergy.hh
• src/core/scoring/methods/MembraneEnvSmoothEnergy.cc