core::scoring::methods::PoissonBoltzmannEnergy Class Reference

#include <PoissonBoltzmannEnergy.hh>

Inheritance diagram for core::scoring::methods::PoissonBoltzmannEnergy:

Collaboration diagram for core::scoring::methods::PoissonBoltzmannEnergy:

List of all members.

Public Types
typedef ContextIndependentLRTwoBodyEnergy	parent
Public Member Functions
	PoissonBoltzmannEnergy ()
	ctor
virtual EnergyMethodOP	clone () const
	clone
methods::LongRangeEnergyType	long_range_type () const
virtual bool	defines_intrares_energy (EnergyMap const &) const
	Two body energies are able to define intra-residue energies, and to do so only in the presence of certain non-zero weights. The ScoreFunction will hand over its weight set as it asks whether the energy method defines an intraresidue energy or not.
virtual bool	defines_residue_pair_energy (pose::Pose const &pose, Size res1, Size res2) const
virtual void	setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const
Real	revamp_weight_by_burial (conformation::Residue const &rsd, pose::Pose const &pose) const
bool	residue_in_chains (conformation::Residue const &rsd, utility::vector1< Size > chains) const
virtual void	eval_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluate the intra-residue energy for a given residue.
virtual void	residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap.
virtual void	indicate_required_context_graphs (utility::vector1< bool > &) const
	PB Energy is context independent and thus indicates that no context graphs need to be maintained by class Energies.

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Member Typedef Documentation

typedef ContextIndependentLRTwoBodyEnergy core::scoring::methods::PoissonBoltzmannEnergy::parent

Reimplemented from core::scoring::methods::ContextIndependentLRTwoBodyEnergy.

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Constructor & Destructor Documentation

core::scoring::methods::PoissonBoltzmannEnergy::PoissonBoltzmannEnergy

(

)

ctor

References core::scoring::get_PB_potential(), and core::scoring::PoissonBoltzmannPotential::isLoaded().

Referenced by clone().

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Member Function Documentation

EnergyMethodOP core::scoring::methods::PoissonBoltzmannEnergy::clone

(

)

const [virtual]

clone

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

References PoissonBoltzmannEnergy().

virtual bool core::scoring::methods::PoissonBoltzmannEnergy::defines_intrares_energy

(

EnergyMap const &

weights

)

const [inline, virtual]

Two body energies are able to define intra-residue energies, and to do so only in the presence of certain non-zero weights. The ScoreFunction will hand over its weight set as it asks whether the energy method defines an intraresidue energy or not.

For example, the Etable method defines intra-residue energies only when one or more of the fa_intra_{atr,rep,sol} weights are non-zero.

Implements core::scoring::methods::TwoBodyEnergy.

bool core::scoring::methods::PoissonBoltzmannEnergy::defines_residue_pair_energy	(	pose::Pose const &	pose,
		Size	res1,
		Size	res2
	)		const [virtual]

void PoissonBoltzmannEnergy::residue_energy( conformation::Residue const & rsd, pose::Pose const &, EnergyMap & emap ) const { Real PB_score_residue, PB_score_backbone, PB_score_sidechain; core::scoring::get_PB_potential().eval_PB_energy_residue( rsd, PB_score_residue, PB_score_backbone, PB_score_sidechain ); emap[ PB_elec ] += PB_score_sidechain; }

Implements core::scoring::methods::LongRangeTwoBodyEnergy.

void core::scoring::methods::PoissonBoltzmannEnergy::eval_intrares_energy	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap
	)		const [virtual]

Evaluate the intra-residue energy for a given residue.

Implements core::scoring::methods::TwoBodyEnergy.

void core::scoring::methods::PoissonBoltzmannEnergy::indicate_required_context_graphs

(

utility::vector1< bool > &

)

const [virtual]

PB Energy is context independent and thus indicates that no context graphs need to be maintained by class Energies.

Energy is context independent and thus indicates that no context graphs need to be maintained by class Energies.

virtual void residue_energy( conformation::Residue const & rsd, pose::Pose const & pose, EnergyMap & emap ) const;

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

methods::LongRangeEnergyType core::scoring::methods::PoissonBoltzmannEnergy::long_range_type

(

)

const [virtual]

Implements core::scoring::methods::LongRangeTwoBodyEnergy.

References core::scoring::methods::PB_elec_lr.

Referenced by setup_for_scoring().

bool core::scoring::methods::PoissonBoltzmannEnergy::residue_in_chains	(	conformation::Residue const &	rsd,
		utility::vector1< Size >	chains
	)		const

References core::conformation::Residue::chain().

Referenced by revamp_weight_by_burial().

void core::scoring::methods::PoissonBoltzmannEnergy::residue_pair_energy	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap
	)		const [virtual]

Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap.

Implements core::scoring::methods::TwoBodyEnergy.

References core::scoring::PoissonBoltzmannPotential::eval_PB_energy_residue(), core::scoring::get_PB_potential(), core::scoring::PB_elec, revamp_weight_by_burial(), and core::conformation::Residue::seqpos().

Real core::scoring::methods::PoissonBoltzmannEnergy::revamp_weight_by_burial	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose
	)		const

References core::kinematics::distance(), core::conformation::Residue::is_virtual(), core::conformation::Residue::is_virtual_residue(), core::conformation::Residue::last_backbone_atom(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), residue_in_chains(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by residue_pair_energy().

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

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

References core::pose::Pose::energies(), long_range_type(), core::scoring::PB_elec, core::pose::Pose::total_residue(), and core::scoring::methods::TR().

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

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