core::scoring::methods::CenHBEnergy Class Reference

#include <CenHBEnergy.hh>

Inheritance diagram for core::scoring::methods::CenHBEnergy:

Collaboration diagram for core::scoring::methods::CenHBEnergy:

List of all members.

Public Types
typedef ContextIndependentTwoBodyEnergy	parent
Public Member Functions
	CenHBEnergy ()
	C-tor, requires options to tell us the atom_type_set_name for the AtomVDW data.
virtual EnergyMethodOP	clone () const
	clone
	CenHBEnergy (CenHBEnergy const &src)
	COPY C-TOR.
virtual void	setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const
virtual void	setup_for_derivatives (pose::Pose &pose, ScoreFunction const &) const
	Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls.
virtual void	residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &, EnergyMap &emap) const
	Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap.
virtual void	eval_residue_pair_derivatives (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &, ResSingleMinimizationData const &, ResPairMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const
	Evaluate the derivative for an atom in rsd1 with respect to rsd2 in the context of a particular pose, and increment the F1 and F2 vectors. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. DEPRECATED. Too slow. Too much overhead for each atom; slowed fast-relax runs by ~40%.
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.
void	eval_intrares_energy (conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const
	Evaluate the intra-residue energy for a given residue.
virtual Distance	atomic_interaction_cutoff () const
	CenHBEnergy distance cutoff.
virtual void	indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const
	CenHBEnergy.

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Member Typedef Documentation

typedef ContextIndependentTwoBodyEnergy core::scoring::methods::CenHBEnergy::parent

Reimplemented from core::scoring::methods::ContextIndependentTwoBodyEnergy.

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Constructor & Destructor Documentation

core::scoring::methods::CenHBEnergy::CenHBEnergy

(

)

C-tor, requires options to tell us the atom_type_set_name for the AtomVDW data.

C-TOR with method options object

Referenced by clone().

core::scoring::methods::CenHBEnergy::CenHBEnergy

(

CenHBEnergy const &

src

)

COPY C-TOR.

copy c-tor

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Member Function Documentation

Distance core::scoring::methods::CenHBEnergy::atomic_interaction_cutoff

(

)

const [virtual]

CenHBEnergy distance cutoff.

Implements core::scoring::methods::ShortRangeTwoBodyEnergy.

EnergyMethodOP core::scoring::methods::CenHBEnergy::clone

(

)

const [virtual]

clone

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

References CenHBEnergy().

virtual bool core::scoring::methods::CenHBEnergy::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.

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

Evaluate the intra-residue energy for a given residue.

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

void core::scoring::methods::CenHBEnergy::eval_residue_pair_derivatives	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		ResSingleMinimizationData const &	,
		ResSingleMinimizationData const &	,
		ResPairMinimizationData const &	min_data,
		pose::Pose const &	pose,
		EnergyMap const &	weights,
		utility::vector1< DerivVectorPair > &	r1_atom_derivs,
		utility::vector1< DerivVectorPair > &	r2_atom_derivs
	)		const [virtual]

Evaluate the derivative for an atom in rsd1 with respect to rsd2 in the context of a particular pose, and increment the F1 and F2 vectors. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. DEPRECATED. Too slow. Too much overhead for each atom; slowed fast-relax runs by ~40%.

Evaluate the derivatives for all atoms on rsd1 and rsd2 with respect to each other and increment the derivatives in atom-derivatives vector1s. The calling function must guarantee that the r1_atom_derivs vector1 holds at least as many entries as there are atoms in rsd1, and that the r2_atom_derivs vector1 holds at least as many entries as there are atoms in rsd2.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

References core::conformation::Residue::aa(), core::chemical::aa_pro, core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), core::scoring::cen_hb, core::conformation::Residue::polymeric_sequence_distance(), and core::conformation::Atom::xyz().

void core::scoring::methods::CenHBEnergy::indicate_required_context_graphs

(

utility::vector1< bool > &

context_graphs_required

)

const [virtual]

CenHBEnergy.

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

void core::scoring::methods::CenHBEnergy::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::conformation::Residue::aa(), core::chemical::aa_pro, core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), core::scoring::cen_hb, core::scoring::CenHBPotential::cutoff(), core::scoring::CenHBPotential::func(), core::conformation::Residue::polymeric_sequence_distance(), and protocols::kinmatch::xyz().

void core::scoring::methods::CenHBEnergy::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::pose::Pose::update_residue_neighbors().

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

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