core::scoring::methods::DNA_BaseEnergy Class Reference

#include <DNA_BaseEnergy.hh>

Inheritance diagram for core::scoring::methods::DNA_BaseEnergy:

Collaboration diagram for core::scoring::methods::DNA_BaseEnergy:

List of all members.

Public Types
typedef ContextIndependentTwoBodyEnergy	parent
Public Member Functions
	DNA_BaseEnergy ()
virtual EnergyMethodOP	clone () const
	clone
virtual void	setup_for_derivatives (pose::Pose &pose, ScoreFunction const &) const
virtual void	setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const
virtual void	setup_for_packing (pose::Pose &pose, utility::vector1< bool > const &, utility::vector1< bool > const &) const
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_intrares_energy (conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const
	Evaluate the intra-residue energy for a given residue.
virtual void	eval_atom_derivative (id::AtomID const &atom_id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &, EnergyMap const &weights, 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 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 Distance	atomic_interaction_cutoff () const
	DNA_BaseEnergy distance cutoff.
virtual void	indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const
	DNA_BaseEnergy.

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Member Typedef Documentation

typedef ContextIndependentTwoBodyEnergy core::scoring::methods::DNA_BaseEnergy::parent

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

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Constructor & Destructor Documentation

core::scoring::methods::DNA_BaseEnergy::DNA_BaseEnergy

(

)

Referenced by clone().

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Member Function Documentation

Distance core::scoring::methods::DNA_BaseEnergy::atomic_interaction_cutoff

(

)

const [virtual]

DNA_BaseEnergy distance cutoff.

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

EnergyMethodOP core::scoring::methods::DNA_BaseEnergy::clone

(

)

const [virtual]

clone

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

References DNA_BaseEnergy().

virtual bool core::scoring::methods::DNA_BaseEnergy::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::DNA_BaseEnergy::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::methods::count_pair_bs(), core::scoring::dna_bp, core::scoring::dna_bs, core::scoring::methods::dna_deriv_atom(), core::scoring::dna::DNA_BasePotential::eval_base_pair_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_step_derivative(), core::pose::Pose::residue(), core::scoring::methods::retrieve_base_partner_from_pose_inline(), core::id::AtomID::rsd(), and core::pose::Pose::total_residue().

virtual void core::scoring::methods::DNA_BaseEnergy::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::DNA_BaseEnergy::indicate_required_context_graphs

(

utility::vector1< bool > &

context_graphs_required

)

const [virtual]

DNA_BaseEnergy.

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

void core::scoring::methods::DNA_BaseEnergy::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::dna::DNA_BasePotential::base_pair_score(), core::scoring::dna::DNA_BasePotential::base_step_score(), core::scoring::methods::count_pair_bs(), core::scoring::dna_bp, core::scoring::dna_bs, core::conformation::Residue::is_DNA(), core::scoring::methods::retrieve_base_partner_from_pose_inline(), and core::conformation::Residue::seqpos().

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

are these really necessary??????????? move to scheme that doesnt depend on nbr calcn

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

References core::scoring::dna::set_base_partner(), and core::pose::Pose::update_residue_neighbors().

void core::scoring::methods::DNA_BaseEnergy::setup_for_packing	(	pose::Pose &	,
		utility::vector1< bool > const &	,
		utility::vector1< bool > const &
	)		const [virtual]

default implementation noop

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

References core::scoring::dna::set_base_partner(), and core::pose::Pose::update_residue_neighbors().

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

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

References core::scoring::dna::set_base_partner(), and 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/DNA_BaseEnergy.hh
• src/core/scoring/methods/DNA_BaseEnergy.cc