core::scoring::rna::RNA_SugarCloseEnergy Class Reference

#include <RNA_SugarCloseEnergy.hh>

Inheritance diagram for core::scoring::rna::RNA_SugarCloseEnergy:

Collaboration diagram for core::scoring::rna::RNA_SugarCloseEnergy:

List of all members.

Public Types
typedef core::scoring::methods::ContextIndependentOneBodyEnergy	parent
Public Member Functions
	RNA_SugarCloseEnergy ()
	ctor
virtual	~RNA_SugarCloseEnergy ()
	dtor
virtual core::scoring::methods::EnergyMethodOP	clone () const
	clone
virtual void	residue_energy (conformation::Residue const &rsd, EnergyMap &emap) const
virtual void	residue_energy (conformation::Residue const &rsd, pose::Pose const &, 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	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	eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &, ScoreFunction const &sfxn, EnergyMap const &weights, Vector &F1, Vector &F2) const
	////////////////////////////////////////////////////////////////////////////
virtual void	indicate_required_context_graphs (utility::vector1< bool > &) const
	RNA_SugarCloseEnergy is context independent; indicates that no context graphs are required.
void	setup_sugar_ring_closure_constraints (pose::Pose &pose) const
void	add_sugar_ring_closure_constraints (conformation::Residue const &rsd, constraints::ConstraintSet &cst_set) const

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Member Typedef Documentation

typedef core::scoring::methods::ContextIndependentOneBodyEnergy core::scoring::rna::RNA_SugarCloseEnergy::parent

Reimplemented from core::scoring::methods::ContextIndependentOneBodyEnergy.

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Constructor & Destructor Documentation

core::scoring::rna::RNA_SugarCloseEnergy::RNA_SugarCloseEnergy

(

)

ctor

Referenced by clone().

core::scoring::rna::RNA_SugarCloseEnergy::~RNA_SugarCloseEnergy

(

)

[virtual]

dtor

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Member Function Documentation

void core::scoring::rna::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints	(	conformation::Residue const &	rsd,
		constraints::ConstraintSet &	cst_set
	)		const

References core::scoring::constraints::ConstraintSet::add_constraint(), core::chemical::rna::RNA_ResidueType::c1star_atom_index(), core::chemical::rna::RNA_ResidueType::c2star_atom_index(), core::chemical::rna::RNA_ResidueType::c4star_atom_index(), core::scoring::rna::first_base_atom_index(), core::conformation::Residue::is_RNA(), core::chemical::rna::RNA_ResidueType::o4star_atom_index(), core::scoring::rna_sugar_close, core::conformation::Residue::RNA_type(), and core::conformation::Residue::seqpos().

Referenced by residue_energy(), and setup_sugar_ring_closure_constraints().

methods::EnergyMethodOP core::scoring::rna::RNA_SugarCloseEnergy::clone

(

)

const [virtual]

clone

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

References RNA_SugarCloseEnergy().

void core::scoring::rna::RNA_SugarCloseEnergy::eval_atom_derivative	(	id::AtomID const &	id,
		pose::Pose const &	pose,
		kinematics::DomainMap const &	,
		ScoreFunction const &	sfxn,
		EnergyMap const &	weights,
		Vector &	F1,
		Vector &	F2
	)		const [virtual]

////////////////////////////////////////////////////////////////////////////

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

void core::scoring::rna::RNA_SugarCloseEnergy::indicate_required_context_graphs

(

utility::vector1< bool > &

)

const [virtual]

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

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

void core::scoring::rna::RNA_SugarCloseEnergy::residue_energy	(	conformation::Residue const &	rsd,
		EnergyMap &	emap
	)		const [virtual]

References add_sugar_ring_closure_constraints(), and core::scoring::constraints::ConstraintSet::eval_intrares_energy().

Referenced by residue_energy().

void core::scoring::rna::RNA_SugarCloseEnergy::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::ContextIndependentOneBodyEnergy.

References residue_energy().

void core::scoring::rna::RNA_SugarCloseEnergy::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 setup_sugar_ring_closure_constraints().

void core::scoring::rna::RNA_SugarCloseEnergy::setup_sugar_ring_closure_constraints

(

pose::Pose &

pose

)

const

References add_sugar_ring_closure_constraints(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by setup_for_derivatives().

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

• src/core/scoring/rna/RNA_SugarCloseEnergy.hh
• src/core/scoring/rna/RNA_SugarCloseEnergy.cc