core::scoring::methods::LinearChainbreakEnergy Class Reference

LinearChainbreakEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by how much their psueduo atoms do not align. More...

#include <LinearChainbreakEnergy.hh>

Inheritance diagram for core::scoring::methods::LinearChainbreakEnergy:

Collaboration diagram for core::scoring::methods::LinearChainbreakEnergy:

List of all members.

Public Types
typedef WholeStructureEnergy	parent
Public Member Functions
	LinearChainbreakEnergy ()
	LinearChainbreakEnergy (Size allowable_sequence_sep)
	LinearChainbreakEnergy (const LinearChainbreakEnergy &)
	The auto-generated copy constructor does not properly handle smart pointer types, so we must explicitly define our own.
LinearChainbreakEnergy &	operator= (const LinearChainbreakEnergy &)
	The auto-generated operator=() method does not properly handle pointer types.
	~LinearChainbreakEnergy ()
virtual EnergyMethodOP	clone () const
	clone
virtual void	finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) const
	called at the end of energy evaluation
virtual void	eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &sfxn, EnergyMap const &weights, Vector &F1, Vector &F2) const
	called during gradient-based minimization inside dfunc
virtual void	indicate_required_context_graphs (utility::vector1< bool > &) const
	LinearChainbreak Energy is context independent and thus indicates that no context graphs need to be maintained by class Energies.

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Detailed Description

LinearChainbreakEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by how much their psueduo atoms do not align.

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Member Typedef Documentation

typedef WholeStructureEnergy core::scoring::methods::LinearChainbreakEnergy::parent

Reimplemented from core::scoring::methods::WholeStructureEnergy.

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Constructor & Destructor Documentation

core::scoring::methods::LinearChainbreakEnergy::LinearChainbreakEnergy

(

)

References core::SZ_MAX.

Referenced by clone().

core::scoring::methods::LinearChainbreakEnergy::LinearChainbreakEnergy

(

Size

allowable_sequence_sep

)

[explicit]

core::scoring::methods::LinearChainbreakEnergy::LinearChainbreakEnergy

(

const LinearChainbreakEnergy &

o

)

The auto-generated copy constructor does not properly handle smart pointer types, so we must explicitly define our own.

core::scoring::methods::LinearChainbreakEnergy::~LinearChainbreakEnergy

(

)

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Member Function Documentation

virtual EnergyMethodOP core::scoring::methods::LinearChainbreakEnergy::clone

(

)

const [inline, virtual]

clone

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

References LinearChainbreakEnergy().

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

called during gradient-based minimization inside dfunc

F1 and F2 are not zeroed -- contributions from this atom are just summed in

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

References core::conformation::Residue::atom(), core::conformation::Residue::atom_name(), core::scoring::methods::is_lower_cutpoint(), core::scoring::methods::is_upper_cutpoint(), core::scoring::linear_chainbreak, core::conformation::Residue::mainchain_atoms(), core::pose::Pose::residue(), protocols::kinmatch::xyz(), core::conformation::Atom::xyz(), and core::pose::Pose::xyz().

void core::scoring::methods::LinearChainbreakEnergy::finalize_total_energy	(	pose::Pose &	pose,
		ScoreFunction const &	,
		EnergyMap &	totals
	)		const [virtual]

called at the end of energy evaluation

called at the end of energy evaluation In this case (LinearChainbreakEnergy), all the calculation is done here

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

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::scoring::methods::find_cutpoint_variants(), core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), boost::tuples::hash_value(), core::scoring::linear_chainbreak, core::conformation::Residue::mainchain_atoms(), core::scoring::overlap_chainbreak, core::pose::Pose::residue(), and core::scoring::methods::tr().

Referenced by protocols::forge::methods::linear_chainbreak(), and protocols::forge::methods::overlap_chainbreak().

void core::scoring::methods::LinearChainbreakEnergy::indicate_required_context_graphs

(

utility::vector1< bool > &

)

const [virtual]

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

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

LinearChainbreakEnergy & core::scoring::methods::LinearChainbreakEnergy::operator=

(

const LinearChainbreakEnergy &

o

)

The auto-generated operator=() method does not properly handle pointer types.

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

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