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>

Public Types
typedef WholeStructureEnergy	parent

Public Types inherited from core::scoring::methods::WholeStructureEnergy
typedef EnergyMethod	parent

Public Types inherited from core::scoring::methods::EnergyMethod
typedef utility::pointer::ReferenceCount	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. More...

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

	~LinearChainbreakEnergy ()

virtual EnergyMethodOP	clone () const
	clone More...

virtual void	finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) const
	called at the end of energy evaluation More...

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 More...

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. More...

Public Member Functions inherited from core::scoring::methods::WholeStructureEnergy
	WholeStructureEnergy (EnergyMethodCreatorOP)
	Constructor with EnergyMethodCreator to list the ScoreTypes computed by this WholeStructureEnergy. More...

virtual	~WholeStructureEnergy ()

EnergyMethodType	method_type () const
	Return one of the 7 kinds of energy methods that exist: e.g. context-dependent-one-body vs whole-structure. More...

virtual Distance	atomic_interaction_cutoff () const
	how far apart must two heavy atoms be to have a zero interaction energy? More...

Public Member Functions inherited from core::scoring::methods::EnergyMethod
	EnergyMethod (EnergyMethodCreatorOP creator)
	Constructor with EnergyMethodCreator, which lists the score types that this energy method is responsible for. More...

	EnergyMethod (EnergyMethod const &src)
	Copy constructor copies over the score types of the source. More...

virtual	~EnergyMethod ()

virtual void	setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const

virtual void	prepare_rotamers_for_packing (pose::Pose const &, conformation::RotamerSetBase &) const

virtual void	update_residue_for_packing (pose::Pose &, Size resid) const
	ensure this function gets called. The default behavior is to do nothing. More...

virtual void	setup_for_scoring (pose::Pose &, ScoreFunction const &) const

virtual void	setup_for_minimizing (pose::Pose &, ScoreFunction const &, kinematics::MinimizerMapBase const &) const
	Called at the beginning of atom tree minimization, this method allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose's Energies object's "use_nblist()" method returns true. More...

virtual void	setup_for_derivatives (pose::Pose &pose, ScoreFunction const &sfxn) const
	Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. More...

virtual void	finalize_after_derivatives (pose::Pose &, ScoreFunction const &) const
	called at the end of derivatives evaluation More...

virtual bool	minimize_in_whole_structure_context (pose::Pose const &) const
	Should this EnergyMethod have score and derivative evaluation evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that's serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return "true" will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction's traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return "true" cannot be included in RTMin. More...

virtual bool	defines_high_order_terms (pose::Pose const &) const
	Should this EnergyMethod have score and derivative evaluation evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta's get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns "false". More...

ScoreTypes const &	score_types () const
	Returns the score types that this energy method computes. More...

Private Member Functions
core::Real	do_score_dev (const core::conformation::Residue &lower_rsd, const core::conformation::Residue &upper_rsd, const core::Size nbb) const

core::Real	do_score_ovp (const core::conformation::Residue &lower_rsd, const core::conformation::Residue &upper_rsd, const core::Size nbb, const core::Size cutpoint, const core::pose::Pose &pose) const

void	initialize (Size allowable_sequence_sep)

virtual core::Size	version () const
	Return the version of the energy method. More...

Private Attributes
Size	allowable_sequence_sep_

scoped_ptr < ShortestPathInFoldTree >	shortest_paths_

std::size_t	previous_hash_value_

Additional Inherited Members
Protected Member Functions inherited from core::scoring::methods::EnergyMethod
void	set_score_types (EnergyMethodCreatorOP creator)
	Override the entirety of the score types list if they were initialized incorrectly in a parent's constructor. More...

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.

Calculates both linear_chainbreak and overlap_chainbreak terms. linear_chainbreak measures 3 distances (cutpoint variants must be added to pose): 1) virt CA res1 -> CA res2 2) virt C res1 -> C res2 3) N res1 -> virt N res2 score = 1 + 2+ 3 /3

For ideal poses, this score should be very close to 0. Real PDBs, however have bond length and angle deviations that will cause this score to be fairly high.

See Also: protocols/forge/chainbreak_eval.hh

Member Typedef Documentation

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

Constructor & Destructor Documentation

core::scoring::methods::LinearChainbreakEnergy::LinearChainbreakEnergy ( )

References initialize().

Referenced by clone().

core::scoring::methods::LinearChainbreakEnergy::LinearChainbreakEnergy ( Size allowable_sequence_sep )

explicit

References initialize().

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.

References allowable_sequence_sep_, previous_hash_value_, and shortest_paths_.

core::scoring::methods::LinearChainbreakEnergy::~LinearChainbreakEnergy ( )

Member Function Documentation

virtual EnergyMethodOP core::scoring::methods::LinearChainbreakEnergy::clone ( ) const

inlinevirtual

clone

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

References LinearChainbreakEnergy().

core::Real core::scoring::methods::LinearChainbreakEnergy::do_score_dev	(	const core::conformation::Residue &	lower_rsd,
		const core::conformation::Residue &	upper_rsd,
		const core::Size	nbb
	)		const

private

References core::conformation::Residue::atom(), core::conformation::Residue::mainchain_atoms(), xyz, and core::conformation::Atom::xyz().

Referenced by finalize_total_energy().

core::Real core::scoring::methods::LinearChainbreakEnergy::do_score_ovp	(	const core::conformation::Residue &	lower_rsd,
		const core::conformation::Residue &	upper_rsd,
		const core::Size	nbb,
		const core::Size	cutpoint,
		const core::pose::Pose &	pose
	)		const

private

References core::kinematics::AtomTree::atom(), core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), core::conformation::Conformation::atom_tree(), core::pose::Pose::conformation(), core::kinematics::distance(), core::kinematics::tree::Atom::get_stub(), core::conformation::Residue::mainchain_atoms(), core::pose::Pose::residue(), core::scoring::methods::tr, xyz, and core::conformation::Atom::xyz().

Referenced by finalize_total_energy().

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 cross(), core::scoring::methods::is_lower_cutpoint(), core::scoring::methods::is_upper_cutpoint(), numeric::xyzVector< class >::length(), core::scoring::linear_chainbreak, match, residue, core::pose::Pose::residue(), 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 allowable_sequence_sep_, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, do_score_dev(), do_score_ovp(), core::scoring::methods::find_cutpoint_variants(), core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), hash_value(), core::scoring::linear_chainbreak, core::conformation::Residue::mainchain_atoms(), core::scoring::overlap_chainbreak, previous_hash_value_, core::pose::Pose::residue(), shortest_paths_, and core::scoring::methods::tr.

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.

void core::scoring::methods::LinearChainbreakEnergy::initialize ( Size allowable_sequence_sep )

private

References allowable_sequence_sep_, previous_hash_value_, and shortest_paths_.

Referenced by LinearChainbreakEnergy().

LinearChainbreakEnergy & core::scoring::methods::LinearChainbreakEnergy::operator= ( const LinearChainbreakEnergy & o )

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

References allowable_sequence_sep_, previous_hash_value_, and shortest_paths_.

core::Size core::scoring::methods::LinearChainbreakEnergy::version ( ) const

privatevirtual

Return the version of the energy method.

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

Member Data Documentation

Size core::scoring::methods::LinearChainbreakEnergy::allowable_sequence_sep_

private

Referenced by finalize_total_energy(), initialize(), LinearChainbreakEnergy(), and operator=().

std::size_t core::scoring::methods::LinearChainbreakEnergy::previous_hash_value_

mutableprivate

Referenced by finalize_total_energy(), initialize(), LinearChainbreakEnergy(), and operator=().

scoped_ptr<ShortestPathInFoldTree> core::scoring::methods::LinearChainbreakEnergy::shortest_paths_

mutableprivate

Referenced by finalize_total_energy(), initialize(), LinearChainbreakEnergy(), and operator=().

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

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

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation