core::scoring::methods::LK_hack Class Reference

#include <LK_hack.hh>

Inheritance diagram for core::scoring::methods::LK_hack:

Collaboration diagram for core::scoring::methods::LK_hack:

List of all members.

Public Types
typedef ContextIndependentTwoBodyEnergy	parent
Public Member Functions
	LK_hack (etable::Etable const &etable_in)
virtual EnergyMethodOP	clone () const
	clone
	LK_hack (LK_hack const &src)
virtual void	setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) 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 &domain_map, ScoreFunction const &sfxn, EnergyMap const &weights, Vector &F1, Vector &F2) const
	called during gradient-based minimization inside dfunc
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 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 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
	how far apart must two heavy atoms be to have a zero interaction energy?
void	indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const
	Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.

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Member Typedef Documentation

typedef ContextIndependentTwoBodyEnergy core::scoring::methods::LK_hack::parent

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

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Constructor & Destructor Documentation

core::scoring::methods::LK_hack::LK_hack

(

etable::Etable const &

etable_in

)

Referenced by clone().

core::scoring::methods::LK_hack::LK_hack

(

LK_hack const &

src

)

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Member Function Documentation

Distance core::scoring::methods::LK_hack::atomic_interaction_cutoff

(

)

const [virtual]

how far apart must two heavy atoms be to have a zero interaction energy?

If hydrogen atoms interact at the same range as heavy atoms, then this distance should build-in a 2 * max-bound-h-distance-cutoff buffer. There is an improper mixing here between run-time aquired chemical knowledge (max-bound-h-distance-cutoff) and compile time aquired scoring knowledge (max atom cutoff); this could be resolved by adding a boolean uses_hydrogen_interaction_distance() to the SRTBEnergy class along with a method of the ChemicalManager max_bound_h_distance_cutoff().

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

References core::scoring::etable::Etable::max_dis().

EnergyMethodOP core::scoring::methods::LK_hack::clone

(

)

const [virtual]

clone

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

References LK_hack().

virtual bool core::scoring::methods::LK_hack::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::LK_hack::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::pose::Pose::residue().

virtual void core::scoring::methods::LK_hack::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::LK_hack::indicate_required_context_graphs

(

utility::vector1< bool > &

context_graphs_required

)

const [virtual]

Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.

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

void core::scoring::methods::LK_hack::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::atom(), core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::atom_type(), core::conformation::Residue::bonded_neighbor(), core::conformation::Residue::connect_map(), core::chemical::ResConnID::connid(), core::scoring::methods::LK_SigmoidalFunc::cos_flipped_ANGLE_CUTOFF_HIGH, core::scoring::methods::LK_SigmoidalFunc::cos_flipped_ANGLE_CUTOFF_LOW, core::scoring::etable::count_pair::CP_CROSSOVER_4, core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_donor(), core::scoring::lk_hack, core::chemical::ResidueType::n_residue_connections_for_atom(), core::conformation::Residue::nheavyatoms(), core::chemical::ResConnID::resid(), core::pose::Pose::residue(), core::chemical::ResidueType::residue_connections_for_atom(), core::conformation::Atom::type(), core::conformation::Residue::type(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

void core::scoring::methods::LK_hack::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::scoring::lk_hack, core::pose::Pose::update_residue_neighbors(), and core::scoring::ScoreFunction::weights().

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

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