core::scoring::methods::LK_BallEnergy Class Reference

#include <LK_BallEnergy.hh>

Inheritance diagram for core::scoring::methods::LK_BallEnergy:

Collaboration diagram for core::scoring::methods::LK_BallEnergy:

List of all members.

Public Types
typedef ContextIndependentTwoBodyEnergy	parent
typedef chemical::ResidueType	ResidueType
	convenience typedefs
typedef utility::vector1< Size >	Sizes
typedef utility::vector1< Vector >	Vectors
Public Member Functions
	LK_BallEnergy (EnergyMethodOptions const &options)
	HACKING //////////////////////////.
virtual EnergyMethodOP	clone () const
	clone
	LK_BallEnergy (LK_BallEnergy const &src)
virtual void	setup_for_packing (pose::Pose &pose, utility::vector1< bool > const &, utility::vector1< bool > const &) const
virtual void	setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const
virtual void	prepare_rotamers_for_packing (pose::Pose const &pose, conformation::RotamerSetBase &rotamer_set) const
virtual void	update_residue_for_packing (pose::Pose &, Size resid) const
	ensure this function gets called. The default behavior is to do nothing.
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.
Real	calculate_lk_desolvation_of_single_atom_by_residue (Size const atom1, conformation::Residue const &rsd1, conformation::Residue const &rsd2)
	helper function for outside use
Real	calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair (Size const atom1, conformation::Residue const &rsd1, conformation::Residue const &rsd2)
void	calculate_lk_ball_atom_energies (Size const atom1, conformation::Residue const &rsd1, Vectors const &atom1_waters, Size const atom2, conformation::Residue const &rsd2, Real &lk_desolvation_of_atom1_by_atom2, Real &lk_ball_desolvation_of_atom1_by_atom2) const
	get the lk-ball desolvation of atom1 by atom2, and the unoriented lk desolvation of atom1 by atom2
Real	get_lk_fractional_contribution_for_single_water (Vector const &atom2_xyz, Size const atom2_type, Vector const &atom1_water) const
void	eval_desolvation_derivs_no_count_pair (Real const d2, Size const atom1, conformation::Residue const &rsd1, Size const atom2, conformation::Residue const &rsd2, Real &atom1_lk_desolvation_by_atom2_deriv, Real &atom2_lk_desolvation_by_atom1_deriv)
virtual void	eval_residue_pair_derivatives (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &, ResSingleMinimizationData const &, ResPairMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const
virtual void	residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &, EnergyMap &emap) const
	This guy is used during scoring.
void	residue_pair_energy (conformation::Residue const &rsd1, LKB_ResidueInfo const &rsd1_info, conformation::Residue const &rsd2, LKB_ResidueInfo const &rsd2_info, EnergyMap &emap) const
void	accumulate_single_atom_contributions (Size const atom1, Size const atom1_type_index, Vectors const &atom1_waters, conformation::Residue const &rsd1, Size const atom2_type_index, Vector const &atom2_xyz, Real const lk_desolvation_of_atom1_by_atom2, EnergyMap &emap) const
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.
Real	eval_lk_fraction (Real const d2_delta) const
Real	eval_d_lk_fraction_dr_over_r (Real const d2_delta) const
Real	get_lk_fractional_contribution (Vector const &atom2_xyz, Size const atom2_type_index, Vectors const &atom1_waters, Size &closest_water, Real &closest_water_dis2) const
Real	get_lk_fractional_contribution (Vector const &atom2_xyz, Size const atom2_type_index, Vectors const &atom1_waters) const
Real	eval_lk_ball_fraction_deriv (Vector const &atom2_xyz, Size const atom2_type_index, Vectors const &atom1_waters, bool const evaluate_deriv, Vector &f1, Vector &f2) const
	for external use
virtual void	evaluate_rotamer_pair_energies (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const
	Batch computation of rotamer pair energies. Need not be overriden in derived class -- by default, iterates over all pairs of rotamers, and calls derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.
virtual void	evaluate_rotamer_background_energies (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< core::PackerEnergy > &energy_vector) const
	Batch computation of rotamer/background energies. Need not be overriden in derived class -- by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.
void	sum_contributions_for_atom_pair_one_way (Size const atom1, conformation::Residue const &rsd1, Vectors const &atom1_waters, Size const atom2, conformation::Residue const &rsd2, scoring::EnergyMap const &weights, Real const weight_factor, Real const d2, Vector &F1, Vector &F2) const
void	sum_contributions_for_atom_pair (Size const atom1, conformation::Residue const &rsd1, LKB_ResidueInfo const &rsd1_info, Size const atom2, conformation::Residue const &rsd2, LKB_ResidueInfo const &rsd2_info, pose::Pose const &pose, scoring::EnergyMap const &weights, Real const cp_weight, Vector &F1, Vector &F2) const
void	setup_d2_bounds ()

---

Member Typedef Documentation

typedef ContextIndependentTwoBodyEnergy core::scoring::methods::LK_BallEnergy::parent

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

typedef chemical::ResidueType core::scoring::methods::LK_BallEnergy::ResidueType

convenience typedefs

typedef utility::vector1< Size > core::scoring::methods::LK_BallEnergy::Sizes

typedef utility::vector1< Vector > core::scoring::methods::LK_BallEnergy::Vectors

---

Constructor & Destructor Documentation

core::scoring::methods::LK_BallEnergy::LK_BallEnergy

(

EnergyMethodOptions const &

options

)

HACKING //////////////////////////.

References setup_d2_bounds().

Referenced by clone().

core::scoring::methods::LK_BallEnergy::LK_BallEnergy

(

LK_BallEnergy const &

src

)

References setup_d2_bounds().

---

Member Function Documentation

void core::scoring::methods::LK_BallEnergy::accumulate_single_atom_contributions	(	Size const	atom1,
		Size const	atom1_type_index,
		Vectors const &	atom1_waters,
		conformation::Residue const &	rsd1,
		Size const	atom2_type_index,
		Vector const &	atom2_xyz,
		Real const	lk_desolvation_of_atom1_by_atom2,
		EnergyMap &	emap
	)		const

References get_lk_fractional_contribution(), core::scoring::lk_ball, and core::scoring::lk_ball_iso.

Referenced by residue_pair_energy().

Distance core::scoring::methods::LK_BallEnergy::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().

void core::scoring::methods::LK_BallEnergy::calculate_lk_ball_atom_energies	(	Size const	atom1,
		conformation::Residue const &	rsd1,
		Vectors const &	atom1_waters,
		Size const	atom2,
		conformation::Residue const &	rsd2,
		Real &	lk_desolvation_of_atom1_by_atom2,
		Real &	lk_ball_desolvation_of_atom1_by_atom2
	)		const

get the lk-ball desolvation of atom1 by atom2, and the unoriented lk desolvation of atom1 by atom2

References core::conformation::Residue::atom(), core::scoring::etable::count_pair::CP_CROSSOVER_4, get_lk_fractional_contribution(), core::conformation::Atom::type(), and core::conformation::Residue::xyz().

Real core::scoring::methods::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue	(	Size const	atom1,
		conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2
	)

helper function for outside use

helper function for outsiders

References core::conformation::Residue::atom(), core::scoring::etable::count_pair::CP_CROSSOVER_4, core::conformation::Residue::nheavyatoms(), core::conformation::Atom::type(), and core::conformation::Residue::xyz().

Real core::scoring::methods::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair	(	Size const	atom1,
		conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2
	)

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

EnergyMethodOP core::scoring::methods::LK_BallEnergy::clone

(

)

const [virtual]

clone

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

References LK_BallEnergy().

virtual bool core::scoring::methods::LK_BallEnergy::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.

Real core::scoring::methods::LK_BallEnergy::eval_d_lk_fraction_dr_over_r

(

Real const

d2_delta

)

const

Referenced by eval_lk_ball_fraction_deriv(), and sum_contributions_for_atom_pair_one_way().

void core::scoring::methods::LK_BallEnergy::eval_desolvation_derivs_no_count_pair	(	Real const	d2,
		Size const	atom1,
		conformation::Residue const &	rsd1,
		Size const	atom2,
		conformation::Residue const &	rsd2,
		Real &	atom1_lk_desolvation_by_atom2_deriv,
		Real &	atom2_lk_desolvation_by_atom1_deriv
	)

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

virtual void core::scoring::methods::LK_BallEnergy::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.

Real core::scoring::methods::LK_BallEnergy::eval_lk_ball_fraction_deriv	(	Vector const &	atom2_xyz,
		Size const	atom2_type,
		Vectors const &	atom1_waters,
		bool const	evaluate_deriv,
		Vector &	f1,
		Vector &	f2
	)		const

for external use

Note that we calculate the lk_ball_iso derivative as well as the lk_ball derivative...

Derivatives are only included for heavyatoms.

For a non-polar heavyatom, the derivs are for all polar atoms that it desolvates

For a polar heavyatom, derivs are for all polar atoms that it desolvates as well as all atoms it's being desolvated by.

Given an atom desolvating a polar atom: the lk_ball_iso deriv is the standard lk deriv, but make sure we use the correct array! (see LK_hack code)

the lk_ball score = wt * lk_polar, so the derivs have two components. One looks like wt * lk_polar deriv contribution. The other looks like the lk_polar term * the derivative of the wt. The derivative of the wt is found by getting the closest water, taking the derivative of the wt term wrt distance and using f1/f2 contributions for the desolvating atom xyz and the water xyz.

Compute the f1 and f2 vectors for the derivative of the lk_fraction term for atom2 desolvating atom1

Note:

f1 and f2 are zeroed and filled within this function, rather than being accumulated into

We pretend that atom1 is the "moving" atom Should eliminate code duplication with next routine... currently this is for outside use.

References eval_d_lk_fraction_dr_over_r(), and get_lk_fractional_contribution().

Referenced by core::scoring::methods::apply_lk_ball_fraction_weight_for_hbonds().

Real core::scoring::methods::LK_BallEnergy::eval_lk_fraction

(

Real const

d2_delta

)

const

Stolen from LK_SigmoidalFunc in lk_hack d2_delta = d2 - d2_low

Referenced by get_lk_fractional_contribution(), and get_lk_fractional_contribution_for_single_water().

void core::scoring::methods::LK_BallEnergy::eval_residue_pair_derivatives	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		ResSingleMinimizationData const &	,
		ResSingleMinimizationData const &	,
		ResPairMinimizationData const &	min_data,
		pose::Pose const &	pose,
		EnergyMap const &	weights,
		utility::vector1< DerivVectorPair > &	r1_atom_derivs,
		utility::vector1< DerivVectorPair > &	r2_atom_derivs
	)		const [virtual]

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

Reimplemented from core::scoring::methods::TwoBodyEnergy.

References core::conformation::Residue::atom_is_hydrogen(), core::scoring::etab_pair_nblist, core::scoring::ResPairMinimizationData::get_data(), core::scoring::ResPairMinimizationData::get_data_ref(), core::conformation::Residue::natoms(), core::scoring::methods::retrieve_residue_info(), core::conformation::Residue::seqpos(), and sum_contributions_for_atom_pair().

void core::scoring::methods::LK_BallEnergy::evaluate_rotamer_background_energies	(	conformation::RotamerSetBase const &	set,
		conformation::Residue const &	residue,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap const &	weights,
		utility::vector1< core::PackerEnergy > &	energy_vector
	)		const [virtual]

Batch computation of rotamer/background energies. Need not be overriden in derived class -- by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.

Reimplemented from core::scoring::methods::ShortRangeTwoBodyEnergy.

References core::scoring::EMapVector::dot(), core::scoring::methods::LKB_ResidueInfo::has_waters(), residue_pair_energy(), core::scoring::methods::retrieve_residue_info(), core::scoring::methods::retrieve_rotamer_set_info(), and core::conformation::Residue::seqpos().

void core::scoring::methods::LK_BallEnergy::evaluate_rotamer_pair_energies	(	conformation::RotamerSetBase const &	set1,
		conformation::RotamerSetBase const &	set2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap const &	weights,
		ObjexxFCL::FArray2D< core::PackerEnergy > &	energy_table
	)		const [virtual]

Batch computation of rotamer pair energies. Need not be overriden in derived class -- by default, iterates over all pairs of rotamers, and calls derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.

Reimplemented from core::scoring::methods::ShortRangeTwoBodyEnergy.

References core::scoring::EMapVector::dot(), core::conformation::RotamerSetBase::get_n_residue_types(), core::conformation::RotamerSetBase::get_n_rotamers_for_residue_type(), core::conformation::RotamerSetBase::get_residue_type_begin(), residue_pair_energy(), core::scoring::methods::retrieve_rotamer_set_info(), and core::conformation::RotamerSetBase::rotamer().

Real core::scoring::methods::LK_BallEnergy::get_lk_fractional_contribution	(	Vector const &	atom2_xyz,
		Size const	atom2_type_index,
		Vectors const &	atom1_waters
	)		const

References get_lk_fractional_contribution().

Real core::scoring::methods::LK_BallEnergy::get_lk_fractional_contribution	(	Vector const &	atom2_xyz,
		Size const	atom2_type,
		Vectors const &	atom1_waters,
		Size &	closest_water,
		Real &	closest_water_d2_delta
	)		const

Note:

closest_water may be set to 0 upon return if none of the waters are within ramp_width_A2_

References eval_lk_fraction().

Referenced by accumulate_single_atom_contributions(), calculate_lk_ball_atom_energies(), eval_lk_ball_fraction_deriv(), get_lk_fractional_contribution(), and sum_contributions_for_atom_pair_one_way().

Real core::scoring::methods::LK_BallEnergy::get_lk_fractional_contribution_for_single_water	(	Vector const &	atom2_xyz,
		Size const	atom2_type,
		Vector const &	atom1_water
	)		const

References eval_lk_fraction().

void core::scoring::methods::LK_BallEnergy::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_BallEnergy::prepare_rotamers_for_packing	(	pose::Pose const &	,
		conformation::RotamerSetBase &
	)		const [virtual]

default implementation noop

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

References core::conformation::RotamerSetBase::data(), core::conformation::RotamerSetCacheableDataType::LK_BALL_ROTAMER_SET_INFO, core::conformation::RotamerSetBase::num_rotamers(), and core::conformation::RotamerSetBase::rotamer().

void core::scoring::methods::LK_BallEnergy::residue_pair_energy	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		pose::Pose const &	pose,
		ScoreFunction const &	,
		EnergyMap &	emap
	)		const [virtual]

This guy is used during scoring.

Implements core::scoring::methods::TwoBodyEnergy.

References core::scoring::methods::retrieve_residue_info(), and core::conformation::Residue::seqpos().

Referenced by evaluate_rotamer_background_energies(), and evaluate_rotamer_pair_energies().

void core::scoring::methods::LK_BallEnergy::residue_pair_energy	(	conformation::Residue const &	rsd1,
		LKB_ResidueInfo const &	rsd1_info,
		conformation::Residue const &	rsd2,
		LKB_ResidueInfo const &	rsd2_info,
		EnergyMap &	emap
	)		const

References accumulate_single_atom_contributions(), core::conformation::Residue::atom(), core::scoring::methods::determine_crossover_behavior(), core::conformation::Residue::nheavyatoms(), core::conformation::Atom::type(), core::scoring::methods::LKB_ResidueInfo::waters(), and core::conformation::Residue::xyz().

void core::scoring::methods::LK_BallEnergy::setup_d2_bounds

(

)

References core::scoring::etable::Etable::atom_set(), core::chemical::AtomType::lj_radius(), make_table_of_pilot_apps::name, core::chemical::AtomType::name(), core::scoring::electron_density::square(), and core::scoring::methods::TR().

Referenced by LK_BallEnergy().

void core::scoring::methods::LK_BallEnergy::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::methods::compute_and_store_pose_waters(), and core::pose::Pose::update_residue_neighbors().

void core::scoring::methods::LK_BallEnergy::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::methods::compute_and_store_pose_waters(), and core::pose::Pose::update_residue_neighbors().

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

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

References core::scoring::methods::compute_and_store_pose_waters(), and core::pose::Pose::update_residue_neighbors().

void core::scoring::methods::LK_BallEnergy::sum_contributions_for_atom_pair	(	Size const	atom1,
		conformation::Residue const &	rsd1,
		LKB_ResidueInfo const &	rsd1_info,
		Size const	atom2,
		conformation::Residue const &	rsd2,
		LKB_ResidueInfo const &	rsd2_info,
		pose::Pose const &	pose,
		scoring::EnergyMap const &	weights,
		Real const	cp_weight,
		Vector &	F1,
		Vector &	F2
	)		const

Note:

Assumes that atom1 is the "moving" atom, ie the atom for which eval_atom_derivative was called

Calculates the water positions for atom2 if d2 < safe_max_dis2

References sum_contributions_for_atom_pair_one_way(), core::scoring::methods::LKB_ResidueInfo::waters(), and core::conformation::Residue::xyz().

Referenced by eval_residue_pair_derivatives().

void core::scoring::methods::LK_BallEnergy::sum_contributions_for_atom_pair_one_way	(	Size const	atom1,
		conformation::Residue const &	rsd1,
		Vectors const &	atom1_waters,
		Size const	atom2,
		conformation::Residue const &	rsd2,
		scoring::EnergyMap const &	weights,
		Real const	weight_factor,
		Real const	d2,
		Vector &	F1,
		Vector &	F2
	)		const

Note:

atom2 is desolvating atom1. atom1_waters is non-empty

Pretend that atom1 is the atom whose derivs are being calculated. weight_factor may include -1 term to switch the order...

References core::conformation::Residue::atom(), eval_d_lk_fraction_dr_over_r(), get_lk_fractional_contribution(), core::scoring::lk_ball, core::scoring::lk_ball_iso, core::conformation::Atom::type(), and core::conformation::Residue::xyz().

Referenced by sum_contributions_for_atom_pair().

void core::scoring::methods::LK_BallEnergy::update_residue_for_packing	(	pose::Pose &	,
		Size	resid
	)		const [virtual]

ensure this function gets called. The default behavior is to do nothing.

default implementation noop

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

References core::scoring::methods::LKB_ResidueInfo::build_waters(), core::pose::Pose::residue(), and core::scoring::methods::retrieve_nonconst_residue_info().

---

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

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