#include <DNA_BasePotential.hh>

Inheritance diagram for core::scoring::dna::DNA_BasePotential:

Public Types
typedef numeric::xyzMatrix< Real >	Matrix

typedef utility::vector1< Real >	Params

typedef conformation::Residue	Residue

typedef ObjexxFCL::FArray3D< Real >	FArray3D_Real

typedef ObjexxFCL::FArray4D< Real >	FArray4D_Real

Public Member Functions
	~DNA_BasePotential () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...

	DNA_BasePotential ()
	ctor More...

Real	base_step_score (Residue const &rsd1, Residue const &rsd2) const

Real	base_pair_score (Residue const &rsd1, Residue const &rsd2) const

void	eval_base_step_derivative (Residue const &rsd1, Residue const &rsd2, Vector &F1, Vector &F2, Real const external_sign_factor) const

void	eval_base_pair_derivative (Residue const &rsd1, Residue const &rsd2, Vector &F1, Vector &F2, Real const sign_factor) const

void	eval_base_pair_Z_scores (Residue const &rsd1, Residue const &rsd2, utility::vector1< Real > &z_scores) const

void	eval_base_step_Z_scores (Residue const &rsd1, Residue const &rsd2, utility::vector1< Real > &z_scores) const

Private Types
enum	InteractionType { BP_type = 1 , BS_type }

Private Member Functions
Real	mean (InteractionType const &t, std::string const &bases, int const p) const

Real	stddev (InteractionType const &t, std::string const &bases, int const p) const

Real	stiffness (InteractionType const &t, std::string const &bases, int const p1, int const p2) const

std::string	base_string (Residue const &rsd) const
	"A","C","T","G" More...

void	get_array_indices (InteractionType const &t, std::string const &bases, int &i1, int &i2) const

void	load_score_tables ()

void	set_mean_and_stddev (InteractionType const &type, std::string const &bases, int const index, Real mean, Real stddev)

void	set_stiffness (InteractionType const &type, std::string const &bases, int const index1, int const index2, Real const val)

Real	base_score (InteractionType const &type, std::string const &bases, utility::vector1< Real > const &params) const

Private Attributes
FArray3D_Real	mean_

FArray3D_Real	stddev_

FArray4D_Real	stiffness_

Member Typedef Documentation

◆ FArray3D_Real

typedef ObjexxFCL::FArray3D< Real > core::scoring::dna::DNA_BasePotential::FArray3D_Real

◆ FArray4D_Real

typedef ObjexxFCL::FArray4D< Real > core::scoring::dna::DNA_BasePotential::FArray4D_Real

◆ Matrix

typedef numeric::xyzMatrix< Real > core::scoring::dna::DNA_BasePotential::Matrix

◆ Params

typedef utility::vector1< Real > core::scoring::dna::DNA_BasePotential::Params

◆ Residue

typedef conformation::Residue core::scoring::dna::DNA_BasePotential::Residue

Member Enumeration Documentation

◆ InteractionType

enum core::scoring::dna::DNA_BasePotential::InteractionType

private

Enumerator
BP_type
BS_type

Constructor & Destructor Documentation

◆ ~DNA_BasePotential()

core::scoring::dna::DNA_BasePotential::~DNA_BasePotential ( )

overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

◆ DNA_BasePotential()

core::scoring::dna::DNA_BasePotential::DNA_BasePotential ( )

ctor

References load_score_tables().

Member Function Documentation

◆ base_pair_score()

Real core::scoring::dna::DNA_BasePotential::base_pair_score	(	Residue const &	rsd1,
		Residue const &	rsd2
	)		const

References base_score(), base_string(), BP_type, and core::scoring::dna::get_base_pair_params().

Referenced by core::energy_methods::DNA_BaseEnergy::residue_pair_energy(), and core::scoring::dna::show_base_pair_params_with_z_scores().

◆ base_score()

Real core::scoring::dna::DNA_BasePotential::base_score	(	InteractionType const &	type,
		std::string const &	bases,
		utility::vector1< Real > const &	params
	)		const

private

References mean(), protocols::hybridization::score, stddev(), and stiffness().

Referenced by base_pair_score(), and base_step_score().

◆ base_step_score()

Real core::scoring::dna::DNA_BasePotential::base_step_score	(	Residue const &	rsd1,
		Residue const &	rsd2
	)		const

References base_score(), base_string(), BS_type, core::scoring::dna::get_base_step_params(), and core::conformation::Residue::seqpos().

Referenced by core::energy_methods::DNA_BaseEnergy::residue_pair_energy(), and core::scoring::dna::show_new_base_step_params().

◆ base_string()

std::string core::scoring::dna::DNA_BasePotential::base_string ( Residue const & rsd ) const

inlineprivate

"A","C","T","G"

References core::conformation::Residue::aa(), core::chemical::na_ade, core::chemical::na_cyt, core::chemical::na_gua, core::chemical::na_thy, and core::conformation::Residue::name().

Referenced by base_pair_score(), base_step_score(), eval_base_pair_derivative(), eval_base_pair_Z_scores(), eval_base_step_derivative(), and eval_base_step_Z_scores().

◆ eval_base_pair_derivative()

void core::scoring::dna::DNA_BasePotential::eval_base_pair_derivative	(	Residue const &	rsd1,
		Residue const &	rsd2,
		Vector &	F1,
		Vector &	F2,
		Real const	sign_factor
	)		const

References base_string(), BP_type, core::pack::interaction_graph::debug, core::chemical::element::F, core::scoring::dna::get_base_pair_params(), core::scoring::dna::get_base_stub(), core::scoring::dna::is_orthonormal(), protocols::antibody::kappa, core::kinematics::Stub::M, protocols::mean_field::max(), mean(), protocols::mean_field::min(), core::scoring::omega, core::conformation::Residue::seqpos(), stddev(), stiffness(), and core::kinematics::Stub::v.

Referenced by core::energy_methods::DNA_BaseEnergy::eval_atom_derivative().

◆ eval_base_pair_Z_scores()

void core::scoring::dna::DNA_BasePotential::eval_base_pair_Z_scores	(	Residue const &	rsd1,
		Residue const &	rsd2,
		utility::vector1< Real > &	z_scores
	)		const

References base_string(), BP_type, core::scoring::dna::get_base_pair_params(), mean(), and stddev().

Referenced by core::scoring::dna::show_base_pair_params_with_z_scores().

◆ eval_base_step_derivative()

void core::scoring::dna::DNA_BasePotential::eval_base_step_derivative	(	Residue const &	rsd1,
		Residue const &	rsd2,
		Vector &	F1,
		Vector &	F2,
		Real const	external_sign_factor
	)		const

References base_string(), BS_type, core::pack::interaction_graph::debug, core::chemical::element::F, core::scoring::dna::get_base_step_params(), core::scoring::dna::get_base_stub(), core::scoring::dna::is_orthonormal(), core::kinematics::Stub::M, protocols::mean_field::max(), mean(), protocols::mean_field::min(), core::conformation::Residue::seqpos(), stddev(), stiffness(), and core::kinematics::Stub::v.

Referenced by core::energy_methods::DNA_BaseEnergy::eval_atom_derivative().

◆ eval_base_step_Z_scores()

void core::scoring::dna::DNA_BasePotential::eval_base_step_Z_scores	(	Residue const &	rsd1,
		Residue const &	rsd2,
		utility::vector1< Real > &	z_scores
	)		const

References base_string(), BS_type, core::scoring::dna::get_base_step_params(), mean(), core::conformation::Residue::seqpos(), and stddev().

Referenced by core::scoring::dna::show_new_base_step_params().

◆ get_array_indices()

void core::scoring::dna::DNA_BasePotential::get_array_indices	(	InteractionType const &	t,
		std::string const &	bases,
		int &	i1,
		int &	i2
	)		const

private

i1 = 1,2 i2 = 1,16

References BP_type, and protocols::hybridization::t.

Referenced by mean(), set_mean_and_stddev(), set_stiffness(), stddev(), and stiffness().

◆ load_score_tables()

void core::scoring::dna::DNA_BasePotential::load_score_tables ( )

private

References BP_type, BS_type, mean(), set_mean_and_stddev(), set_stiffness(), and stddev().

Referenced by DNA_BasePotential().

◆ mean()

Real core::scoring::dna::DNA_BasePotential::mean	(	InteractionType const &	t,
		std::string const &	bases,
		int const	p
	)		const

inlineprivate

References get_array_indices(), mean_, and protocols::hybridization::t.

Referenced by base_score(), eval_base_pair_derivative(), eval_base_pair_Z_scores(), eval_base_step_derivative(), eval_base_step_Z_scores(), load_score_tables(), and set_mean_and_stddev().

◆ set_mean_and_stddev()

void core::scoring::dna::DNA_BasePotential::set_mean_and_stddev	(	InteractionType const &	type,
		std::string const &	bases,
		int const	index,
		Real	mean,
		Real	stddev
	)

private

References get_array_indices(), mean(), mean_, stddev(), and stddev_.

Referenced by load_score_tables().

◆ set_stiffness()

void core::scoring::dna::DNA_BasePotential::set_stiffness	(	InteractionType const &	type,
		std::string const &	bases,
		int const	index1,
		int const	index2,
		Real const	val
	)

private

References get_array_indices(), stiffness_, and protocols::hybridization::val.

Referenced by load_score_tables().

◆ stddev()

Real core::scoring::dna::DNA_BasePotential::stddev	(	InteractionType const &	t,
		std::string const &	bases,
		int const	p
	)		const

inlineprivate

References get_array_indices(), stddev_, and protocols::hybridization::t.

Referenced by base_score(), eval_base_pair_derivative(), eval_base_pair_Z_scores(), eval_base_step_derivative(), eval_base_step_Z_scores(), load_score_tables(), and set_mean_and_stddev().

◆ stiffness()

Real core::scoring::dna::DNA_BasePotential::stiffness	(	InteractionType const &	t,
		std::string const &	bases,
		int const	p1,
		int const	p2
	)		const

inlineprivate

References get_array_indices(), stiffness_, and protocols::hybridization::t.

Referenced by base_score(), eval_base_pair_derivative(), and eval_base_step_derivative().

Member Data Documentation

◆ mean_

FArray3D_Real core::scoring::dna::DNA_BasePotential::mean_

private

Referenced by mean(), and set_mean_and_stddev().

◆ stddev_

FArray3D_Real core::scoring::dna::DNA_BasePotential::stddev_

private

Referenced by set_mean_and_stddev(), and stddev().

◆ stiffness_

FArray4D_Real core::scoring::dna::DNA_BasePotential::stiffness_

private

Referenced by set_stiffness(), and stiffness().

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

src/core/scoring/dna/DNA_BasePotential.hh
src/core/scoring/dna/DNA_BasePotential.cc

Public Types

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Member Typedef Documentation

◆ FArray3D_Real

◆ FArray4D_Real

◆ Matrix

◆ Params

◆ Residue

Member Enumeration Documentation

◆ InteractionType

Constructor & Destructor Documentation

◆ ~DNA_BasePotential()

◆ DNA_BasePotential()

Member Function Documentation

◆ base_pair_score()

◆ base_score()

◆ base_step_score()

◆ base_string()

◆ eval_base_pair_derivative()

◆ eval_base_pair_Z_scores()

◆ eval_base_step_derivative()

◆ eval_base_step_Z_scores()

◆ get_array_indices()

◆ load_score_tables()

◆ mean()

◆ set_mean_and_stddev()

◆ set_stiffness()

◆ stddev()

◆ stiffness()

Member Data Documentation

◆ mean_

◆ stddev_

◆ stiffness_