#include <DNA_BasePotential.hh>

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

Collaboration 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
virtual	~DNA_BasePotential ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. 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_

Detailed Description

Definition at line 35 of file DNA_BasePotential.hh.

Member Typedef Documentation

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

Definition at line 42 of file DNA_BasePotential.hh.

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

Definition at line 43 of file DNA_BasePotential.hh.

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

Definition at line 39 of file DNA_BasePotential.hh.

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

Definition at line 40 of file DNA_BasePotential.hh.

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

Definition at line 41 of file DNA_BasePotential.hh.

Member Enumeration Documentation

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

private

Enumerator
BP_type
BS_type

Definition at line 100 of file DNA_BasePotential.hh.

Constructor & Destructor Documentation

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

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Definition at line 46 of file DNA_BasePotential.cc.

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

ctor

Definition at line 50 of file DNA_BasePotential.cc.

References load_score_tables().

Member Function Documentation

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

Definition at line 320 of file DNA_BasePotential.cc.

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

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

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

private

Definition at line 220 of file DNA_BasePotential.cc.

References mean(), stddev(), and stiffness().

Referenced by base_pair_score(), and base_step_score().

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

Definition at line 265 of file DNA_BasePotential.cc.

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

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

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

inlineprivate

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

Definition at line 59 of file DNA_BasePotential.cc.

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().

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

Definition at line 631 of file DNA_BasePotential.cc.

References base_string(), BP_type, core::pack::dunbrack::c, core::pack::interaction_graph::debug, core::kinematics::distance(), core::scoring::dna::get_base_pair_params(), core::scoring::dna::get_base_stub(), core::scoring::dna::is_orthonormal(), core::kinematics::Stub::M, mean(), core::scoring::omega, core::conformation::Residue::seqpos(), stddev(), stiffness(), and core::kinematics::Stub::v.

Referenced by core::scoring::methods::DNA_BaseEnergy::eval_atom_derivative().

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

Definition at line 301 of file DNA_BasePotential.cc.

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().

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

Definition at line 338 of file DNA_BasePotential.cc.

References base_string(), BS_type, core::pack::dunbrack::c, core::pack::interaction_graph::debug, core::kinematics::distance(), core::scoring::dna::get_base_step_params(), core::scoring::dna::get_base_stub(), core::scoring::dna::is_orthonormal(), mean(), core::conformation::Residue::seqpos(), stddev(), and stiffness().

Referenced by core::scoring::methods::DNA_BaseEnergy::eval_atom_derivative().

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

Definition at line 280 of file DNA_BasePotential.cc.

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().

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

Definition at line 81 of file DNA_BasePotential.cc.

References BP_type.

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

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

private

Definition at line 162 of file DNA_BasePotential.cc.

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

Referenced by DNA_BasePotential().

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

inlineprivate

Definition at line 108 of file DNA_BasePotential.hh.

References get_array_indices(), and mean_.

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().

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

Definition at line 127 of file DNA_BasePotential.cc.

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

Referenced by load_score_tables().

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