core::scoring::dna::DNA_BasePotential Class Reference

#include <DNA_BasePotential.hh>

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_

Member Typedef Documentation

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

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

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

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

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

Member Enumeration Documentation

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

private

Enumerator
BP_type
BS_type

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

core::scoring::dna::DNA_BasePotential::DNA_BasePotential

(

)

ctor

References load_score_tables().

Member Function Documentation

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

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

References mean(), score, 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

References base_score(), base_string(), BS_type, core::scoring::dna::get_base_step_params(), 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"

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

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

References numeric::arccos(), arccos(), base_string(), BP_type, core::pack::dunbrack::c, numeric::xyzMatrix< class >::col_x(), numeric::xyzMatrix< class >::col_y(), numeric::xyzMatrix< class >::col_z(), cross(), numeric::cross(), core::pack::interaction_graph::debug, degrees(), numeric::conversions::degrees(), core::kinematics::distance(), dot(), core::chemical::element::F, 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, params, rad2deg, numeric::conversions::radians(), radians(), rotation_matrix(), core::conformation::Residue::seqpos(), stddev(), stiffness(), numeric::xyzMatrix< class >::transposed(), 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

References base_string(), BP_type, core::scoring::dna::get_base_pair_params(), mean(), params, 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

References numeric::arccos(), arccos(), base_string(), BS_type, core::pack::dunbrack::c, numeric::xyzMatrix< class >::col_z(), numeric::cross(), cross(), core::pack::interaction_graph::debug, degrees(), numeric::conversions::degrees(), core::kinematics::distance(), dot(), core::chemical::element::F, core::scoring::dna::get_base_step_params(), core::scoring::dna::get_base_stub(), core::scoring::dna::is_orthonormal(), length, mean(), params, rad2deg, numeric::conversions::radians(), radians(), rotation_matrix(), runtime_assert, core::conformation::Residue::seqpos(), stddev(), stiffness(), numeric::xyzMatrix< class >::transposed(), verbose, z1, and z2.

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

References base_string(), BS_type, core::scoring::dna::get_base_step_params(), mean(), params, 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

References BP_type, and utility_exit_with_message.

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

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

private

References BP_type, BS_type, getline(), l, mean(), basic::database::open(), set_mean_and_stddev(), set_stiffness(), stddev(), tag, type, and utility_exit_with_message.

Referenced by DNA_BasePotential().

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

inlineprivate

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

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  )

private

References get_array_indices(), and stiffness_.

Referenced by load_score_tables().

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

inlineprivate

References get_array_indices(), and stddev_.

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().

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(), and stiffness_.

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

Member Data Documentation

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

private

Referenced by mean(), and set_mean_and_stddev().

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

private

Referenced by set_mean_and_stddev(), and stddev().

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

private

Referenced by set_stiffness(), and stiffness().

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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