A class for holding values for all helical parameters. More...

#include <Containers.h>

Public Member Functions
	HelicalParameters ()
	Empty constructor. More...

void	computeHelicalParameters ()
	A function to compute the helical parameters. This should be called when the the step parameters are provided. More...

OpenBabel::vector3	getGlobalTranslationVec (bool is_base_pair=false, bool is_second_strand=false)
	Get the global translation vector. More...

OpenBabel::vector3	getStepTranslationVec (unsigned n=0, bool is_base_pair=false, bool is_second_strand=false)
	Get the step translation vector. More...

OpenBabel::matrix3x3	getGlobalRotationMatrix (bool is_base_pair=false, bool is_second_strand=false)
	Get the global rotation matrix. More...

OpenBabel::matrix3x3	getStepRotationMatrix (unsigned n=0, bool is_base_pair=false, bool is_second_strand=false)
	Get the step rotation matrix. More...

Public Attributes
double	inclination
	Inclination. More...

double	tip
	Tip. More...

double	h_twist
	Helical twist. More...

double	x_displacement
	X-Displacement. More...

double	y_displacement
	Y-Displacement. More...

double	h_rise
	Helical rise. More...

double	shift
	Shift. More...

double	slide
	Slide. More...

double	rise
	Rise. More...

double	tilt
	Tilt. More...

double	roll
	Roll. More...

double	twist
	Twist. More...

double	buckle
	Buckle. More...

double	propeller
	Propeller twist. More...

double	opening
	Opening. More...

double	shear
	Shear. More...

double	stretch
	Stretch. More...

double	stagger
	Stagger. More...

bool	is_helical
	Are the base parameters helical or step parameters. More...

Private Member Functions
OpenBabel::matrix3x3	rodrigues_formula (OpenBabel::vector3 axis_vector, double theta)
	Rodrigues rotation formula for rotating a vector in space. More...

std::vector< OpenBabel::vector3 >	StepParametersToReferenceFrame ()
	Computes the origin and direction vectors given a set of step parameters. More...

void	ReferenceFrameToHelicalParameters (OpenBabel::vector3 origin2, OpenBabel::vector3 x2, OpenBabel::vector3 y2, OpenBabel::vector3 z2)
	Computes the helical parameters given the origin and direction vectors of the second base. More...

Detailed Description

A class for holding values for all helical parameters.

The helical parameters are used for generating the geometries of the nucleobases in the strands. This class holds the value for six helical parameters (helical twist, inclination, tip, helical rise, x-displacement, and y-displacement). It can also compute the helical parameters given the step parameters (twist, roll, tilt, rise, slide, shift). Internally, when the step parameters are provided, the helical parameters are computed. The helical parameters are used for generating the geometries. This class also implements the base-pair parameters (buckle, propeller, opening, shear, stretch, and stagger). The class holds functions to generate the geometries.

See also: Chain::setCoordsForChain; ConformationSearch::measureDistance

Constructor & Destructor Documentation

◆ HelicalParameters()

PNAB::HelicalParameters::HelicalParameters ( )

inline

Empty constructor.

This empty constructor can be used. After that, values for the member variables should be specified.

Member Function Documentation

◆ computeHelicalParameters()

void HelicalParameters::computeHelicalParameters ( )

A function to compute the helical parameters. This should be called when the the step parameters are provided.

See also: is_helical; StepParametersToReferenceFrame; ReferenceFrameToHelicalParameters

◆ getGlobalRotationMatrix()

matrix3x3 HelicalParameters::getGlobalRotationMatrix	(	bool	is_base_pair = `false`,
		bool	is_second_strand = `false`
	)

Get the global rotation matrix.

For the base step transformation, the HelicalParameters::tip and HelicalParameters::inclination are used. For the base-pair transformation, the HelicalParameters::buckle and HelicalParameters::propeller are used. The base pair parameters are divided by two and set to positive or negative values depending on which strand is being constructed.

Parameters

is_base_pair	Whetehr the vector requested is for base-pair transformation
is_second_strand	Whether the strand being constructed is the second strand. Used only for base-pair parameters

Returns: The global rotation matrix

See also: rodrigues_formula

◆ getGlobalTranslationVec()

vector3 HelicalParameters::getGlobalTranslationVec	(	bool	is_base_pair = `false`,
		bool	is_second_strand = `false`
	)

Get the global translation vector.

For the base step transformation, the HelicalParameters::x_displacement and HelicalParameters::y_displacement are used. For the base-pair transformation, the HelicalParameters::shear and HelicalParameters::stretch are used. The base pair parameters are divided by two and set to positive or negative values depending on which strand is being constructed.

Parameters

is_base_pair	Whetehr the vector requested is for base-pair transformation
is_second_strand	Whether the strand being constructed is the second strand. Used only for base-pair parameters

Returns: The translation vector

◆ getStepRotationMatrix()

matrix3x3 HelicalParameters::getStepRotationMatrix	(	unsigned	n = `0`,
		bool	is_base_pair = `false`,
		bool	is_second_strand = `false`
	)

Get the step rotation matrix.

For the base step transformation, the HelicalParameters::twist is used. For the base-pair transformation, the HelicalParameters::opening is used. The base pair parameters are divided by two and set to positive or negative values depending on which strand is being constructed.

Parameters

n	The sequence of the nucleobase in the strand. Used only for the base step transformation
is_base_pair	Whetehr the vector requested is for base-pair transformation
is_second_strand	Whether the strand being constructed is the second strand. Used only for base-pair parameters

Returns: The step rotation matrix

◆ getStepTranslationVec()

vector3 HelicalParameters::getStepTranslationVec	(	unsigned	n = `0`,
		bool	is_base_pair = `false`,
		bool	is_second_strand = `false`
	)

Get the step translation vector.

For the base step transformation, the HelicalParameters::h_rise is used. For the base-pair transformation, the HelicalParameters::stagger is used. The base pair parameters are divided by two and set to positive or negative values depending on which strand is being constructed.

Parameters

n	The sequence of the nucleobase in the strand. Used only for the base step transformation
is_base_pair	Whetehr the vector requested is for base-pair transformation
is_second_strand	Whether the strand being constructed is the second strand. Used only for base-pair parameters

Returns: The step translation vector

◆ ReferenceFrameToHelicalParameters()

void HelicalParameters::ReferenceFrameToHelicalParameters	(	OpenBabel::vector3	origin2,
		OpenBabel::vector3	x2,
		OpenBabel::vector3	y2,
		OpenBabel::vector3	z2
	)

private

Computes the helical parameters given the origin and direction vectors of the second base.

This function computes the helical parameters and set the values for the appropriate member variables

Reference: Lu, Xiang-Jun, M. A. El Hassan, and C. A. Hunter. "Structure and conformation of helical nucleic acids: analysis program (SCHNAaP)." Journal of molecular biology 273.3 (1997): 668-680.

Parameters

origin2	The coordinates of the origin of the second base pair
x2	The x direction vector for the second base pair
y2	The y direction vector for the second base pair
z2	The z direction vector for the second base pair

See also: StepParametersToReferenceFrame

◆ rodrigues_formula()

matrix3x3 HelicalParameters::rodrigues_formula	(	OpenBabel::vector3	axis_vector,
		double	theta
	)

private

Rodrigues rotation formula for rotating a vector in space.

Outputs a 3x3 rotation matrix.

Parameters

axis_vector	A unit vector defining the axis about which to rotate by angle theta
theta	The angle at which to rotate about vector given by axis

Returns: The new rotation matrix

◆ StepParametersToReferenceFrame()

vector< vector3 > HelicalParameters::StepParametersToReferenceFrame ( )

private

Computes the origin and direction vectors given a set of step parameters.

Outputs a list containing the new origin, and x, y, and z direction vectors. It uses the class member variables to access the step parameters.

Reference: El Hassan, M. A., and C. R. Calladine. "The assessment of the geometry of dinucleotide steps in double-helical DNA; a new local calculation scheme." Journal of molecular biology 251.5 (1995): 648-664.

Returns: The origin and direction vectors

See also: ReferenceFrameToHelicalParameters

Member Data Documentation

◆ buckle

double PNAB::HelicalParameters::buckle

Buckle.

◆ h_rise

double PNAB::HelicalParameters::h_rise

Helical rise.

◆ h_twist

double PNAB::HelicalParameters::h_twist

Helical twist.

◆ inclination

double PNAB::HelicalParameters::inclination

Inclination.

◆ is_helical

bool PNAB::HelicalParameters::is_helical

Are the base parameters helical or step parameters.

◆ opening

double PNAB::HelicalParameters::opening

Opening.

◆ propeller

double PNAB::HelicalParameters::propeller

Propeller twist.

◆ rise

double PNAB::HelicalParameters::rise

Rise.

◆ roll

double PNAB::HelicalParameters::roll

Roll.

◆ shear

double PNAB::HelicalParameters::shear

Shear.

◆ shift

double PNAB::HelicalParameters::shift

Shift.

◆ slide

double PNAB::HelicalParameters::slide

Slide.

◆ stagger

double PNAB::HelicalParameters::stagger

Stagger.

◆ stretch

double PNAB::HelicalParameters::stretch

Stretch.

◆ tilt

double PNAB::HelicalParameters::tilt

Tilt.

◆ tip

double PNAB::HelicalParameters::tip

Tip.

◆ twist

double PNAB::HelicalParameters::twist

Twist.

◆ x_displacement

double PNAB::HelicalParameters::x_displacement

X-Displacement.

◆ y_displacement

double PNAB::HelicalParameters::y_displacement

Y-Displacement.

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

Public Member Functions

Public Attributes

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ HelicalParameters()

Member Function Documentation

◆ computeHelicalParameters()

◆ getGlobalRotationMatrix()

◆ getGlobalTranslationVec()

◆ getStepRotationMatrix()

◆ getStepTranslationVec()

◆ ReferenceFrameToHelicalParameters()

◆ rodrigues_formula()

◆ StepParametersToReferenceFrame()

Member Data Documentation

◆ buckle

◆ h_rise

◆ h_twist

◆ inclination

◆ is_helical

◆ opening

◆ propeller

◆ rise

◆ roll

◆ shear

◆ shift

◆ slide

◆ stagger

◆ stretch

◆ tilt

◆ tip

◆ twist

◆ x_displacement

◆ y_displacement