angle Class Reference

Residual and gradient calculations for angle restraint. More...

#include <angle.h>

List of all members.

Public Member Functions

angle ()

Default constructor. Some data members are not initialized!

angle (af::tiny< scitbx::vec3< double >, 3 > const &sites_, double angle_ideal_, double weight_)

Constructor.

angle (af::const_ref< scitbx::vec3< double > > const &sites_cart, angle_proxy const &proxy)

Coordinates are copied from sites_cart according to proxy.i_seqs, parameters are copied from proxy.

double residual () const

weight * delta**2.

af::tiny< scitbx::vec3< double >, 3 > gradients (double epsilon=1.e-100) const

Gradients with respect to the three sites.

void add_gradients (af::ref< scitbx::vec3< double > > const &gradient_array, angle_proxy::i_seqs_type const &i_seqs) const

Support for angle_residual_sum.

Public Attributes

af::tiny< scitbx::vec3< double >, 3 > sites

Cartesian coordinates of sites forming the angle.

double angle_ideal

Parameter (usually as passed to the constructor).

double weight

Parameter (usually as passed to the constructor).

bool have_angle_model

false in singular situations.

double angle_model

Value of angle formed by the sites.

double delta

Smallest difference between angle_model and angle_ideal taking the periodicity into account.

Detailed Description

Residual and gradient calculations for angle restraint.

Member Function Documentation

double residual ( ) const [inline]

weight * delta**2.

See also: Hendrickson, W.A. (1985). Meth. Enzym. 115, 252-270.

References angle::delta, and angle::weight.

af::tiny<scitbx::vec3<double>, 3> gradients ( double epsilon = 1.e-100 ) const [inline]

Gradients with respect to the three sites.

The formula for the gradients is singular at delta = 0 and delta = 180. However, the gradients converge to zero near these singularities. To avoid numerical problems, the gradients are set to zero exactly if the intermediate result 1/(1-cos(angle_model)**2) < epsilon.

See also: http://salilab.org/modeller/manual/manual.html, "Features and their derivatives"

References angle::delta, angle::have_angle_model, and angle::weight.

Referenced by angle::add_gradients().

void add_gradients	(	af::ref< scitbx::vec3< double > > const &	gradient_array,
		angle_proxy::i_seqs_type const &	i_seqs
	)			const `[inline]`

Support for angle_residual_sum.

Not available in Python.

References angle::gradients().

Member Data Documentation

double delta

Smallest difference between angle_model and angle_ideal taking the periodicity into account.


Public Member Functions
	angle ()
	Default constructor. Some data members are not initialized!
	angle (af::tiny< scitbx::vec3< double >, 3 > const &sites_, double angle_ideal_, double weight_)
	Constructor.
	angle (af::const_ref< scitbx::vec3< double > > const &sites_cart, angle_proxy const &proxy)
	Coordinates are copied from sites_cart according to proxy.i_seqs, parameters are copied from proxy.
double	residual () const
	weight * delta**2.
af::tiny< scitbx::vec3< double >, 3 >	gradients (double epsilon=1.e-100) const
	Gradients with respect to the three sites.
void	add_gradients (af::ref< scitbx::vec3< double > > const &gradient_array, angle_proxy::i_seqs_type const &i_seqs) const
	Support for angle_residual_sum.
Public Attributes
af::tiny< scitbx::vec3< double >, 3 >	sites
	Cartesian coordinates of sites forming the angle.
double	angle_ideal
	Parameter (usually as passed to the constructor).
double	weight
	Parameter (usually as passed to the constructor).
bool	have_angle_model
	false in singular situations.
double	angle_model
	Value of angle formed by the sites.
double	delta
	Smallest difference between angle_model and angle_ideal taking the periodicity into account.