bond Class Reference

Residual and gradient calculations for harmonically restraint bonds. More...

#include <bond.h>

Inheritance diagram for bond:

List of all members.

Public Types
typedef scitbx::vec3< double >	vec3
	Convenience typedef.
Public Member Functions
	bond ()
	Default constructor. Some data members are not initialized!
	bond (af::tiny< scitbx::vec3< double >, 2 > const &sites_, double distance_ideal_, double weight_, double slack_=0)
	Constructor.
	bond (af::const_ref< scitbx::vec3< double > > const &sites_cart, bond_simple_proxy const &proxy)
	Coordinates are copied from sites_cart according to proxy.i_seqs, parameters are copied from proxy.
	bond (uctbx::unit_cell const &unit_cell, af::const_ref< scitbx::vec3< double > > const &sites_cart, bond_sym_proxy const &proxy)
	Coordinates are copied from sites_cart according to proxy.i_seqs and proxy.rt_mx_ji, parameters are copied from proxy.
	bond (af::const_ref< scitbx::vec3< double > > const &sites_cart, direct_space_asu::asu_mappings<> const &asu_mappings, bond_asu_proxy const &proxy)
	Coordinates are copied from sites_cart according to proxy.i_seq, proxy.j_seq, parameters are copied from proxy.
	bond (asu_cache<> const &cache, bond_asu_proxy const &proxy)
	For fast processing. Not available in Python.
double	residual () const
	weight * delta_slack**2.
scitbx::vec3< double >	gradient_0 (double epsilon=1.e-100) const
	Gradient with respect to sites[0].
af::tiny< scitbx::vec3< double >, 2 >	gradients () const
	Gradients with respect to both sites.
void	add_gradients (af::ref< scitbx::vec3< double > > const &gradient_array, af::tiny< unsigned, 2 > const &i_seqs) const
	Support for bond_residual_sum.
void	add_gradients (af::ref< scitbx::vec3< double > > const &gradient_array, direct_space_asu::asu_mappings<> const &asu_mappings, asu_mapping_index_pair const &pair) const
	Support for bond_residual_sum.
void	add_gradients (asu_cache<> &cache, asu_mapping_index_pair const &pair) const
	Support for bond_residual_sum.
Public Attributes
af::tiny< scitbx::vec3< double >, 2 >	sites
	Cartesian coordinates of bonded sites.
double	distance_model
	Distance between sites.
double	delta
	Difference distance_ideal - distance_model.
double	delta_slack
	sign(delta) * max(0, (abs(delta) - slack)).

---

Detailed Description

Residual and gradient calculations for harmonically restraint bonds.

---

Member Function Documentation

double residual

(

)

const [inline]

weight * delta_slack**2.

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

References bond::delta_slack, and bond_params::weight.

Referenced by cctbx::geometry_restraints::bond_residuals().

scitbx::vec3<double> gradient_0

(

double

epsilon = 1.e-100

)

const [inline]

Gradient with respect to sites[0].

Not available in Python.

References bond::delta_slack, bond::distance_model, bond::sites, bond_params::slack, and bond_params::weight.

Referenced by bond::add_gradients(), and bond::gradients().

void add_gradients	(	af::ref< scitbx::vec3< double > > const &	gradient_array,
		af::tiny< unsigned, 2 > const &	i_seqs
	)			const [inline]

Support for bond_residual_sum.

Not available in Python.

References bond::gradient_0().

void add_gradients	(	af::ref< scitbx::vec3< double > > const &	gradient_array,
		direct_space_asu::asu_mappings<> const &	asu_mappings,
		asu_mapping_index_pair const &	pair
	)			const [inline]

Support for bond_residual_sum.

Not available in Python.

References bond::gradient_0(), asu_mapping_index_pair::i_seq, asu_mapping_index_pair::j_seq, asu_mapping_index_pair::j_sym, and asu_mappings::r_inv_cart().

void add_gradients	(	asu_cache<> &	cache,
		asu_mapping_index_pair const &	pair
	)			const [inline]

Support for bond_residual_sum.

Not available in Python.

References bond::gradient_0(), asu_cache::gradients, asu_mapping_index_pair::i_seq, asu_mapping_index_pair::j_seq, and asu_mapping_index_pair::j_sym.

---

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

• cctbx/geometry_restraints/bond.h