#include <bond_similarity.h>
Public Types | |
| typedef scitbx::vec3< double > | vec3 |
| Convenience typedef. | |
Public Member Functions | |
| bond_similarity () | |
| Default constructor. Some data members are not initialized! | |
| bond_similarity (af::shared< af::tiny< vec3, 2 > > const &sites_array_, af::shared< double > const &weights_) | |
| Constructor. | |
| bond_similarity (af::const_ref< vec3 > const &sites_cart, bond_similarity_proxy const &proxy) | |
| Coordinates are copied from sites_cart according to proxy.i_seqs, parameters are copied from proxy. | |
| bond_similarity (uctbx::unit_cell const &unit_cell, af::const_ref< vec3 > const &sites_cart, bond_similarity_proxy const &proxy) | |
| Coordinates are obtained from sites_cart according to proxy.i_seqs by applying proxy.sym_ops and unit_cell, parameters are copied from proxy. | |
| af::shared< double > const & | deltas () const |
| Array of deviation from mean bond distance for each pair. | |
| double | rms_deltas () const |
| sqrt(mean_sq(deltas)) | |
| double | residual () const |
| sum(weight_i * delta_i**2) / sum(weights). | |
| af::shared< af::tiny< vec3, 2 > > | gradients () const |
| Gradients with respect to the sites. | |
| void | add_gradients (af::ref< scitbx::vec3< double > > const &gradient_array, bond_similarity_proxy::i_seqs_type const &i_seqs) const |
| Support for bond_similarity_residual_sum. | |
| void | add_gradients (uctbx::unit_cell const &unit_cell, af::ref< scitbx::vec3< double > > const &gradient_array, bond_similarity_proxy const &proxy) const |
| Support for bond_similarity_residual_sum. | |
| double | mean_distance () const |
| Weighted mean of the bond lengths. | |
Public Attributes | |
| af::shared< af::tiny< vec3, 2 > > | sites_array |
| Cartesian coordinates of bonded sites. | |
| af::shared< double > | weights |
| Array of weights for each pair. | |
| void add_gradients | ( | af::ref< scitbx::vec3< double > > const & | gradient_array, | |
| bond_similarity_proxy::i_seqs_type const & | i_seqs | |||
| ) | const [inline] |
Support for bond_similarity_residual_sum.
Not available in Python.
References bond_similarity::gradients().
| void add_gradients | ( | uctbx::unit_cell const & | unit_cell, | |
| af::ref< scitbx::vec3< double > > const & | gradient_array, | |||
| bond_similarity_proxy const & | proxy | |||
| ) | const [inline] |
Support for bond_similarity_residual_sum.
Not available in Python.
Inefficient implementation, r_inv_cart is not cached. TODO: use asu_mappings to take advantage of caching of r_inv_cart.
References optional_copy::get(), bond_similarity::gradients(), bond_similarity_proxy::i_seqs, cctbx::geometry_restraints::r_inv_cart(), and bond_similarity_proxy::sym_ops.
1.5.6