cctbx::geometry_restraints Namespace Reference

Geometry restraints (bond, angle, etc.). More...

Classes
struct	angle_proxy
	Grouping of indices into array of sites (i_seqs) and angle_params. More...
class	angle
	Residual and gradient calculations for angle restraint. More...
class	asu_cache
	Asymmetric unit cache to facilitate speed optimizations. More...
struct	bond_params
	Grouping of bond parameters distance_ideal and weight. More...
struct	bond_simple_proxy
	Grouping of indices into array of sites (i_seqs) and bond_params. More...
struct	bond_sym_proxy
	Grouping of bond_simple_proxy and symmetry operation (rt_mx_ji). More...
struct	bond_asu_proxy
	Grouping of asu_mapping_index_pair and bond_params. More...
class	bond
	Residual and gradient calculations for harmonically restrained bonds. More...
struct	bond_similarity_proxy
class	bond_similarity
	Residual and gradient calculations for harmonically restrained bonds. More...
class	bond_sorted_asu_proxies
	Generation of sorted bond proxies. More...
struct	chirality_proxy
	Grouping of indices into array of sites (i_seqs) and parameters. More...
class	chirality
	Residual and gradient calculations for chirality restraint. More...
struct	dihedral_proxy
	Grouping of indices into array of sites (i_seqs) and dihedral_params. More...
class	dihedral
	Residual and gradient calculations for dihedral angle restraint. More...
struct	motif
struct	nonbonded_params
	Grouping of parameters for the generation of nonbonded pair interactions. More...
struct	nonbonded_simple_proxy
	Grouping of indices into array of sites (i_seqs) and vdw_distance. More...
struct	nonbonded_asu_proxy
	Grouping of asu_mapping_index_pair and vdw_distance. More...
struct	prolsq_repulsion_function
	General repulsive function (see PROLSQ and CNS). More...
struct	inverse_power_repulsion_function
	energy(delta) = k_rep*vdw_distance/(delta**irexp) repulsive function. More...
struct	cos_repulsion_function
	energy(delta) = max_residual*((cos(pi*delta)+1)/2)**exponent More...
struct	gaussian_repulsion_function
	energy(delta) = max_residual*exp(-delta**2/f_sq) More...
class	nonbonded
	Residual and gradient calculations for nonbonded restraints. More...
class	nonbonded_sorted_asu_proxies
	Generation of sorted nonbonded proxies. More...
struct	planarity_proxy
	Grouping of indices into array of sites (i_seqs) and weights. More...
class	planarity
	Residual and gradient calculations for planarity restraint. More...
class	sorted_asu_proxies
	Managed group of simple proxies and asu proxies. More...
Typedefs
typedef std::map< unsigned, bond_params >	bond_params_dict
	Dictionary of bond parameters for a given index i_seq.
typedef af::shared < bond_params_dict >	bond_params_table
	Array of dictionary of bond parameters. The index i_seq is implied.
typedef sorted_asu_proxies < bond_simple_proxy, bond_asu_proxy >	bond_sorted_asu_proxies_base
	Managed group of bond_simple_proxy and bond_asu_proxy arrays.
typedef std::map< std::string, double >	nonbonded_distance_dict
	Dictionary of VdW distances (element of nonbonded_distance_table).
typedef std::map< std::string, std::map< std::string, double > >	nonbonded_distance_table
	Table of VdW distances (given two energy types).
typedef std::map< std::string, double >	nonbonded_radius_table
	Table of VdW radii (given one energy type).
typedef sorted_asu_proxies < nonbonded_simple_proxy, nonbonded_asu_proxy >	nonbonded_sorted_asu_proxies_base
	Managed group of nonbonded_simple_proxy and nonbonded_asu_proxy arrays.
typedef direct_space_asu::asu_mapping_index	asu_mapping_index
	Convenience typedef.
typedef direct_space_asu::asu_mapping_index_pair	asu_mapping_index_pair
	Convenience typedef.
typedef direct_space_asu::asu_mappings	asu_mappings
	Convenience typedef.
Functions
af::shared< double >	angle_deltas (af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< angle_proxy > const &proxies)
af::shared< double >	angle_deltas (uctbx::unit_cell const &unit_cell, af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< angle_proxy > const &proxies)
af::shared< double >	angle_residuals (af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< angle_proxy > const &proxies)
af::shared< double >	angle_residuals (uctbx::unit_cell const &unit_cell, af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< angle_proxy > const &proxies)
double	angle_residual_sum (af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< angle_proxy > const &proxies, af::ref< scitbx::vec3< double > > const &gradient_array)
double	angle_residual_sum (uctbx::unit_cell const &unit_cell, af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< angle_proxy > const &proxies, af::ref< scitbx::vec3< double > > const &gradient_array)
bond_params_table	extract_bond_params (std::size_t n_seq, af::const_ref< bond_simple_proxy > const &bond_simple_proxies)
	Extracts bond parameters from array of simple proxies.
af::shared< double >	bond_distances_model (af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< bond_simple_proxy > const &proxies)
	Fast computation of bond::distance_model given an array of bond proxies.
af::shared< double >	bond_deltas (af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< bond_simple_proxy > const &proxies)
	Fast computation of bond::delta given an array of bond proxies.
af::shared< double >	bond_residuals (af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< bond_simple_proxy > const &proxies)
	Fast computation of bond::residual() given an array of bond proxies.
double	bond_residual_sum (af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< bond_simple_proxy > const &proxies, af::ref< scitbx::vec3< double > > const &gradient_array)
af::shared< double >	bond_distances_model (af::const_ref< scitbx::vec3< double > > const &sites_cart, bond_sorted_asu_proxies_base const &sorted_asu_proxies)
	Fast computation of bond::distance_model given managed proxies.
af::shared< double >	bond_deltas (af::const_ref< scitbx::vec3< double > > const &sites_cart, bond_sorted_asu_proxies_base const &sorted_asu_proxies)
	Fast computation of bond::delta given managed proxies.
af::shared< double >	bond_residuals (af::const_ref< scitbx::vec3< double > > const &sites_cart, bond_sorted_asu_proxies_base const &sorted_asu_proxies)
	Fast computation of bond::residual() given managed proxies.
double	bond_residual_sum (af::const_ref< scitbx::vec3< double > > const &sites_cart, bond_sorted_asu_proxies_base const &sorted_asu_proxies, af::ref< scitbx::vec3< double > > const &gradient_array, bool disable_cache=false)
af::shared< double >	bond_similarity_deltas_rms (af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< bond_similarity_proxy > const &proxies)
	Fast computation of bond_similarity::rms_deltas() given an array of bond_similarity proxies, ignoring proxy.sym_ops.
af::shared< double >	bond_similarity_residuals (af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< bond_similarity_proxy > const &proxies)
	Fast computation of bond_similarity::residual() given an array of bond_similarity proxies, ignoring proxy.sym_ops.
double	bond_similarity_residual_sum (af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< bond_similarity_proxy > const &proxies, af::ref< scitbx::vec3< double > > const &gradient_array)
af::shared< double >	bond_similarity_deltas_rms (uctbx::unit_cell const &unit_cell, af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< bond_similarity_proxy > const &proxies)
	Fast computation of bond_similarity::rms_deltas() given an array of bond_similarity proxies, taking account of proxy.sym_ops.
af::shared< double >	bond_similarity_residuals (uctbx::unit_cell const &unit_cell, af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< bond_similarity_proxy > const &proxies)
	Fast computation of bond_similarity::residual() given an array of bond_similarity proxies, taking account of proxy.sym_ops.
double	bond_similarity_residual_sum (uctbx::unit_cell const &unit_cell, af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< bond_similarity_proxy > const &proxies, af::ref< scitbx::vec3< double > > const &gradient_array)
void	add_pairs (crystal::pair_asu_table<> &pair_asu_table, af::const_ref< bond_simple_proxy > const &bond_simple_proxies)
	Adds all pairs defined by bond_simple_proxies[i].i_seqs.
af::shared< double >	chirality_deltas (af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< chirality_proxy > const &proxies)
	Fast computation of chirality::delta given an array of chirality proxies.
af::shared< double >	chirality_residuals (af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< chirality_proxy > const &proxies)
double	chirality_residual_sum (af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< chirality_proxy > const &proxies, af::ref< scitbx::vec3< double > > const &gradient_array)
std::size_t	dihedral_count_harmonic (af::const_ref< dihedral_proxy > const &proxies)
	Number of proxies with periodicity <= 0.
af::shared< double >	dihedral_deltas (af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< dihedral_proxy > const &proxies)
af::shared< double >	dihedral_residuals (af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< dihedral_proxy > const &proxies)
double	dihedral_residual_sum (af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< dihedral_proxy > const &proxies, af::ref< scitbx::vec3< double > > const &gradient_array)
af::shared< double >	dihedral_deltas (uctbx::unit_cell const &unit_cell, af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< dihedral_proxy > const &proxies)
af::shared< double >	dihedral_residuals (uctbx::unit_cell const &unit_cell, af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< dihedral_proxy > const &proxies)
double	dihedral_residual_sum (uctbx::unit_cell const &unit_cell, af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< dihedral_proxy > const &proxies, af::ref< scitbx::vec3< double > > const &gradient_array)
af::shared< double >	nonbonded_deltas (af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< nonbonded_simple_proxy > const &proxies)
	Fast computation of nonbonded::delta given an array of nonbonded proxies.
template<typename NonbondedFunction>
af::shared< double >	nonbonded_residuals (af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< nonbonded_simple_proxy > const &proxies, NonbondedFunction const &function)
	Fast computation of nonbonded::residual() given an array of nonbonded proxies.
template<typename NonbondedFunction>
double	nonbonded_residual_sum (af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< nonbonded_simple_proxy > const &proxies, af::ref< scitbx::vec3< double > > const &gradient_array, NonbondedFunction const &function)
af::shared< double >	nonbonded_deltas (af::const_ref< scitbx::vec3< double > > const &sites_cart, nonbonded_sorted_asu_proxies_base const &sorted_asu_proxies)
	Fast computation of nonbonded::delta given managed proxies.
template<typename NonbondedFunction>
af::shared< double >	nonbonded_residuals (af::const_ref< scitbx::vec3< double > > const &sites_cart, nonbonded_sorted_asu_proxies_base const &sorted_asu_proxies, NonbondedFunction const &function)
	Fast computation of nonbonded::residual() given managed proxies.
template<typename NonbondedFunction>
double	nonbonded_residual_sum (af::const_ref< scitbx::vec3< double > > const &sites_cart, nonbonded_sorted_asu_proxies_base const &sorted_asu_proxies, af::ref< scitbx::vec3< double > > const &gradient_array, NonbondedFunction const &function, bool disable_cache=false)
af::shared< double >	planarity_deltas_rms (af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< planarity_proxy > const &proxies)
	Fast computation of planarity::rms_deltas() given an array of planarity proxies, ignoring proxy.sym_ops.
af::shared< double >	planarity_residuals (af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< planarity_proxy > const &proxies)
	Fast computation of planarity::residual() given an array of planarity proxies, ignoring proxy.sym_ops.
double	planarity_residual_sum (af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< planarity_proxy > const &proxies, af::ref< scitbx::vec3< double > > const &gradient_array)
af::shared< double >	planarity_deltas_rms (uctbx::unit_cell const &unit_cell, af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< planarity_proxy > const &proxies)
	Fast computation of planarity::rms_deltas() given an array of planarity sym proxies, taking account of proxy.sym_ops.
af::shared< double >	planarity_residuals (uctbx::unit_cell const &unit_cell, af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< planarity_proxy > const &proxies)
	Fast computation of planarity::residual() given an array of planarity sym proxies, taking account of proxy.sym_ops.
double	planarity_residual_sum (uctbx::unit_cell const &unit_cell, af::const_ref< scitbx::vec3< double > > const &sites_cart, af::const_ref< planarity_proxy > const &proxies, af::ref< scitbx::vec3< double > > const &gradient_array)
template<typename ProxyType>
af::shared< ProxyType >	shared_proxy_select (af::const_ref< ProxyType > const &self, std::size_t n_seq, af::const_ref< std::size_t > const &iselection)
	Applies selection on array of atoms to array of angle, dihedral or chirality proxies.
template<typename ProxyType>
af::shared< ProxyType >	shared_planarity_proxy_select (af::const_ref< ProxyType > const &self, std::size_t n_seq, af::const_ref< std::size_t > const &iselection)
	Applies selection on array of atoms to array of planarity proxies.
template<typename ProxyType>
af::shared< ProxyType >	shared_proxy_remove (af::const_ref< ProxyType > const &self, af::const_ref< bool > const &selection)
scitbx::mat3< double >	r_inv_cart (uctbx::unit_cell const &unit_cell, sgtbx::rt_mx const &rt_mx)
	Rotation part of rt_mx.inverse() in the cartesian system.
double	angle_delta_deg (double angle_1, double angle_2, int periodicity=1)
	Difference between angle_1 and angle_2 (in degrees) taking the periodicity into account.

---

Detailed Description

Geometry restraints (bond, angle, etc.).

---

Function Documentation

af::shared<double> cctbx::geometry_restraints::angle_deltas	(	uctbx::unit_cell const &	unit_cell,
		af::const_ref< scitbx::vec3< double > > const &	sites_cart,
		af::const_ref< angle_proxy > const &	proxies
	)			[inline]

Fast computation of angle::delta given an array of angle proxies. taking into account proxy.sym_ops.

af::shared<double> cctbx::geometry_restraints::angle_deltas	(	af::const_ref< scitbx::vec3< double > > const &	sites_cart,
		af::const_ref< angle_proxy > const &	proxies
	)			[inline]

Fast computation of angle::delta given an array of angle proxies, ignoring proxy.sym_ops.

double cctbx::geometry_restraints::angle_residual_sum	(	uctbx::unit_cell const &	unit_cell,
		af::const_ref< scitbx::vec3< double > > const &	sites_cart,
		af::const_ref< angle_proxy > const &	proxies,
		af::ref< scitbx::vec3< double > > const &	gradient_array
	)			[inline]

Fast computation of sum of angle::residual() and gradients given an array of angle proxies, taking into account proxy.sym_ops.

The angle::gradients() are added to the gradient_array if gradient_array.size() == sites_cart.size(). gradient_array must be initialized before this function is called. No gradient calculations are performed if gradient_array.size() == 0.

double cctbx::geometry_restraints::angle_residual_sum	(	af::const_ref< scitbx::vec3< double > > const &	sites_cart,
		af::const_ref< angle_proxy > const &	proxies,
		af::ref< scitbx::vec3< double > > const &	gradient_array
	)			[inline]

Fast computation of sum of angle::residual() and gradients given an array of angle proxies, ignoring proxy.sym_ops.

The angle::gradients() are added to the gradient_array if gradient_array.size() == sites_cart.size(). gradient_array must be initialized before this function is called. No gradient calculations are performed if gradient_array.size() == 0.

af::shared<double> cctbx::geometry_restraints::angle_residuals	(	uctbx::unit_cell const &	unit_cell,
		af::const_ref< scitbx::vec3< double > > const &	sites_cart,
		af::const_ref< angle_proxy > const &	proxies
	)			[inline]

Fast computation of angle::residual() given an array of angle proxies, taking account of proxy.sym_ops.

af::shared<double> cctbx::geometry_restraints::angle_residuals	(	af::const_ref< scitbx::vec3< double > > const &	sites_cart,
		af::const_ref< angle_proxy > const &	proxies
	)			[inline]

Fast computation of angle::residual() given an array of angle proxies, ignoring proxy.sym_ops.

double cctbx::geometry_restraints::bond_residual_sum	(	af::const_ref< scitbx::vec3< double > > const &	sites_cart,
		bond_sorted_asu_proxies_base const &	sorted_asu_proxies,
		af::ref< scitbx::vec3< double > > const &	gradient_array,
		bool	disable_cache = false
	)			[inline]

Fast computation of sum of bond::residual() and gradients given managed proxies.

The bond::gradients() are added to the gradient_array if gradient_array.size() == sites_cart.size(). gradient_array must be initialized before this function is called. No gradient calculations are performed if gradient_array.size() == 0.

Intermediate results are accumulated in an asu cache until disable_cache=true. The accumulated results are mapped back to the original sites at the end of the calculation. This is faster but requires more memory.

References sorted_asu_proxies::asu, sorted_asu_proxies::asu_active_flags, sorted_asu_proxies::asu_mappings(), bond_residual_sum(), and sorted_asu_proxies::simple.

double cctbx::geometry_restraints::bond_residual_sum	(	af::const_ref< scitbx::vec3< double > > const &	sites_cart,
		af::const_ref< bond_simple_proxy > const &	proxies,
		af::ref< scitbx::vec3< double > > const &	gradient_array
	)			[inline]

Fast computation of sum of bond::residual() and gradients given an array of bond proxies.

The bond::gradients() are added to the gradient_array if gradient_array.size() == sites_cart.size(). gradient_array must be initialized before this function is called. No gradient calculations are performed if gradient_array.size() == 0.

Referenced by bond_residual_sum().

double cctbx::geometry_restraints::bond_similarity_residual_sum	(	uctbx::unit_cell const &	unit_cell,
		af::const_ref< scitbx::vec3< double > > const &	sites_cart,
		af::const_ref< bond_similarity_proxy > const &	proxies,
		af::ref< scitbx::vec3< double > > const &	gradient_array
	)			[inline]

Fast computation of sum of bond_similarity::residual() and gradients given an array of bond_similarity proxies, taking account of proxy.sym_ops.

The bond_similarity::gradients() are added to the gradient_array if gradient_array.size() == sites_cart.size(). gradient_array must be initialized before this function is called. No gradient calculations are performed if gradient_array.size() == 0.

double cctbx::geometry_restraints::bond_similarity_residual_sum	(	af::const_ref< scitbx::vec3< double > > const &	sites_cart,
		af::const_ref< bond_similarity_proxy > const &	proxies,
		af::ref< scitbx::vec3< double > > const &	gradient_array
	)			[inline]

Fast computation of sum of bond_similarity::residual() and gradients given an array of bond_similarity proxies, ignoring proxy.sym_ops.

The bond_similarity::gradients() are added to the gradient_array if gradient_array.size() == sites_cart.size(). gradient_array must be initialized before this function is called. No gradient calculations are performed if gradient_array.size() == 0.

double cctbx::geometry_restraints::chirality_residual_sum	(	af::const_ref< scitbx::vec3< double > > const &	sites_cart,
		af::const_ref< chirality_proxy > const &	proxies,
		af::ref< scitbx::vec3< double > > const &	gradient_array
	)			[inline]

Fast computation of sum of chirality::residual() and gradients given an array of chirality proxies.

The chirality::gradients() are added to the gradient_array if gradient_array.size() == sites_cart.size(). gradient_array must be initialized before this function is called. No gradient calculations are performed if gradient_array.size() == 0.

af::shared<double> cctbx::geometry_restraints::chirality_residuals	(	af::const_ref< scitbx::vec3< double > > const &	sites_cart,
		af::const_ref< chirality_proxy > const &	proxies
	)			[inline]

Fast computation of chirality::residual() given an array of chirality proxies.

af::shared<double> cctbx::geometry_restraints::dihedral_deltas	(	uctbx::unit_cell const &	unit_cell,
		af::const_ref< scitbx::vec3< double > > const &	sites_cart,
		af::const_ref< dihedral_proxy > const &	proxies
	)			[inline]

Fast computation of dihedral::delta given an array of dihedral proxies, taking into account proxy.sym_ops.

af::shared<double> cctbx::geometry_restraints::dihedral_deltas	(	af::const_ref< scitbx::vec3< double > > const &	sites_cart,
		af::const_ref< dihedral_proxy > const &	proxies
	)			[inline]

Fast computation of dihedral::delta given an array of dihedral proxies, ignoring proxy.sym_ops.

double cctbx::geometry_restraints::dihedral_residual_sum	(	uctbx::unit_cell const &	unit_cell,
		af::const_ref< scitbx::vec3< double > > const &	sites_cart,
		af::const_ref< dihedral_proxy > const &	proxies,
		af::ref< scitbx::vec3< double > > const &	gradient_array
	)			[inline]

Fast computation of sum of dihedral::residual() and gradients given an array of dihedral proxies, taking into account proxy.sym_ops.

The dihedral::gradients() are added to the gradient_array if gradient_array.size() == sites_cart.size(). gradient_array must be initialized before this function is called. No gradient calculations are performed if gradient_array.size() == 0.

double cctbx::geometry_restraints::dihedral_residual_sum	(	af::const_ref< scitbx::vec3< double > > const &	sites_cart,
		af::const_ref< dihedral_proxy > const &	proxies,
		af::ref< scitbx::vec3< double > > const &	gradient_array
	)			[inline]

Fast computation of sum of dihedral::residual() and gradients given an array of dihedral proxies, ignoring proxy.sym_ops.

The dihedral::gradients() are added to the gradient_array if gradient_array.size() == sites_cart.size(). gradient_array must be initialized before this function is called. No gradient calculations are performed if gradient_array.size() == 0.

af::shared<double> cctbx::geometry_restraints::dihedral_residuals	(	uctbx::unit_cell const &	unit_cell,
		af::const_ref< scitbx::vec3< double > > const &	sites_cart,
		af::const_ref< dihedral_proxy > const &	proxies
	)			[inline]

Fast computation of dihedral::residual() given an array of dihedral proxies, taking into account proxy.sym_ops.

af::shared<double> cctbx::geometry_restraints::dihedral_residuals	(	af::const_ref< scitbx::vec3< double > > const &	sites_cart,
		af::const_ref< dihedral_proxy > const &	proxies
	)			[inline]

Fast computation of dihedral::residual() given an array of dihedral proxies, ignoring proxy.sym_ops.

double cctbx::geometry_restraints::nonbonded_residual_sum	(	af::const_ref< scitbx::vec3< double > > const &	sites_cart,
		nonbonded_sorted_asu_proxies_base const &	sorted_asu_proxies,
		af::ref< scitbx::vec3< double > > const &	gradient_array,
		NonbondedFunction const &	function,
		bool	disable_cache = false
	)			[inline]

Fast computation of sum of nonbonded::residual() and gradients given managed proxies.

The nonbonded::gradients() are added to the gradient_array if gradient_array.size() == sites_cart.size(). gradient_array must be initialized before this function is called. No gradient calculations are performed if gradient_array.size() == 0.

Intermediate results are accumulated in an asu cache until disable_cache=true. The accumulated results are mapped back to the original sites at the end of the calculation. This is faster but requires more memory.

References sorted_asu_proxies::asu, sorted_asu_proxies::asu_active_flags, sorted_asu_proxies::asu_mappings(), nonbonded_residual_sum(), and sorted_asu_proxies::simple.

double cctbx::geometry_restraints::nonbonded_residual_sum	(	af::const_ref< scitbx::vec3< double > > const &	sites_cart,
		af::const_ref< nonbonded_simple_proxy > const &	proxies,
		af::ref< scitbx::vec3< double > > const &	gradient_array,
		NonbondedFunction const &	function
	)			[inline]

Fast computation of sum of nonbonded::residual() and gradients given an array of nonbonded proxies.

The nonbonded::gradients() are added to the gradient_array if gradient_array.size() == sites_cart.size(). gradient_array must be initialized before this function is called. No gradient calculations are performed if gradient_array.size() == 0.

References nonbonded::add_gradients(), and nonbonded::residual().

Referenced by nonbonded_residual_sum().

double cctbx::geometry_restraints::planarity_residual_sum	(	uctbx::unit_cell const &	unit_cell,
		af::const_ref< scitbx::vec3< double > > const &	sites_cart,
		af::const_ref< planarity_proxy > const &	proxies,
		af::ref< scitbx::vec3< double > > const &	gradient_array
	)			[inline]

Fast computation of sum of planarity::residual() and gradients given an array of planarity sym proxies, taking account of proxy.sym_ops.

The planarity::gradients() are added to the gradient_array if gradient_array.size() == sites_cart.size(). gradient_array must be initialized before this function is called. No gradient calculations are performed if gradient_array.size() == 0.

double cctbx::geometry_restraints::planarity_residual_sum	(	af::const_ref< scitbx::vec3< double > > const &	sites_cart,
		af::const_ref< planarity_proxy > const &	proxies,
		af::ref< scitbx::vec3< double > > const &	gradient_array
	)			[inline]

Fast computation of sum of planarity::residual() and gradients given an array of planarity proxies, ignoring proxy.sym_ops.

The planarity::gradients() are added to the gradient_array if gradient_array.size() == sites_cart.size(). gradient_array must be initialized before this function is called. No gradient calculations are performed if gradient_array.size() == 0.

scitbx::mat3<double> cctbx::geometry_restraints::r_inv_cart	(	uctbx::unit_cell const &	unit_cell,
		sgtbx::rt_mx const &	rt_mx
	)			[inline]

Rotation part of rt_mx.inverse() in the cartesian system.

Useful for mapping gradients in cartesian space from the asymmetric unit to the original sites.

Inefficient implementation, the rotation matrices are NOT cached.

References unit_cell::fractionalization_matrix(), unit_cell::orthogonalization_matrix(), and rt_mx::r().

Referenced by planarity::add_gradients(), dihedral::add_gradients(), bond_similarity::add_gradients(), and angle::add_gradients().