cctbx.geometry_restraints
index
/net/chevy/raid1/nat/src/cctbx_project/cctbx/geometry_restraints/__init__.py

 
Package Contents
       
distance_least_squares
energies
flags
lbfgs
manager
tst_angle_derivs
tst_ext
tst_motif
tst_nb_clashscore
tst_proxy_registry

 
Classes
       
__builtin__.object
pair_proxies
proxy_registry_base
angle_proxy_registry
bond_simple_proxy_registry
chirality_proxy_registry
dihedral_proxy_registry
planarity_proxy_registry
proxy_registry_process_result

 
class angle_proxy_registry(proxy_registry_base)
    
Method resolution order:
angle_proxy_registry
proxy_registry_base
__builtin__.object

Methods defined here:
__init__(self, strict_conflict_handling)
lookup_i_proxy(self, i_seqs)
See also: cctbx::geometry_restraints::angle_proxy::sort_i_seqs()
process(self, source_info, proxy, tolerance=1e-06)

Methods inherited from proxy_registry_base:
append_custom_proxy(self, proxy)
discard_table(self)
initialize_table(self)

Data descriptors inherited from proxy_registry_base:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class bond_simple_proxy_registry(proxy_registry_base)
    
Method resolution order:
bond_simple_proxy_registry
proxy_registry_base
__builtin__.object

Methods defined here:
__init__(self, n_seq, strict_conflict_handling)
initialize_table(self)
is_any_proxy_set(self, i_seqs, j_seqs)
is_proxy_set(self, i_seqs)
process(self, source_info, proxy, tolerance=1e-06)

Methods inherited from proxy_registry_base:
append_custom_proxy(self, proxy)
discard_table(self)

Data descriptors inherited from proxy_registry_base:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class chirality_proxy_registry(proxy_registry_base)
    
Method resolution order:
chirality_proxy_registry
proxy_registry_base
__builtin__.object

Methods defined here:
__init__(self, strict_conflict_handling)
process(self, source_info, proxy, tolerance=1e-06)

Methods inherited from proxy_registry_base:
append_custom_proxy(self, proxy)
discard_table(self)
initialize_table(self)

Data descriptors inherited from proxy_registry_base:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class dihedral_proxy_registry(proxy_registry_base)
    
Method resolution order:
dihedral_proxy_registry
proxy_registry_base
__builtin__.object

Methods defined here:
__init__(self, strict_conflict_handling)
lookup_i_proxy(self, i_seqs)
See also: cctbx::geometry_restraints::dihedral_proxy::sort_i_seqs()
process(self, source_info, proxy, tolerance=1e-06)

Methods inherited from proxy_registry_base:
append_custom_proxy(self, proxy)
discard_table(self)
initialize_table(self)

Data descriptors inherited from proxy_registry_base:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class pair_proxies(__builtin__.object)
     Methods defined here:
__init__(self, flags=None, bond_params_table=None, shell_asu_tables=None, model_indices=None, conformer_indices=None, sym_excl_indices=None, donor_acceptor_excl_groups=None, nonbonded_params=None, nonbonded_types=None, nonbonded_charges=None, nonbonded_distance_cutoff_plus_buffer=None, min_cubicle_edge=5)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class planarity_proxy_registry(proxy_registry_base)
    
Method resolution order:
planarity_proxy_registry
proxy_registry_base
__builtin__.object

Methods defined here:
__init__(self, strict_conflict_handling)
process(self, source_info, proxy, tolerance=1e-06)

Methods inherited from proxy_registry_base:
append_custom_proxy(self, proxy)
discard_table(self)
initialize_table(self)

Data descriptors inherited from proxy_registry_base:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class proxy_registry_base(__builtin__.object)
     Methods defined here:
__init__(self, proxies, strict_conflict_handling)
append_custom_proxy(self, proxy)
discard_table(self)
initialize_table(self)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class proxy_registry_process_result(__builtin__.object)
     Methods defined here:
__init__(self, tabulated_proxy=None, is_new=False, is_conflicting=False, conflict_source_labels=None)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
Functions
       
add_pairs(...)
add_pairs( (pair_asu_table)pair_asu_table, (shared_bond_simple_proxy)bond_simple_proxies) -> None :
 
    C++ signature :
        void add_pairs(cctbx::crystal::pair_asu_table<double, int> {lvalue},scitbx::af::const_ref<cctbx::geometry_restraints::bond_simple_proxy, scitbx::af::trivial_accessor>)
angle_delta_deg(angle_1, angle_2, periodicity=1)
angle_deltas(...)
angle_deltas( (vec3_double)sites_cart, (shared_angle_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> angle_deltas(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::angle_proxy, scitbx::af::trivial_accessor>)
 
angle_deltas( (unit_cell)unit_cell, (vec3_double)sites_cart, (shared_angle_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> angle_deltas(cctbx::uctbx::unit_cell,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::angle_proxy, scitbx::af::trivial_accessor>)
angle_residual_sum(...)
angle_residual_sum( (vec3_double)sites_cart, (shared_angle_proxy)proxies, (vec3_double)gradient_array) -> float :
 
    C++ signature :
        double angle_residual_sum(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::angle_proxy, scitbx::af::trivial_accessor>,scitbx::af::ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>)
 
angle_residual_sum( (unit_cell)unit_cell, (vec3_double)sites_cart, (shared_angle_proxy)proxies, (vec3_double)gradient_array) -> float :
 
    C++ signature :
        double angle_residual_sum(cctbx::uctbx::unit_cell,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::angle_proxy, scitbx::af::trivial_accessor>,scitbx::af::ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>)
angle_residuals(...)
angle_residuals( (vec3_double)sites_cart, (shared_angle_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> angle_residuals(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::angle_proxy, scitbx::af::trivial_accessor>)
 
angle_residuals( (unit_cell)unit_cell, (vec3_double)sites_cart, (shared_angle_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> angle_residuals(cctbx::uctbx::unit_cell,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::angle_proxy, scitbx::af::trivial_accessor>)
bond_deltas(...)
bond_deltas( (vec3_double)sites_cart, (shared_bond_simple_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> bond_deltas(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::bond_simple_proxy, scitbx::af::trivial_accessor>)
 
bond_deltas( (unit_cell)unit_cell, (vec3_double)sites_cart, (shared_bond_simple_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> bond_deltas(cctbx::uctbx::unit_cell,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::bond_simple_proxy, scitbx::af::trivial_accessor>)
 
bond_deltas( (vec3_double)sites_cart, (bond_sorted_asu_proxies_base)sorted_asu_proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> bond_deltas(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::sorted_asu_proxies<cctbx::geometry_restraints::bond_simple_proxy, cctbx::geometry_restraints::bond_asu_proxy>)
bond_distances_model(...)
bond_distances_model( (vec3_double)sites_cart, (shared_bond_simple_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> bond_distances_model(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::bond_simple_proxy, scitbx::af::trivial_accessor>)
 
bond_distances_model( (vec3_double)sites_cart, (bond_sorted_asu_proxies_base)sorted_asu_proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> bond_distances_model(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::sorted_asu_proxies<cctbx::geometry_restraints::bond_simple_proxy, cctbx::geometry_restraints::bond_asu_proxy>)
bond_residual_sum(...)
bond_residual_sum( (vec3_double)sites_cart, (shared_bond_simple_proxy)proxies, (vec3_double)gradient_array) -> float :
 
    C++ signature :
        double bond_residual_sum(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::bond_simple_proxy, scitbx::af::trivial_accessor>,scitbx::af::ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>)
 
bond_residual_sum( (unit_cell)unit_cell, (vec3_double)sites_cart, (shared_bond_simple_proxy)proxies, (vec3_double)gradient_array) -> float :
 
    C++ signature :
        double bond_residual_sum(cctbx::uctbx::unit_cell,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::bond_simple_proxy, scitbx::af::trivial_accessor>,scitbx::af::ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>)
 
bond_residual_sum( (vec3_double)sites_cart, (bond_sorted_asu_proxies_base)sorted_asu_proxies, (vec3_double)gradient_array [, (bool)disable_cache=False]) -> float :
 
    C++ signature :
        double bond_residual_sum(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::sorted_asu_proxies<cctbx::geometry_restraints::bond_simple_proxy, cctbx::geometry_restraints::bond_asu_proxy>,scitbx::af::ref<scitbx::vec3<double>, scitbx::af::trivial_accessor> [,bool=False])
bond_residuals(...)
bond_residuals( (vec3_double)sites_cart, (shared_bond_simple_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> bond_residuals(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::bond_simple_proxy, scitbx::af::trivial_accessor>)
 
bond_residuals( (unit_cell)unit_cell, (vec3_double)sites_cart, (shared_bond_simple_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> bond_residuals(cctbx::uctbx::unit_cell,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::bond_simple_proxy, scitbx::af::trivial_accessor>)
 
bond_residuals( (vec3_double)sites_cart, (bond_sorted_asu_proxies_base)sorted_asu_proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> bond_residuals(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::sorted_asu_proxies<cctbx::geometry_restraints::bond_simple_proxy, cctbx::geometry_restraints::bond_asu_proxy>)
bond_similarity_deltas_rms(...)
bond_similarity_deltas_rms( (vec3_double)sites_cart, (shared_bond_similarity_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> bond_similarity_deltas_rms(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::bond_similarity_proxy, scitbx::af::trivial_accessor>)
 
bond_similarity_deltas_rms( (unit_cell)unit_cell, (vec3_double)sites_cart, (shared_bond_similarity_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> bond_similarity_deltas_rms(cctbx::uctbx::unit_cell,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::bond_similarity_proxy, scitbx::af::trivial_accessor>)
bond_similarity_residual_sum(...)
bond_similarity_residual_sum( (vec3_double)sites_cart, (shared_bond_similarity_proxy)proxies, (vec3_double)gradient_array) -> float :
 
    C++ signature :
        double bond_similarity_residual_sum(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::bond_similarity_proxy, scitbx::af::trivial_accessor>,scitbx::af::ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>)
 
bond_similarity_residual_sum( (unit_cell)unit_cell, (vec3_double)sites_cart, (shared_bond_similarity_proxy)proxies, (vec3_double)gradient_array) -> float :
 
    C++ signature :
        double bond_similarity_residual_sum(cctbx::uctbx::unit_cell,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::bond_similarity_proxy, scitbx::af::trivial_accessor>,scitbx::af::ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>)
bond_similarity_residuals(...)
bond_similarity_residuals( (vec3_double)sites_cart, (shared_bond_similarity_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> bond_similarity_residuals(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::bond_similarity_proxy, scitbx::af::trivial_accessor>)
 
bond_similarity_residuals( (unit_cell)unit_cell, (vec3_double)sites_cart, (shared_bond_similarity_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> bond_similarity_residuals(cctbx::uctbx::unit_cell,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::bond_similarity_proxy, scitbx::af::trivial_accessor>)
chirality_deltas(...)
chirality_deltas( (vec3_double)sites_cart, (shared_chirality_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> chirality_deltas(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::chirality_proxy, scitbx::af::trivial_accessor>)
chirality_residual_sum(...)
chirality_residual_sum( (vec3_double)sites_cart, (shared_chirality_proxy)proxies, (vec3_double)gradient_array) -> float :
 
    C++ signature :
        double chirality_residual_sum(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::chirality_proxy, scitbx::af::trivial_accessor>,scitbx::af::ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>)
chirality_residuals(...)
chirality_residuals( (vec3_double)sites_cart, (shared_chirality_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> chirality_residuals(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::chirality_proxy, scitbx::af::trivial_accessor>)
dihedral_deltas(...)
dihedral_deltas( (vec3_double)sites_cart, (shared_dihedral_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> dihedral_deltas(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::dihedral_proxy, scitbx::af::trivial_accessor>)
 
dihedral_deltas( (unit_cell)unit_cell, (vec3_double)sites_cart, (shared_dihedral_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> dihedral_deltas(cctbx::uctbx::unit_cell,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::dihedral_proxy, scitbx::af::trivial_accessor>)
dihedral_residual_sum(...)
dihedral_residual_sum( (vec3_double)sites_cart, (shared_dihedral_proxy)proxies, (vec3_double)gradient_array) -> float :
 
    C++ signature :
        double dihedral_residual_sum(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::dihedral_proxy, scitbx::af::trivial_accessor>,scitbx::af::ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>)
 
dihedral_residual_sum( (unit_cell)unit_cell, (vec3_double)sites_cart, (shared_dihedral_proxy)proxies, (vec3_double)gradient_array) -> float :
 
    C++ signature :
        double dihedral_residual_sum(cctbx::uctbx::unit_cell,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::dihedral_proxy, scitbx::af::trivial_accessor>,scitbx::af::ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>)
dihedral_residuals(...)
dihedral_residuals( (vec3_double)sites_cart, (shared_dihedral_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> dihedral_residuals(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::dihedral_proxy, scitbx::af::trivial_accessor>)
 
dihedral_residuals( (unit_cell)unit_cell, (vec3_double)sites_cart, (shared_dihedral_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> dihedral_residuals(cctbx::uctbx::unit_cell,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::dihedral_proxy, scitbx::af::trivial_accessor>)
extract_bond_params(...)
extract_bond_params( (int)n_seq, (shared_bond_simple_proxy)bond_simple_proxies) -> bond_params_table :
 
    C++ signature :
        scitbx::af::shared<std::map<unsigned int, cctbx::geometry_restraints::bond_params, std::less<unsigned int>, std::allocator<std::pair<unsigned int const, cctbx::geometry_restraints::bond_params> > > > extract_bond_params(unsigned long,scitbx::af::const_ref<cctbx::geometry_restraints::bond_simple_proxy, scitbx::af::trivial_accessor>)
home_restraints_summation_skip_special_positions(...)
home_restraints_summation_skip_special_positions( (vec3_double)sites_cart, (vec3_double)gradients, (size_t)site_symmetry_table_indices, (vec3_double)home_sites_cart, (size_t)iselection, (float)weight, (float)slack) -> float :
 
    C++ signature :
        double home_restraints_summation_skip_special_positions(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<unsigned long, scitbx::af::trivial_accessor>,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<unsigned long, scitbx::af::trivial_accessor>,double,double)
nonbonded_deltas(...)
nonbonded_deltas( (vec3_double)sites_cart, (shared_nonbonded_simple_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> nonbonded_deltas(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::nonbonded_simple_proxy, scitbx::af::trivial_accessor>)
 
nonbonded_deltas( (vec3_double)sites_cart, (nonbonded_sorted_asu_proxies_base)sorted_asu_proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> nonbonded_deltas(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::sorted_asu_proxies<cctbx::geometry_restraints::nonbonded_simple_proxy, cctbx::geometry_restraints::nonbonded_asu_proxy>)
 
nonbonded_deltas( (vec3_double)sites_cart, (shared_nonbonded_simple_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> nonbonded_deltas(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::nonbonded_simple_proxy, scitbx::af::trivial_accessor>)
 
nonbonded_deltas( (vec3_double)sites_cart, (nonbonded_sorted_asu_proxies_base)sorted_asu_proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> nonbonded_deltas(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::sorted_asu_proxies<cctbx::geometry_restraints::nonbonded_simple_proxy, cctbx::geometry_restraints::nonbonded_asu_proxy>)
 
nonbonded_deltas( (vec3_double)sites_cart, (shared_nonbonded_simple_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> nonbonded_deltas(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::nonbonded_simple_proxy, scitbx::af::trivial_accessor>)
 
nonbonded_deltas( (vec3_double)sites_cart, (nonbonded_sorted_asu_proxies_base)sorted_asu_proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> nonbonded_deltas(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::sorted_asu_proxies<cctbx::geometry_restraints::nonbonded_simple_proxy, cctbx::geometry_restraints::nonbonded_asu_proxy>)
 
nonbonded_deltas( (vec3_double)sites_cart, (shared_nonbonded_simple_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> nonbonded_deltas(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::nonbonded_simple_proxy, scitbx::af::trivial_accessor>)
 
nonbonded_deltas( (vec3_double)sites_cart, (nonbonded_sorted_asu_proxies_base)sorted_asu_proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> nonbonded_deltas(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::sorted_asu_proxies<cctbx::geometry_restraints::nonbonded_simple_proxy, cctbx::geometry_restraints::nonbonded_asu_proxy>)
nonbonded_residual_sum(...)
nonbonded_residual_sum( (vec3_double)sites_cart, (shared_nonbonded_simple_proxy)proxies, (vec3_double)gradient_array, (prolsq_repulsion_function)function) -> float :
 
    C++ signature :
        double nonbonded_residual_sum(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::nonbonded_simple_proxy, scitbx::af::trivial_accessor>,scitbx::af::ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::prolsq_repulsion_function)
 
nonbonded_residual_sum( (vec3_double)sites_cart, (nonbonded_sorted_asu_proxies_base)sorted_asu_proxies, (vec3_double)gradient_array, (prolsq_repulsion_function)function [, (bool)disable_cache=False]) -> float :
 
    C++ signature :
        double nonbonded_residual_sum(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::sorted_asu_proxies<cctbx::geometry_restraints::nonbonded_simple_proxy, cctbx::geometry_restraints::nonbonded_asu_proxy>,scitbx::af::ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::prolsq_repulsion_function [,bool=False])
 
nonbonded_residual_sum( (vec3_double)sites_cart, (shared_nonbonded_simple_proxy)proxies, (vec3_double)gradient_array, (inverse_power_repulsion_function)function) -> float :
 
    C++ signature :
        double nonbonded_residual_sum(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::nonbonded_simple_proxy, scitbx::af::trivial_accessor>,scitbx::af::ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::inverse_power_repulsion_function)
 
nonbonded_residual_sum( (vec3_double)sites_cart, (nonbonded_sorted_asu_proxies_base)sorted_asu_proxies, (vec3_double)gradient_array, (inverse_power_repulsion_function)function [, (bool)disable_cache=False]) -> float :
 
    C++ signature :
        double nonbonded_residual_sum(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::sorted_asu_proxies<cctbx::geometry_restraints::nonbonded_simple_proxy, cctbx::geometry_restraints::nonbonded_asu_proxy>,scitbx::af::ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::inverse_power_repulsion_function [,bool=False])
 
nonbonded_residual_sum( (vec3_double)sites_cart, (shared_nonbonded_simple_proxy)proxies, (vec3_double)gradient_array, (cos_repulsion_function)function) -> float :
 
    C++ signature :
        double nonbonded_residual_sum(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::nonbonded_simple_proxy, scitbx::af::trivial_accessor>,scitbx::af::ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::cos_repulsion_function)
 
nonbonded_residual_sum( (vec3_double)sites_cart, (nonbonded_sorted_asu_proxies_base)sorted_asu_proxies, (vec3_double)gradient_array, (cos_repulsion_function)function [, (bool)disable_cache=False]) -> float :
 
    C++ signature :
        double nonbonded_residual_sum(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::sorted_asu_proxies<cctbx::geometry_restraints::nonbonded_simple_proxy, cctbx::geometry_restraints::nonbonded_asu_proxy>,scitbx::af::ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::cos_repulsion_function [,bool=False])
 
nonbonded_residual_sum( (vec3_double)sites_cart, (shared_nonbonded_simple_proxy)proxies, (vec3_double)gradient_array, (gaussian_repulsion_function)function) -> float :
 
    C++ signature :
        double nonbonded_residual_sum(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::nonbonded_simple_proxy, scitbx::af::trivial_accessor>,scitbx::af::ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::gaussian_repulsion_function)
 
nonbonded_residual_sum( (vec3_double)sites_cart, (nonbonded_sorted_asu_proxies_base)sorted_asu_proxies, (vec3_double)gradient_array, (gaussian_repulsion_function)function [, (bool)disable_cache=False]) -> float :
 
    C++ signature :
        double nonbonded_residual_sum(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::sorted_asu_proxies<cctbx::geometry_restraints::nonbonded_simple_proxy, cctbx::geometry_restraints::nonbonded_asu_proxy>,scitbx::af::ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::gaussian_repulsion_function [,bool=False])
nonbonded_residuals(...)
nonbonded_residuals( (vec3_double)sites_cart, (shared_nonbonded_simple_proxy)proxies, (prolsq_repulsion_function)function) -> double :
 
    C++ signature :
        scitbx::af::shared<double> nonbonded_residuals(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::nonbonded_simple_proxy, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::prolsq_repulsion_function)
 
nonbonded_residuals( (vec3_double)sites_cart, (nonbonded_sorted_asu_proxies_base)sorted_asu_proxies, (prolsq_repulsion_function)function) -> double :
 
    C++ signature :
        scitbx::af::shared<double> nonbonded_residuals(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::sorted_asu_proxies<cctbx::geometry_restraints::nonbonded_simple_proxy, cctbx::geometry_restraints::nonbonded_asu_proxy>,cctbx::geometry_restraints::prolsq_repulsion_function)
 
nonbonded_residuals( (vec3_double)sites_cart, (shared_nonbonded_simple_proxy)proxies, (inverse_power_repulsion_function)function) -> double :
 
    C++ signature :
        scitbx::af::shared<double> nonbonded_residuals(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::nonbonded_simple_proxy, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::inverse_power_repulsion_function)
 
nonbonded_residuals( (vec3_double)sites_cart, (nonbonded_sorted_asu_proxies_base)sorted_asu_proxies, (inverse_power_repulsion_function)function) -> double :
 
    C++ signature :
        scitbx::af::shared<double> nonbonded_residuals(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::sorted_asu_proxies<cctbx::geometry_restraints::nonbonded_simple_proxy, cctbx::geometry_restraints::nonbonded_asu_proxy>,cctbx::geometry_restraints::inverse_power_repulsion_function)
 
nonbonded_residuals( (vec3_double)sites_cart, (shared_nonbonded_simple_proxy)proxies, (cos_repulsion_function)function) -> double :
 
    C++ signature :
        scitbx::af::shared<double> nonbonded_residuals(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::nonbonded_simple_proxy, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::cos_repulsion_function)
 
nonbonded_residuals( (vec3_double)sites_cart, (nonbonded_sorted_asu_proxies_base)sorted_asu_proxies, (cos_repulsion_function)function) -> double :
 
    C++ signature :
        scitbx::af::shared<double> nonbonded_residuals(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::sorted_asu_proxies<cctbx::geometry_restraints::nonbonded_simple_proxy, cctbx::geometry_restraints::nonbonded_asu_proxy>,cctbx::geometry_restraints::cos_repulsion_function)
 
nonbonded_residuals( (vec3_double)sites_cart, (shared_nonbonded_simple_proxy)proxies, (gaussian_repulsion_function)function) -> double :
 
    C++ signature :
        scitbx::af::shared<double> nonbonded_residuals(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::nonbonded_simple_proxy, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::gaussian_repulsion_function)
 
nonbonded_residuals( (vec3_double)sites_cart, (nonbonded_sorted_asu_proxies_base)sorted_asu_proxies, (gaussian_repulsion_function)function) -> double :
 
    C++ signature :
        scitbx::af::shared<double> nonbonded_residuals(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,cctbx::geometry_restraints::sorted_asu_proxies<cctbx::geometry_restraints::nonbonded_simple_proxy, cctbx::geometry_restraints::nonbonded_asu_proxy>,cctbx::geometry_restraints::gaussian_repulsion_function)
planarity_deltas_rms(...)
planarity_deltas_rms( (vec3_double)sites_cart, (shared_planarity_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> planarity_deltas_rms(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::planarity_proxy, scitbx::af::trivial_accessor>)
 
planarity_deltas_rms( (unit_cell)unit_cell, (vec3_double)sites_cart, (shared_planarity_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> planarity_deltas_rms(cctbx::uctbx::unit_cell,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::planarity_proxy, scitbx::af::trivial_accessor>)
planarity_residual_sum(...)
planarity_residual_sum( (vec3_double)sites_cart, (shared_planarity_proxy)proxies, (vec3_double)gradient_array) -> float :
 
    C++ signature :
        double planarity_residual_sum(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::planarity_proxy, scitbx::af::trivial_accessor>,scitbx::af::ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>)
 
planarity_residual_sum( (unit_cell)unit_cell, (vec3_double)sites_cart, (shared_planarity_proxy)proxies, (vec3_double)gradient_array) -> float :
 
    C++ signature :
        double planarity_residual_sum(cctbx::uctbx::unit_cell,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::planarity_proxy, scitbx::af::trivial_accessor>,scitbx::af::ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>)
planarity_residuals(...)
planarity_residuals( (vec3_double)sites_cart, (shared_planarity_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> planarity_residuals(scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::planarity_proxy, scitbx::af::trivial_accessor>)
 
planarity_residuals( (unit_cell)unit_cell, (vec3_double)sites_cart, (shared_planarity_proxy)proxies) -> double :
 
    C++ signature :
        scitbx::af::shared<double> planarity_residuals(cctbx::uctbx::unit_cell,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<cctbx::geometry_restraints::planarity_proxy, scitbx::af::trivial_accessor>)
sigma_as_weight(sigma)
weight_as_sigma(weight)

 
Data
        division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)