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

 
Package Contents
       
burzlaff_zimmermann_dewolff
close_packing
coordination_sequences
crystal_model (package)
direct_space_asu
distance_based_connectivity
find_best_cell
reindex
tst_distance_based_connectivity
tst_ext

 
Classes
       
__builtin__.object
calculate_angles
calculate_distances
show_angles
symmetry
special_position_settings
_clustering_mix_in(__builtin__.object)
distance_based_clustering
incremental_clustering
libtbx.slots_getstate_setstate(__builtin__.object)
show_distances
sym_pair

 
class calculate_angles(__builtin__.object)
     Methods defined here:
__init__(self, pair_asu_table, sites_frac, skip_j_seq_less_than_i_seq=True, covariance_matrix=None, cell_covariance_matrix=None, parameter_map=None, conformer_indices=None)
__iter__(self)
next(self)

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

 
class calculate_distances(__builtin__.object)
     Methods defined here:
__init__(self, pair_asu_table, sites_frac, skip_j_seq_less_than_i_seq=True, covariance_matrix=None, cell_covariance_matrix=None, parameter_map=None)
__iter__(self)
next(self)

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

 
class distance_based_clustering(_clustering_mix_in)
    
Method resolution order:
distance_based_clustering
_clustering_mix_in
__builtin__.object

Methods defined here:
__init__(self, special_position_settings, sites_cart, distance_cutoff, discard_special_positions=False)

Methods inherited from _clustering_mix_in:
sites_cart(self)
tidy_index_groups_in_place(self)

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

 
class incremental_clustering(_clustering_mix_in)
    
Method resolution order:
incremental_clustering
_clustering_mix_in
__builtin__.object

Methods defined here:
__init__(self, special_position_settings, sites_cart, distance_cutoffs, scores=None, discard_special_positions=False, discard_not_strictly_inside_asu=False, initial_required_cluster_size=0)

Methods inherited from _clustering_mix_in:
sites_cart(self)
tidy_index_groups_in_place(self)

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

 
class show_angles(__builtin__.object)
     Methods defined here:
__init__(self, pair_asu_table, site_labels=None, sites_frac=None, sites_cart=None, show_cartesian=False, keep_pair_asu_table=False, out=None)

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

 
class show_distances(libtbx.slots_getstate_setstate)
    
Method resolution order:
show_distances
libtbx.slots_getstate_setstate
__builtin__.object

Methods defined here:
__init__(self, pair_asu_table, site_labels=None, sites_frac=None, sites_cart=None, show_cartesian=False, keep_pair_asu_table=False, skip_j_seq_less_than_i_seq=False, out=None)

Data descriptors defined here:
distances_info
have_sym
pair_asu_table

Methods inherited from libtbx.slots_getstate_setstate:
__getstate__(self)
__setstate__(self, state)

 
class special_position_settings(symmetry)
    
Method resolution order:
special_position_settings
symmetry
__builtin__.object

Methods defined here:
__init__(self, crystal_symmetry, min_distance_sym_equiv=0.5, u_star_tolerance=0, assert_min_distance_sym_equiv=True)
assert_min_distance_sym_equiv(self)
asu_mappings(self, buffer_thickness, sites_frac=None, sites_cart=None, site_symmetry_table=None, asu_is_inside_epsilon=None)
change_basis(self, cb_op)
incremental_pairs(self, distance_cutoff, asu_is_inside_epsilon=None, asu_mappings_buffer_thickness=-1, cubicle_epsilon=-1)
min_distance_sym_equiv(self)
pair_asu_table(self, distance_cutoff, sites_frac=None, sites_cart=None, site_symmetry_table=None, asu_mappings_buffer_thickness=None, asu_is_inside_epsilon=None, min_cubicle_edge=5, distance_cutoff_epsilon=None)
pair_generator(self, distance_cutoff, sites_frac=None, sites_cart=None, site_symmetry_table=None, asu_mappings_buffer_thickness=None, asu_is_inside_epsilon=None, minimal=False)
site_cluster_analysis(self, min_distance=None, min_cross_distance=None, min_self_distance=None, general_positions_only=False, estimated_reduction_factor=4, asu_is_inside_epsilon=None, asu_mappings_buffer_thickness=-1, min_cubicle_edge=5, cubicle_epsilon=-1)
site_symmetry(self, site=None, site_cart=None)
site_symmetry_table(self, sites_frac=None, sites_cart=None, unconditional_general_position_flags=None)
sym_equiv_sites(self, site)
u_star_tolerance(self)
xray_structure(self, scatterers=None)

Methods inherited from symmetry:
as_cif_block(self)
as_py_code(self, indent='')
as_reference_setting(self)
average_b_cart(self, b_cart)
average_u_cart(self, u_cart)
best_cell(self, angular_tolerance=None)
build_miller_set(self, anomalous_flag, d_min, d_max=None)
cell_equivalent_p1(self)
change_of_basis_op_to_best_cell(self, angular_tolerance=None, best_monoclinic_beta=True)
change_of_basis_op_to_inverse_hand(self)
change_of_basis_op_to_minimum_cell(self)
change_of_basis_op_to_niggli_cell(self, relative_epsilon=None, iteration_limit=None)
change_of_basis_op_to_primitive_setting(self)
change_of_basis_op_to_reference_setting(self)
customized_copy(self, unit_cell=<class libtbx.utils.Keep>, space_group_info=<class libtbx.utils.Keep>, raise_sorry_if_incompatible_unit_cell=False)
direct_space_asu(self)
gridding(self, d_min=None, resolution_factor=None, step=None, symmetry_flags=None, mandatory_factors=None, max_prime=5, assert_shannon_sampling=True)
inverse_hand(self)
is_compatible_unit_cell(self)
is_patterson_symmetry(self)
is_similar_symmetry(self, other, relative_length_tolerance=0.01, absolute_angle_tolerance=1.0)
join_symmetry(self, other_symmetry, force=False, raise_sorry_if_incompatible_unit_cell=False)
miller_set(self, indices, anomalous_flag)
minimum_cell(self)
niggli_cell(self, relative_epsilon=None, iteration_limit=None)
patterson_symmetry(self)
primitive_setting(self)
reflection_intensity_symmetry(self, anomalous_flag)
show_summary(self, f=None, prefix='')
space_group(self)
space_group_info(self)
special_position_settings(self, min_distance_sym_equiv=0.5, u_star_tolerance=0, assert_min_distance_sym_equiv=True)
subtract_continuous_allowed_origin_shifts(self, translation_cart)
unit_cell(self)

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

 
class sym_pair(libtbx.slots_getstate_setstate)
    
Method resolution order:
sym_pair
libtbx.slots_getstate_setstate
__builtin__.object

Methods defined here:
__init__(self, i_seq, j_seq, rt_mx_ji)
i_seqs(self)

Data descriptors defined here:
i_seq
j_seq
rt_mx_ji

Methods inherited from libtbx.slots_getstate_setstate:
__getstate__(self)
__setstate__(self, state)

 
class symmetry(__builtin__.object)
    This class represents the symmetry of a crystal and bundles information on its unit cell and space group.
 
  Methods defined here:
__init__(self, unit_cell=None, space_group_symbol=None, space_group_info=None, space_group=None, correct_rhombohedral_setting_if_necessary=False, assert_is_compatible_unit_cell=True, raise_sorry_if_incompatible_unit_cell=False, force_compatible_unit_cell=True)
Initialises a new crystal.symmetry class object from different input data. Only one of space_group, space_group_info and space_group_symbol may be used.
 
:param unit_cell:          object specifying the unit_cell properties
:type unit_cell:           cctbc.uctbx.ext.unit_cell or tuple(lattice parameters)
:param space_group_symbol: Hermann-Mauguin symbol of the crystallographic space group
:type space_group_symbol:  string
:param space_group_info:   object describing the desired space group
:type space_group_info:    cctbx.sgtbx.space_group_info
:param space_group:        the desired space group of the symmetry class
:type space_group:         cctbx.sgtbx.space_group
:param correct_rhombohedral_setting_if_necessary: If set to 'True' an automatic conversion between rhombohedral and hexagonal basis will be done
:type correct_rhombohedral_setting_if_necessary:  boolean
:param assert_is_compatible_unit_cell: If set to 'True' a consistency check will be performed on the relation of space group to lattice parameters
:type assert_is_compatible_unit_cell:  boolean
:param force_compatible_unit_cell:     If set to 'True' the crystal parameters will be averaged to comply with the restrictions of the space group
:type force_compatible_unit_cell:      boolean
 
:returns: a new crystal.symmetry class with desired properties
:rtype: cctbx.crystal.symmetry
as_cif_block(self)
as_py_code(self, indent='')
as_reference_setting(self)
asu_mappings(self, buffer_thickness, asu_is_inside_epsilon=None)
average_b_cart(self, b_cart)
average_u_cart(self, u_cart)
best_cell(self, angular_tolerance=None)
build_miller_set(self, anomalous_flag, d_min, d_max=None)
cell_equivalent_p1(self)
change_basis(self, cb_op)
change_of_basis_op_to_best_cell(self, angular_tolerance=None, best_monoclinic_beta=True)
change_of_basis_op_to_inverse_hand(self)
change_of_basis_op_to_minimum_cell(self)
change_of_basis_op_to_niggli_cell(self, relative_epsilon=None, iteration_limit=None)
change_of_basis_op_to_primitive_setting(self)
change_of_basis_op_to_reference_setting(self)
customized_copy(self, unit_cell=<class libtbx.utils.Keep>, space_group_info=<class libtbx.utils.Keep>, raise_sorry_if_incompatible_unit_cell=False)
direct_space_asu(self)
gridding(self, d_min=None, resolution_factor=None, step=None, symmetry_flags=None, mandatory_factors=None, max_prime=5, assert_shannon_sampling=True)
inverse_hand(self)
is_compatible_unit_cell(self)
is_patterson_symmetry(self)
is_similar_symmetry(self, other, relative_length_tolerance=0.01, absolute_angle_tolerance=1.0)
join_symmetry(self, other_symmetry, force=False, raise_sorry_if_incompatible_unit_cell=False)
miller_set(self, indices, anomalous_flag)
minimum_cell(self)
niggli_cell(self, relative_epsilon=None, iteration_limit=None)
patterson_symmetry(self)
primitive_setting(self)
reflection_intensity_symmetry(self, anomalous_flag)
show_summary(self, f=None, prefix='')
space_group(self)
space_group_info(self)
special_position_settings(self, min_distance_sym_equiv=0.5, u_star_tolerance=0, assert_min_distance_sym_equiv=True)
subtract_continuous_allowed_origin_shifts(self, translation_cart)
unit_cell(self)

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

 
Functions
       
cluster_erosion(sites_cart, box_size, fraction_to_be_retained)
coordination_sequences_shell_asu_tables(...)
coordination_sequences_shell_asu_tables( (pair_asu_table)pair_asu_table, (int)max_shell) -> tuple :
 
    C++ signature :
        std::vector<cctbx::crystal::pair_asu_table<double, int>, std::allocator<cctbx::crystal::pair_asu_table<double, int> > > coordination_sequences_shell_asu_tables(cctbx::crystal::pair_asu_table<double, int>,unsigned int)
coordination_sequences_shell_sym_tables(...)
coordination_sequences_shell_sym_tables( (pair_sym_table)full_pair_sym_table, (site_symmetry_table)site_symmetry_table, (int)max_shell) -> tuple :
 
    C++ signature :
        std::vector<scitbx::af::shared<std::map<unsigned int, std::vector<cctbx::sgtbx::rt_mx, std::allocator<cctbx::sgtbx::rt_mx> >, std::less<unsigned int>, std::allocator<std::pair<unsigned int const, std::vector<cctbx::sgtbx::rt_mx, std::allocator<cctbx::sgtbx::rt_mx> > > > > >, std::allocator<scitbx::af::shared<std::map<unsigned int, std::vector<cctbx::sgtbx::rt_mx, std::allocator<cctbx::sgtbx::rt_mx> >, std::less<unsigned int>, std::allocator<std::pair<unsigned int const, std::vector<cctbx::sgtbx::rt_mx, std::allocator<cctbx::sgtbx::rt_mx> > > > > > > > coordination_sequences_shell_sym_tables(scitbx::af::shared<std::map<unsigned int, std::vector<cctbx::sgtbx::rt_mx, std::allocator<cctbx::sgtbx::rt_mx> >, std::less<unsigned int>, std::allocator<std::pair<unsigned int const, std::vector<cctbx::sgtbx::rt_mx, std::allocator<cctbx::sgtbx::rt_mx> > > > > >,cctbx::sgtbx::site_symmetry_table,unsigned int)
coordination_sequences_simple(...)
coordination_sequences_simple( (pair_asu_table)pair_asu_table, (int)max_shell) -> stl_vector_unsigned :
 
    C++ signature :
        scitbx::af::shared<std::vector<unsigned int, std::allocator<unsigned int> > > coordination_sequences_simple(cctbx::crystal::pair_asu_table<double, int>,unsigned int)
coordination_sequences_simple_sym(...)
coordination_sequences_simple_sym( (pair_sym_table)full_pair_sym_table, (site_symmetry_table)site_symmetry_table, (int)max_shell) -> stl_vector_unsigned :
 
    C++ signature :
        scitbx::af::shared<std::vector<unsigned int, std::allocator<unsigned int> > > coordination_sequences_simple_sym(scitbx::af::shared<std::map<unsigned int, std::vector<cctbx::sgtbx::rt_mx, std::allocator<cctbx::sgtbx::rt_mx> >, std::less<unsigned int>, std::allocator<std::pair<unsigned int const, std::vector<cctbx::sgtbx::rt_mx, std::allocator<cctbx::sgtbx::rt_mx> > > > > >,cctbx::sgtbx::site_symmetry_table,unsigned int)
correct_special_position(crystal_symmetry, special_op, site_frac=None, site_cart=None, site_label=None, tolerance=1, error_message='Excessive special position correction:')
cubicles_max_memory_allocation_get(...)
cubicles_max_memory_allocation_get() -> int :
 
    C++ signature :
        unsigned long cubicles_max_memory_allocation_get()
cubicles_max_memory_allocation_set(...)
cubicles_max_memory_allocation_set( (int)number_of_bytes) -> None :
 
    C++ signature :
        void cubicles_max_memory_allocation_set(unsigned long)
get_distances(...)
get_distances( (pair_sym_table)pair_sym_table, (object)orthogonalization_matrix, (vec3_double)sites_frac) -> double :
 
    C++ signature :
        scitbx::af::shared<double> get_distances(scitbx::af::const_ref<std::map<unsigned int, std::vector<cctbx::sgtbx::rt_mx, std::allocator<cctbx::sgtbx::rt_mx> >, std::less<unsigned int>, std::allocator<std::pair<unsigned int const, std::vector<cctbx::sgtbx::rt_mx, std::allocator<cctbx::sgtbx::rt_mx> > > > >, scitbx::af::trivial_accessor>,scitbx::mat3<double>,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>)
 
get_distances( (pair_sym_table)pair_sym_table, (vec3_double)sites_cart) -> double :
 
    C++ signature :
        scitbx::af::shared<double> get_distances(scitbx::af::const_ref<std::map<unsigned int, std::vector<cctbx::sgtbx::rt_mx, std::allocator<cctbx::sgtbx::rt_mx> >, std::less<unsigned int>, std::allocator<std::pair<unsigned int const, std::vector<cctbx::sgtbx::rt_mx, std::allocator<cctbx::sgtbx::rt_mx> > > > >, scitbx::af::trivial_accessor>,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>)
non_crystallographic_symmetry(sites_cart=None, sites_cart_min=None, sites_cart_max=None, buffer_layer=None, default_buffer_layer=0.5, min_unit_cell_length=0)
select_crystal_symmetry(from_command_line=None, from_parameter_file=None, from_coordinate_files=[None], from_reflection_files=[None])
Select/construct a crystal symmetry from a list of various options

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