light_atom_types: set
fused_ring_dispatch_table: dict
symmetry_type_dispatch: dict

__init__(self, atoms, bonds, base_coords=None, rings=None, fragments=None, light_atoms=None, backbone=None, neighbor_count=3): 

@property
coords(self): 

generate_coords(self): 

@classmethod
canonicalize_coord(cls, coord): 

@classmethod
prep_unique_coords(cls, coords): 

@classmethod
prune_excess_coords(cls, coord_set, canonicalized=False): 

@classmethod
ring_coordinates(cls, ring_atoms): 

@classmethod
unfused_ring_coordinates(cls, ring_atoms1, ring_atoms2, shared_atoms, shared_indices1, shared_indices2): 

@classmethod
pivot_fused_ring_coordinates(cls, ring_atoms1, ring_atoms2, shared_atoms, shared_indices1, shared_indices2): 

@classmethod
simple_fused_ring_coordinates(cls, ring_atoms1, ring_atoms2, shared_atoms, shared_indices1, shared_indices2): 

@classmethod
fused_ring_coordinates(cls, ring_atoms1, ring_atoms2): 

fragment_connection_coords(self, frag_1, frag_2): 

get_neighborhood_symmetries(self, atoms, ignored=None, neighborhood=3): 

chain_coords(self, R, y): 

RYX2_coords(self, R, y, X): 

RYX3_coords(self, R, y, X): 

get_precedent_chains(self, atom, num_precs=2, ring_atoms=None, light_atoms=None, ignored=None, backbone=None): 

@classmethod
get_symmetry_groups(cls, neighbors, matches): 

symmetry_coords(self, atom, neighborhood=3, backbone=None):