biotite.structure.AtomArrayStack¶

class biotite.structure.AtomArrayStack(depth, length)[source]¶

Bases: _AtomArrayBase

A collection of multiple AtomArray instances, where each atom array has equal annotation arrays.

Effectively, this means that each atom is occuring in every array in the stack at differing coordinates. This situation arises e.g. in NMR-elucidated or simulated structures. Since the annotations are equal for each array, the annotation arrays are 1-D, while the coordinate array is 3-D (m x n x 3). A detailed description of each annotation category can be viewed here.

Indexing works similar to AtomArray, with the difference, that two index dimensions are possible: The first index dimension specifies the array(s), the second index dimension specifies the atoms in each array (same as the index in AtomArray). Using a single integer as first dimension index returns a single AtomArray instance.

Concatenation of atoms for each array in the stack is done using the ‘+’ operator. For addition of atom arrays onto the stack use the stack() method.

The box attribute has the shape m x 3 x 3, as the cell might be different for each frame in the atom array stack.

Parameters

depthint: The fixed amount of arrays in the stack. When indexing, this is the length of the first dimension.
lengthint: The fixed amount of atoms in each array in the stack. When indexing, this is the length of the second dimension.

See also

AtomArray

Examples

Creating an atom array stack from two arrays:

>>> atom1 = Atom([1,2,3], chain_id="A")
>>> atom2 = Atom([2,3,4], chain_id="A")
>>> atom3 = Atom([3,4,5], chain_id="B")
>>> atom_array1 = array([atom1, atom2, atom3])
>>> print(atom_array1.coord)
[[1. 2. 3.]
 [2. 3. 4.]
 [3. 4. 5.]]
>>> atom_array2 = atom_array1.copy()
>>> atom_array2.coord += 3
>>> print(atom_array2.coord)
[[4. 5. 6.]
 [5. 6. 7.]
 [6. 7. 8.]]
>>> array_stack = stack([atom_array1, atom_array2])
>>> print(array_stack.coord)
[[[1. 2. 3.]
  [2. 3. 4.]
  [3. 4. 5.]]

 [[4. 5. 6.]
  [5. 6. 7.]
  [6. 7. 8.]]]

Attributes

{annot}ndarray, shape=(n,): Mutliple n-length annotation arrays.
coordndarray, dtype=float, shape=(m,n,3): ndarray containing the x, y and z coordinate of the atoms.
bonds: BondList or None: A BondList, specifying the indices of atoms that form a chemical bond.
box: ndarray, dtype=float, shape=(m,3,3) or None: The surrounding box. May represent a MD simulation box or a crystallographic unit cell.
shapetuple of int: Tuple of array dimensions.

add_annotation(category, dtype)¶

Add an annotation category, if not already existing.

Initially the new annotation is filled with the zero representation of the given type.

Parameters

categorystr: The annotation category to be added.
dtypetype or str: A type instance or a valid NumPy dtype string. Defines the type of the annotation