def test_list_assemblies():
"""
Test the :func:`list_assemblies()` function based on a known
example.
"""
path = join(data_dir("structure"), "1f2n.cif")
pdbx_file = pdbx.PDBxFile.read(path)
assembly_list = pdbx.list_assemblies(pdbx_file)
assert assembly_list == {
"1": "complete icosahedral assembly",
"2": "icosahedral asymmetric unit",
"3": "icosahedral pentamer",
"4": "icosahedral 23 hexamer",
"5": "icosahedral asymmetric unit, std point frame",
"6": "crystal asymmetric unit, crystal frame",
}
At first we will check, which assemblies are available to us.
"""
# Code source: Patrick Kunzmann
# License: BSD 3 clause
import numpy as np
import biotite.structure as struc
import biotite.structure.io.pdbx as pdbx
import biotite.structure.io as strucio
import biotite.database.rcsb as rcsb
pdbx_file = pdbx.PDBxFile.read(rcsb.fetch("1M4X", "mmcif"))
assemblies = pdbx.list_assemblies(pdbx_file)
print("ID name")
print()
for assembly_id, name in assemblies.items():
print(f"{assembly_id:2} {name}")
########################################################################
# ``'complete icosahedral assembly'`` sounds good.
# In fact, often the first assembly is the complete one.
# Hence, the :func:`get_assembly()` function builds the first assembly
# by default.
# Since we know the ID we want (``'1'``), we will provide it to this
# function anyway.
# It returns the chosen assembly as :class:`AtomArray`.
# Note that the assembly ID is a string, not an integer.