def load_structure(fpath, chain=None):
"""
Args:
fpath: filepath to either pdb or cif file
chain: the chain id
Returns:
biotite.structure.AtomArray
"""
if fpath.endswith('cif'):
with open(fpath) as fin:
pdbxf = pdbx.PDBxFile.read(fin)
structure = pdbx.get_structure(pdbxf, model=1)
elif fpath.endswith('pdb'):
with open(fpath) as fin:
pdbf = pdb.PDBFile.read(fin)
structure = pdb.get_structure(pdbf, model=1)
issolvent = filter_solvent(structure)
structure = structure[~issolvent]
chains = get_chains(structure)
print(f'Found {len(chains)} chains:', chains, '\n')
if len(chains) == 0:
raise ValueError('No chains found in the input file.')
if chain is None:
chain = chains[0]
if chain not in chains:
raise ValueError(f'Chain {chain} not found in input file')
structure = structure[structure.chain_id == chain]
print(f'Loaded chain {chain}\n')
return structure
def test_chain_iter(array):
n = 0
for chain in struc.get_chains(array):
n += 1
assert isinstance(array, struc.AtomArray)
assert n == 6
def test_get_chains(array):
assert struc.get_chains(array).tolist() == ["A", "B", "C", "D", "E", "F"]