def from_json(cls, in_json: str):
"""Construct instance from JSON.
Parameters:
in_json: JSON-formatted string representing a ParentsSequences.
Return:
ParentsSequences instance created from in_json.
"""
records, alignment, pdb = json.loads(in_json)
seq_records = []
for sr_list in records:
sr_seq, sr_id, sr_name, sr_desc = sr_list
seq = Seq(sr_seq)
sr = SeqRecord(seq, id=sr_id, name=sr_name, description=sr_desc)
seq_records.append(sr)
if pdb is not None:
pdb = PDBStructure.from_json(pdb)
new_instance = cls(seq_records, pdb)
if alignment is not None:
# This will renumber the pdb_structure but that's okay.
alignment = [tuple(ele) for ele in alignment]
new_instance._alignment = alignment
return new_instance
def test_json(self, amino_acid_list, bgl3_fasta_filename):
in_pdb = PDBStructure(amino_acid_list)
json_str = in_pdb.to_json()
assert json_str
out_pdb = PDBStructure.from_json(json_str)
assert in_pdb.seq == out_pdb.seq
with pytest.raises(AttributeError):
out_pdb.unrenumbered_amino_acids
with pytest.raises(AttributeError):
out_pdb.renumbering_seq
p1 = str(list(SeqIO.parse(bgl3_fasta_filename, 'fasta'))[0].seq)
p1_short = p1[:400]
renum_pdb = PDBStructure(amino_acid_list)
renum_pdb.renumber(p1_short)
json_str2 = renum_pdb.to_json()
assert json_str2
out_pdb2 = PDBStructure.from_json(json_str2)
assert renum_pdb.seq == out_pdb2.seq
assert renum_pdb.renumbering_seq == out_pdb2.renumbering_seq