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
def test_from_pdb_file(self, bgl3_pdb_filename, amino_acid_list):
pdb_s = PDBStructure.from_pdb_file(str(bgl3_pdb_filename))
with open(bgl3_pdb_filename) as f:
pdb_f = PDBStructure.from_pdb_file(f)
pdb_p = PDBStructure.from_pdb_file(bgl3_pdb_filename)
pdb = PDBStructure(amino_acid_list)
assert pdb.seq == pdb_s.seq
assert pdb.seq == pdb_f.seq
assert pdb.seq == pdb_p.seq
def test_renumbering(self, bgl3_fasta_filename, amino_acid_list):
# TODO: Probably want to do this one with multiple PDBs.
assert amino_acid_list
# Test PDBStructure init.
pdb = PDBStructure(amino_acid_list)
assert pdb.amino_acids
with pytest.raises(AttributeError):
pdb.unrenumbered_amino_acids
with pytest.raises(AttributeError):
pdb.renumbering_seq
assert pdb.seq
assert pdb.contacts
renum_pdb = copy.deepcopy(pdb)
p1 = str(list(SeqIO.parse(bgl3_fasta_filename, 'fasta'))[0].seq)
renum_pdb.renumber(p1)
assert len(pdb.amino_acids) == len(renum_pdb.amino_acids) \
+ len(renum_pdb.unrenumbered_amino_acids)
# Technically this could be true, but not for this PDB.
assert pdb.seq != renum_pdb.seq
assert renum_pdb.renumbering_seq == p1
assert pdb.contacts
# Most important!
assert all(aa == p1[i] for i, aa in enumerate(renum_pdb.seq)
if aa != '-')
renum_pdb.derenumber()
with pytest.raises(AttributeError):
pdb.unrenumbered_amino_acids
with pytest.raises(AttributeError):
pdb.renumbering_seq
assert pdb.seq == renum_pdb.seq
assert len(pdb.contacts) == len(renum_pdb.contacts)
pdb_contacts = set(pdb.contacts)
for contact in renum_pdb.contacts:
assert contact in pdb_contacts
# Derenumbering when not renumbered.
with pytest.raises(AttributeError):
pdb.derenumber()
def test_double_renum(self, bgl3_fasta_filename, amino_acid_list):
"""Same as test_renumbering but double renum with two reduced p1."""
pdb = PDBStructure(amino_acid_list)
p1 = str(list(SeqIO.parse(bgl3_fasta_filename, 'fasta'))[0].seq)
renum_pdb = copy.deepcopy(pdb)
p1_short = p1[:400]
renum_pdb.renumber(p1_short)
assert renum_pdb.unrenumbered_amino_acids # Should be occupied now.
assert len(pdb.amino_acids) == len(renum_pdb.amino_acids) \
+ len(renum_pdb.unrenumbered_amino_acids)
assert pdb.seq != renum_pdb.seq
assert renum_pdb.renumbering_seq == p1_short
assert all(aa == p1_short[i] for i, aa in enumerate(renum_pdb.seq)
if aa != '-')
# Renumber again.
p1_middle_removed = p1_short[:150] + p1_short[250:]
renum_pdb.renumber(p1_middle_removed)
assert renum_pdb.unrenumbered_amino_acids
assert len(pdb.amino_acids) == len(renum_pdb.amino_acids) \
+ len(renum_pdb.unrenumbered_amino_acids)
assert pdb.seq != renum_pdb.seq
assert renum_pdb.renumbering_seq == p1_middle_removed
assert all(aa == p1_middle_removed[i] for i, aa
in enumerate(renum_pdb.seq) if aa != '-')
renum_pdb.derenumber()
with pytest.raises(AttributeError):
pdb.unrenumbered_amino_acids
with pytest.raises(AttributeError):
pdb.renumbering_seq
assert pdb.seq == renum_pdb.seq
assert len(pdb.contacts) == len(renum_pdb.contacts)
# pdb_contacts = set(pdb.contacts)
for contact in renum_pdb.contacts:
assert contact in pdb.contacts
def invalid_init(self, bgl3_fasta_filename, amino_acid_list):
p1 = str(list(SeqIO.parse(bgl3_fasta_filename, 'fasta'))[0].seq)
with pytest.raises(ValueError):
PDBStructure(amino_acid_list, None, p1)
p1_short = p1[:400]
renum_pdb = PDBStructure(amino_acid_list)
renum_pdb.renumber(p1_short)
amino_acids = renum_pdb.amino_acids
unrenum = renum_pdb.unrenumbered_amino_acids
with pytest.raises(ValueError):
PDBStructure(amino_acids, unrenum, None)
# Empty unrenumbered_amino_acids.
with pytest.raises(ValueError):
PDBStructure(amino_acids, [], p1_short)
# p1 too short.
with pytest.raises(ValueError):
PDBStructure(amino_acids, unrenum, p1_short[:200])
# p1 too long.
with pytest.raises(ValueError):
PDBStructure(amino_acids, unrenum, p1)