def test_record_linkage(self):
cluster = CandidateCluster(CandidateCluster.kinds.INTERLEAVED,
self.record.get_protoclusters())
with self.assertRaisesRegex(
ValueError, "CandidateCluster not contained in record"):
cluster.get_candidate_cluster_number()
self.record.add_candidate_cluster(cluster)
assert cluster.get_candidate_cluster_number() == 1
def test_conversion(self):
kind = CandidateClusterKind.INTERLEAVED
original = CandidateCluster(kind,
self.record.get_protoclusters(),
smiles="dummy smiles",
polymer="dummy polymer")
self.record.add_candidate_cluster(original)
assert original.products == ["a"]
assert len(original.protoclusters) == 1
bios = original.to_biopython()
assert len(bios) == 1
bio = bios[0]
assert bio.qualifiers["product"] == ["a"]
assert bio.qualifiers["kind"] == [str(kind)]
assert bio.qualifiers["candidate_cluster_number"] == [
str(original.get_candidate_cluster_number())
]
assert bio.qualifiers["SMILES"] == ["dummy smiles"]
assert bio.qualifiers["polymer"] == ["dummy polymer"]
assert bio.qualifiers["contig_edge"] == ["True"]
regenerated = CandidateCluster.from_biopython(bio)
assert isinstance(regenerated, TemporaryCandidateCluster)
assert regenerated.products == original.products
assert regenerated.location == original.location
assert regenerated.smiles_structure == original.smiles_structure
assert regenerated.polymer == original.polymer
proto_numbers = [
cluster.get_protocluster_number()
for cluster in self.record.get_protoclusters()
]
assert regenerated.protoclusters == proto_numbers
assert regenerated.kind == original.kind
real = regenerated.convert_to_real_feature(self.record)
assert isinstance(real, CandidateCluster)
assert len(real.protoclusters) == len(self.record.get_protoclusters())
for reference, record_cluster in zip(real.protoclusters,
self.record.get_protoclusters()):
assert reference is record_cluster
# attempt a conversion with a record missing the cluster
self.record.clear_protoclusters()
with self.assertRaisesRegex(ValueError,
"Not all referenced clusters are present"):
regenerated.convert_to_real_feature(self.record)
def test_conversion(self):
kind = CandidateClusterKind.INTERLEAVED
original = CandidateCluster(kind,
self.record.get_protoclusters(),
smiles="dummy smiles",
polymer="dummy polymer")
self.record.add_candidate_cluster(original)
assert original.products == ["a"]
assert len(original.protoclusters) == 1
bios = original.to_biopython()
assert len(bios) == 1
bio = bios[0]
assert bio.qualifiers["product"] == ["a"]
assert bio.qualifiers["kind"] == [str(kind)]
assert bio.qualifiers["candidate_cluster_number"] == [
str(original.get_candidate_cluster_number())
]
assert bio.qualifiers["SMILES"] == ["dummy smiles"]
assert bio.qualifiers["polymer"] == ["dummy polymer"]
assert bio.qualifiers["contig_edge"] == ["True"]
real = CandidateCluster.from_biopython(bio, record=self.record)
assert isinstance(real, CandidateCluster)
assert len(real.protoclusters) == len(self.record.get_protoclusters())
for reference, record_cluster in zip(real.protoclusters,
self.record.get_protoclusters()):
assert reference is record_cluster
# attempt a conversion with a record missing the cluster
self.record.clear_protoclusters()
with self.assertRaisesRegex(
ValueError,
"record does not contain all expected protoclusters"):
CandidateCluster.from_biopython(bio, record=self.record)
# and with no record
with self.assertRaisesRegex(ValueError, "record instance required"):
CandidateCluster.from_biopython(bio)