def compound_name_match(self, compound):
"""
Query NP Atlas DB to see if there is a name match
Return boolean match
"""
res = None
if compound.name != "Not named":
res = atlas_api.search_name(compound.name)
return bool(res)
def longest_substring_name_match(self, compound):
res = None
struct_inchi = compound.inchikey.split("-")[0]
if compound.name != "Not named":
longest_substring = next(
iter(sorted((compound.name.split()), key=len, reverse=True))
)
comps = atlas_api.search_name(longest_substring)
res = any(struct_inchi in c.get("inchikey", "") for c in comps)
return bool(res)
def get_npa_compounds(compound):
compounds = []
if compound.npaid:
res = atlas_api.get_compound(compound.npaid)
if res:
compounds.append(
NPACompound(
res.get("id"),
res.get("original_name"),
atlas_api.get_compound_molblock(compound.npaid),
res.get("inchikey"),
)
)
struct_res = atlas_api.search_inchikey(compound.inchikey.split("-")[0])
for r in struct_res:
id_ = r.get("npaid")
if id_ not in [x.npaid for x in compounds]:
compounds.append(
NPACompound(
id_,
r.get("original_name"),
atlas_api.get_compound_molblock(id_),
r.get("inchikey"),
)
)
if compound.name != "Not named":
name_res = atlas_api.search_name(compound.name)
for r in name_res:
id_ = r.get("npaid")
if id_ not in [x.npaid for x in compounds]:
compounds.append(
NPACompound(
id_,
r.get("original_name"),
atlas_api.get_compound_molblock(id_),
r.get("inchikey"),
)
)
return compounds
def test_search_name_bad():
name = "Not named!"
res = atlas_api.search_name(name)
assert len(res) == 0
def test_search_name():
name = "Not named"
res = atlas_api.search_name(name)
assert len(res) > 0