def __init__(self, id_a, id_b, mechanism, effect, direct, relation, pmid,
linenum):
self.id_a = id_a
self.id_b = id_b
self.effect = effect
self.direct = direct
self.relation = relation
self.pmid = pmid
self.linenum = linenum
self.complex_a = None
try:
if NamingConvention.is_complex(
self.id_a) and self.id_a in COMPLEXES:
self.complex_a = COMPLEXES[self.id_a]
except TypeError as err:
print(self.id_a)
raise err
self.complex_b = None
if NamingConvention.is_complex(self.id_b) and self.id_b in COMPLEXES:
self.complex_b = COMPLEXES[self.id_b]
# by default mechanism = molecular function
mechanism_term = "GO:0003674"
if self.direct == "YES":
if (mechanism):
mechanism_term = MECHANISM_GO_MAPPING[mechanism]
self.mechanism = {
"name": mechanism,
"uri": None,
"term": mechanism_term
}
self.regulated_activity = {"name": None, "uri": None, "term": None}
self.individuals = {}
self.enabled_by_stmt_a = None
def b_is_complex(self):
return NamingConvention.is_complex(self.id_b)
def determine_entity(cls, entity_id: str, entity_name: str,
entity_type: str) -> SignorEntity:
if NamingConvention.is_complex(entity_id):
return SignorEntityFactory.complex_from_id(entity_id)
else:
return cls.entity_type_map[entity_type](entity_id, entity_name)