def __init__(self, aa, loc=None, state=None, test=True):
"""Init residue object."""
self.aa = normalize_to_set(aa)
if loc is not None:
self.loc = int(loc)
else:
self.loc = None
self.state = state
self.test = normalize_to_set(test)
def meta_data(self):
"""Get a dictionary with site's meta-data."""
res = dict()
if self.interproid:
res["interproid"] = self.interproid
if self.name:
res["name"] = normalize_to_set(self.name)
if self.label:
res["label"] = normalize_to_set(self.label)
return res
def from_json(cls, json_data):
"""Create Site object from JSON representation."""
name = json_data["name"]
test = True
if "test" in json_data.keys():
test = normalize_to_set(json_data["test"])
return cls(name, test)
def meta_data(self):
"""Convert agent object to attrs."""
agent_attrs = {
"uniprotid": {self.uniprotid}
}
if self.hgnc_symbol is not None:
agent_attrs["hgnc_symbol"] = normalize_to_set(self.hgnc_symbol)
if self.synonyms is not None:
agent_attrs["synonyms"] = normalize_to_set(self.synonyms)
if self.xrefs is not None:
xrefs = []
for k, v in self.xrefs.items():
if type(v) == list:
for vv in v:
xrefs.append((k, vv))
else:
xrefs.append((k, v))
agent_attrs["xrefs"] = normalize_to_set(xrefs)
return agent_attrs
def from_json(cls, json_data):
"""Create Residue object from JSON representation."""
aa = json_data["aa"]
loc = None
if "loc" in json_data.keys():
loc = json_data["loc"]
state = None
if "state" in json_data.keys():
state = State.from_json(json_data["state"])
test = True
if "test" in json_data.keys():
test = normalize_to_set(json_data["test"])
return cls(aa, loc, state, test)
def meta_data(self):
"""Convert agent object to attrs."""
return {
"name": normalize_to_set(self.name),
"test": normalize_to_set(self.test)
}