def __init__(self, rules: Union[str, dict], logger=app_logger):
if isinstance(rules, dict):
pass
elif isinstance(rules, str):
rules = get_json(rules)
else:
raise TypeError
self.logger = logger
self.raw_rules = rules
self.sources = self.raw_rules["SOURCES"]
self.date = self.raw_rules.get("_DATE", 20200214)
self.authors = self.raw_rules.get("_AUTHORS",
["*****@*****.**"])
mods = self.raw_rules.get("MODS", {})
if mods:
self.supported_mods = list(mods.keys())
else:
self.supported_mods = []
self.supported_residues = list(self.raw_rules["RESIDUES"].keys())
self.supported_classes = list(self.raw_rules["LIPID_CLASSES"].keys())
self.supported_keys = (self.supported_mods + self.supported_residues +
self.supported_classes)
self.separators = self.raw_rules["SEPARATORS"]
self.rules = {}
self.is_structure_valid = self.__check__()
if self.is_structure_valid:
pass
else:
raise ValueError(
"Cannot find valid sections for key [SOURCE, RESIDUES, LIPID_CLASSES]"
)
self.rules = self.build()
self.is_validated = self.validate()
def __init__(self, rules: Union[str, dict]):
if isinstance(rules, dict):
pass
elif isinstance(rules, str):
rules = get_json(rules)
else:
raise TypeError
self.raw_rules = rules
self.date = self.raw_rules.get("_DATE", 20200214)
self.authors = self.raw_rules.get("_AUTHORS",
["*****@*****.**"])
self.nomenclature = self.raw_rules.get("NOMENCLATURE", "LipidLynxX")
self.supported_lmsd_classes = list(
self.raw_rules["LMSD_CLASSES"].keys())
self.separators = self.raw_rules["SEPARATORS"]
self.mods = self.raw_rules.get("MODS", {})
self.residues = self.raw_rules.get("RESIDUES", {})
self.rules = self.build()
self.is_structure_valid = self.__check__()
def __load_raw__(self) -> dict:
raw_cv_info = {}
raw_cv_dct = get_json(self.cv_file)
for raw_cv in raw_cv_dct:
order = raw_cv.get("order", None)
cv = raw_cv.get("cv", None)
level = raw_cv.get("level", 0)
elements_dct = raw_cv.get("elements", {})
alias_lst = raw_cv.get("alias", [])
if cv:
if cv not in alias_lst:
alias_lst.append(cv)
alias_lst = list(set(alias_lst))
raw_cv_info[cv] = {
"ORDER": order,
"ALIAS": alias_lst,
"LEVEL": level,
"ELEMENTS": elements_dct,
}
return raw_cv_info
def __load__(self) -> dict:
cv_info = {}
raw_cv_info = get_json(self.cv_file)
for raw_cv in raw_cv_info:
order = raw_cv.get("order", None)
cv = raw_cv.get("cv", None)
level = raw_cv.get("level", 0)
elements_dct = raw_cv.get("elements", {})
alias_lst = raw_cv.get("alias", [])
if cv:
if cv not in alias_lst:
alias_lst.append(cv)
alias_lst = list(set(alias_lst))
for alias in alias_lst:
cv_info[alias] = {
"MATCH": re.compile("^" + alias + "$"),
"ORDER": order,
"CV": cv,
"LEVEL": level,
"ELEMENTS": elements_dct,
}
return cv_info
def __load_raw__(self) -> dict:
if not self._raw_cv:
return get_json(self.alias_file)
else:
return self._raw_cv