def composition(self):
composition = CompositionType()
for element_relation in self.elements:
symbol = element_relation.element
isotope, element = re.search(r"(?P<isotope>\d*)?(?P<element>\S+)", symbol).groups()
if isotope != "":
isotope = int(isotope)
iso_str = _make_isotope_string(element, isotope)
else:
iso_str = element
count = element_relation.count
composition[str(iso_str)] = count
return composition
def _formula_parser(formula, session):
'''
Parse a unimod formula composed of elements,
isotopes, and other bricks.
In order to look up a Brick's composition, this
function must have access to a session.
Parameters
----------
formula: str
A Unimod formula of the form `A(n) B(m)...`
where A, B, ... are element names or bricks and
(n), (m)... are parenthesized possibly signed integers or
omitted in which case they are interpreted as 1
session: Session
An active SQLAlchemy session for looking up bricks in the database
Returns
-------
CompositionType
'''
composition = CompositionType()
for token in formula.split(" "):
match = re.search(r"(?P<isotope>\d+)?(?P<elemet>[^\(]+)(?:\((?P<count>-?\d+)\))?", token)
if match:
isotope, element, count = match.groups()
if count is not None:
count = int(count)
else:
count = 1
if isotope is not None:
name = _make_isotope_string(element, int(isotope))
else:
name = element
is_brick = session.query(Brick).filter(Brick.brick == name).first()
if is_brick is None:
composition[str(name)] += count
else:
composition += is_brick.composition * count
return composition
def composition(self):
composition = CompositionType()
session = object_session(self)
for fragment_composition_relation in self._fragment_composition:
symbol = fragment_composition_relation.brick_string
isotope, element = re.search(r"(?P<isotope>\d*)?(?P<element>\S+)", symbol).groups()
count = fragment_composition_relation.count
if count is not None:
count = int(count)
else:
count = 1
if isotope != "":
name = _make_isotope_string(element, isotope)
else:
name = element
is_brick = session.query(Brick).filter(Brick.brick == name).first()
if is_brick is None:
composition[str(name)] += count
else:
composition += is_brick.composition * count
return composition
