def to_reaction(line, substance_keys, token, Cls, globals_=None, **kwargs):
""" Parses a string into a Reaction object and substances
Reac1 + 2 Reac2 + (2 Reac1) -> Prod1 + Prod2; 10**3.7; ref='doi:12/ab'
Reac1 = Prod1; 2.1;
Parameters
----------
line: str
string representation to be parsed
substance_keys: iterable of strings
Allowed names, e.g. ('H2O', 'H+', 'OH-')
token : str
delimiter token between reactant and product side
Cls : class
e.g. subclass of Reaction
globals_: dict (optional)
Globals passed on to :func:`eval`, when ``None``:
`chempy.units.default_units` is used with 'chempy'
and 'default_units' extra entries.
Notes
-----
This function calls :func:`eval`, hence there are severe security concerns
with running this on untrusted data.
"""
if globals_ is None:
import chempy
from chempy.kinetics import rates
from chempy.units import default_units
globals_ = {k: getattr(rates, k) for k in dir(rates)}
globals_.update({'chempy': chempy})
if default_units is not None:
globals_.update({k: v for k, v in chempy.__dict__.items()
if not k.startswith('_')})
globals_.update(default_units.as_dict())
import numpy as np
globals_['array'] = np.array
parts = line.rstrip('\n').split(';')
stoich = parts[0].strip()
if len(parts) > 2:
kwargs.update(eval('dict('+';'.join(parts[2:])+')', globals_ or {}))
if len(parts) > 1:
param = parts[1].strip()
else:
param = kwargs.pop('param', 'None')
if isinstance(param, str):
if param.startswith("'") and param.endswith("'") and "'" not in param[1:-1]:
from ..kinetics.rates import MassAction
param = MassAction(unique_keys=(param[1:-1],))
else:
param = None if globals_ is False else eval(param, globals_)
if token not in stoich:
raise ValueError("Missing token: %s" % token)
reac_prod = [[y.strip() for y in x.split(' + ')] for x in stoich.split(token)]
act, inact = [], []
for elements in reac_prod:
act.append(_parse_multiplicity([x for x in elements if not x.startswith('(')], substance_keys))
inact.append(_parse_multiplicity(
[x[1:-1] for x in elements if x.startswith('(') and x.endswith(')')],
substance_keys
))
# stoich coeff -> dict
return Cls(act[0], act[1], param, inact_reac=inact[0],
inact_prod=inact[1], **kwargs)
def to_reaction(line, substance_keys, token, Cls, globals_=None, **kwargs):
""" Parses a string into a Reaction object and substances
Reac1 + 2 Reac2 + (2 Reac1) -> Prod1 + Prod2; 10**3.7; ref='doi:12/ab'
Reac1 = Prod1; 2.1;
Parameters
----------
line: str
string representation to be parsed
substance_keys: iterable of strings
Allowed names, e.g. ('H2O', 'H+', 'OH-')
token : str
delimiter token between reactant and product side
Cls : class
e.g. subclass of Reaction
globals_: dict (optional)
Globals passed on to :func:`eval`, when ``None``:
`chempy.units.default_units` is used with 'chempy'
and 'default_units' extra entries.
Notes
-----
This function calls :func:`eval`, hence there are severe security concerns
with running this on untrusted data.
"""
# TODO: add handling of units.
if globals_ is None:
import chempy
from chempy.kinetics import rates
from chempy.units import default_units
globals_ = {k: getattr(rates, k) for k in dir(rates)}
globals_.update({'chempy': chempy, 'default_units': default_units})
if default_units is not None:
globals_.update(default_units.as_dict())
try:
stoich, param, kw = map(str.strip, line.rstrip('\n').split(';'))
except ValueError:
if ';' in line:
stoich, param = map(str.strip, line.rstrip('\n').split(';'))
else:
stoich, param = line.strip(), kwargs.pop('param', 'None')
else:
kwargs.update({} if globals_ is False else eval('dict('+kw+')', globals_))
if isinstance(param, str):
param = None if globals_ is False else eval(param, globals_)
if token not in stoich:
raise ValueError("Missing token: %s" % token)
reac_prod = [[y.strip() for y in x.split(' + ')] for
x in stoich.split(token)]
act, inact = [], []
for side in reac_prod:
if side[-1].startswith('('):
if not side[-1].endswith(')'):
raise ValueError("Bad format (missing closing paren)")
inact.append(_parse_multiplicity(side[-1][1:-1].split(' + '),
substance_keys))
act.append(_parse_multiplicity(side[:-1], substance_keys))
else:
inact.append({})
act.append(_parse_multiplicity(side, substance_keys))
# stoich coeff -> dict
return Cls(act[0], act[1], param, inact_reac=inact[0],
inact_prod=inact[1], **kwargs)