def get_h(self, keep1=True):
"""
c = h(p)
"""
hs = [poly.get_h(keep1=keep1) for poly in self]
yids = butil.flatten([h_.yids for h_ in hs])
coefstrs = butil.flatten([h_.frepr.tolist() for h_ in hs])
senstrs = [[exprmanip.simplify_expr(exprmanip.diff_expr(coefstr, pid))
for pid in self.pids] for coefstr in coefstrs]
hstr = str(coefstrs).replace("'", "")
Dhstr = str(senstrs).replace("'", "")
subs0 = dict(butil.flatten([poly.convarvals.items() for poly in self],
depth=1))
def f(p):
subs = subs0.copy()
subs.update(dict(zip(self.pids, p)))
return np.array(eval(hstr, subs))
def Df(p):
subs = subs0.copy()
subs.update(dict(zip(self.pids, p)))
return np.array(eval(Dhstr, subs))
h = predict.Predict(f=f, Df=Df, pids=self.pids, p0=self.p0,
yids=yids, frepr=butil.Series(coefstrs, yids),
Dfrepr=butil.DF(senstrs, yids, self.pids))
return h
def _sub_var_names(self, input):
mapping_dict = {}
for id in ExprManip.extract_vars(input):
# convert it back to something key_column will recognize
# had to use a form dynVarName__derivWRT__optParamName for the
# sensitivity variable because otherwise,
# extract_vars gets confused
splitId = id.split('__derivWRT__')
if len(splitId) == 1:
idname = splitId[0]
elif len(splitId) == 2:
idname = tuple(splitId)
else:
raise 'Problem with id %s in Trajectory._sub_var_names' % id
if idname in self.key_column.keys():
mapping = 'values[start:end, %i]' % self.key_column.get(idname)
elif idname in self.const_var_values.keys():
# Don't substitute for constant variable names. Those will
# be taken care of earlier in the method.
continue
elif idname == 'time':
mapping = 'times[start:end]'
else:
raise 'Problem with idname %s in Trajectory._sub_var_names' % id
mapping_dict[id] = mapping
input = ExprManip.sub_for_vars(input, mapping_dict)
return input
def list2predict2(l, pids, uids=None, us=None, yids=None, c=None, p0=None):
"""
pred = list2predict(['exp(-p1*1)+exp(-p2*1)', 'exp(-p1*2)+exp(-p2*2)', 'exp(-p1*1)-exp(-p2*1)'],
pids=['p1','p2'], p0=None)
pred = list2predict(['(k1f*C1-k1r*X1)-(k2f*X1-k2r*X2)',
'(k2f*X1-k2r*X2)-(k3f*X2-k3r*C2)'],
uids=['X1','X2'],
us=butil.get_product([1,2,3],[1,2,3]),
pids=['k1f','k1r','k2f','k2r','k3f','k3r'],
c={'C1':2,'C2':1})
Input:
c: a mapping
"""
if c is not None:
l = [exprmanip.sub_for_vars(s, c) for s in l]
ystr = str(l).replace("'", "")
ycode = compile(ystr, '', 'eval')
def f(p):
return np.array(eval(ycode, dict(zip(pids, p)), mathsubs))
jaclist = []
for s in l:
jacrow = [exprmanip.simplify_expr(exprmanip.diff_expr(s, pid))
for pid in pids]
jaclist.append(jacrow)
if us is not None:
jaclist = [[[exprmanip.sub_for_vars(jacentry, dict(zip(uids, u)))
for jacentry in jacrow]
for jacrow in jaclist]
for u in us]
jaclist = butil.flatten(jaclist, depth=1)
jacstr = str(jaclist).replace("'", "")
jaccode = compile(jacstr, '', 'eval')
def Df(p):
return np.array(eval(jaccode, dict(zip(pids, p)), mathsubs))
if p0 is None:
p0 = [1] * len(pids)
if yids is None:
yids = ['y%d'%i for i in range(1, len(l)+1)]
if us is not None:
uids = ['u%d'%i for i in range(1, len(us)+1)]
yids = butil.get_product(yids, uids)
return Predict(f=f, Df=Df, p0=p0, pids=pids, yids=yids)
def get_Ep_str(net):
"""
"""
Ep = []
for rxnid in net.rxnids:
ratelaw = exprmanip.sub_for_vars(net.rxns[rxnid].kineticLaw,
net.asgrules.to_od())
Ep_rxn = []
for pid in net.pids:
Ep_rxn.append(exprmanip.simplify_expr(exprmanip.diff_expr(ratelaw, pid)))
Ep.append(Ep_rxn)
Ep_str = str(Ep).replace("'", "")
Ep_code = compile(Ep_str, '', 'eval') # compile to code object
net.Ep_str, net.Ep_code = Ep_str, Ep_code
return Ep_str, Ep_code
def doKwargsSubstitution(self, kwargs):
oldStoichiometry = self.stoichiometry
self.stoichiometry = {}
for base in oldStoichiometry:
self.stoichiometry[kwargs[base]] = oldStoichiometry[base]
self.kineticLaw = ExprManip.sub_for_vars(self.kineticLaw, kwargs)
def test_diff_expr(self):
cases = [('x', 'x'), ('+x', 'x'), ('y', 'x'), ('x+y', 'x'),
('x*y', 'x'), ('x/y', 'x'), ('x**y', 'x'), ('x**x', 'x'),
('y**x', 'x'), ('acos(x)', 'x'), ('asin(x)', 'x'),
('atan(x)', 'x'), ('cos(x)', 'x'), ('cosh(x)', 'x'),
('exp(x)', 'x'), ('log(x)', 'x'), ('log10(x)', 'x'),
('sin(x)', 'x'), ('sinh(x)', 'x'), ('sqrt(x)', 'x'),
('tan(x)', 'x'), ('tanh(x)', 'x'), ('pow(x, 2)', 'x'),
('pow(y, x)', 'x'), ('y**2 - 4*x*z', 'x'),
('(-y + sqrt(y**2 - 4*x*z))/(2*x)', 'x'),
('(-y + sqrt(y**2 - 4*x*z))/(2*x)', 'y'),
('(-y + sqrt(y**2 - 4*x*z))/(2*x)', 'z'),
('sqrt(y - x)', 'x'), ('f(x)', 'x'),
('f(x - y*x + cos(x*z))', 'x'),
('g(x - y*x + cos(x*z), y, x)', 'x'),
('g(x - y*x + cos(x*z), y, x)', 'y'),
('g(x - y*x + cos(x*z), y**z, x - 14*z)', 'y'),
('g(x - y*x + cos(x*z), y, x)', 'y'),
('g(x*y, x*y**2, y)', 'z')]
for expr, wrt in cases:
d = ExprManip.diff_expr(expr, wrt)
ad = eval(d)
fd = self._num_diff(expr, wrt, x=x, y=y, z=z)
# We test that our numeric and analytic derivatives differ by less
# than 0.1%
if ad != 0:
assert abs(fd - ad) / (0.5 * (ad + fd)) < 1e-3
else:
assert ad == fd
def parseTrigger(self, trigger):
if '<' in trigger or '>' in trigger or '=' in trigger:
raise ValueError('Event triggers must use the functions gt and lt, '
'rather than the symbols > and <. For example, '
'to trigger when B becomes less than A, use '
'lt(B,A).')
# Figures out if the event is time-triggered and parses it to niceness.
# 'and' is a reserved keyword in python, so the parser will break
# unless we substitute the name here.
trigger = trigger.replace('and(', 'and_func(')
self.trigger = trigger
if ExprManip.extract_vars(trigger) == sets.Set(['time']):
self.timeTriggered = True
ast = ExprManip.AST.strip_parse(trigger)
firstArg = ExprManip.AST.ast2str(ast.args[0])
secondArg = ExprManip.AST.ast2str(ast.args[1])
if firstArg == 'time':
self.triggeringTime = eval(secondArg)
elif secondArg == 'time':
self.triggeringTime = eval(firstArg)
else:
raise 'Problem in time triggered events'
def parseTrigger(self, trigger):
if '<' in trigger or '>' in trigger or '=' in trigger:
raise ValueError(
'Event triggers must use the functions gt and lt, '
'rather than the symbols > and <. For example, '
'to trigger when B becomes less than A, use '
'lt(B,A).')
# Figures out if the event is time-triggered and parses it to niceness.
# 'and' is a reserved keyword in python, so the parser will break
# unless we substitute the name here.
trigger = trigger.replace('and(', 'and_func(')
self.trigger = trigger
if ExprManip.extract_vars(trigger) == set(['time']):
self.timeTriggered = True
ast = ExprManip.AST.strip_parse(trigger)
firstArg = ExprManip.AST.ast2str(ast.args[0])
secondArg = ExprManip.AST.ast2str(ast.args[1])
if firstArg == 'time':
self.triggeringTime = eval(secondArg)
elif secondArg == 'time':
self.triggeringTime = eval(firstArg)
else:
raise NameError('Problem in time triggered events')
def get_h(self, keep1=True):
"""
"""
coefs = self.get_coefs()
if not keep1:
coefs = butil.get_submapping(coefs, f_value=lambda s: s != '1')
subcoefids, subcoefstrs = coefs.keys(), coefs.values()
yids = ['%s, %s, %s'%((self.polyid,)+subcoefid)
for subcoefid in subcoefids]
senstrs = [[exprmanip.diff_expr(subcoefstr, pid)
for pid in self.pids] for subcoefstr in subcoefstrs]
hstr = str(subcoefstrs).replace("'", "")
Dhstr = str(senstrs).replace("'", "")
subs0 = self.convarvals.to_dict()
def h(p):
subs = subs0.copy()
subs.update(dict(zip(self.pids, p)))
return np.array(eval(hstr, subs))
def Dh(p):
subs = subs0.copy()
subs.update(dict(zip(self.pids, p)))
return np.array(eval(Dhstr, subs))
h = predict.Predict(f=h, Df=Dh, pids=self.pids, p0=self.p0,
yids=yids, frepr=butil.Series(subcoefstrs, yids),
Dfrepr=butil.DF(senstrs, yids, self.pids))
return h
def test_sub_for_vars(self):
cases = [
('x', {
'x': 'y'
}, 'y'),
('x + 1', {
'x': 'y'
}, 'y + 1'),
('f(x)**2 - y + z', {
'x': 'y*z/(x-2)'
}, 'f(y*z/(x-2))**2 - y + z'),
('x**2', {
'x': 'y+2'
}, '(y+2)**2'),
('p[0]**x', {
'x': 'y+2'
}, 'p[0]**(y+2)'),
# In these cases substituting one-by-one will fail
('x*y', {
'x': 'y',
'y': 'z'
}, 'y*z'),
('z*y', {
'z': 'y',
'y': 'z'
}, 'y*z'),
]
for expr, mapping, answer in cases:
subbed = ExprManip.sub_for_vars(expr, mapping)
assert eval(answer) == eval(subbed)
def get_concentration_elasticity_string(net):
"""
"""
Ex = []
for rxnid in net.rxnids:
ratelaw = exprmanip.sub_for_vars(net.rxns[rxnid].kineticLaw,
net.asgrules.to_dict())
Ex_rxn = []
for xid in net.xids:
Ex_rxn.append(
exprmanip.simplify_expr(exprmanip.diff_expr(ratelaw, xid)))
Ex.append(Ex_rxn)
Ex_str = str(Ex).replace("'", "")
Ex_code = compile(Ex_str, '', 'eval') # compile to code object
net.Ex_str, net.Ex_code = Ex_str, Ex_code
return Ex_str, Ex_code
def test_expr2Tex(self):
lines.append(r'\section{Basic expressions}')
lines.append(r'\begin{longtable}{rl}')
cases = [
'x',
'x+y',
'x-y',
'x*y',
'x/y',
'x**y',
'-x',
'x**-y',
'x**(-y + z)',
'f(x)',
'g(x,y,z)',
'x**(y**z)',
'(x**y)**z',
'x**y**z',
'x - (x+y)',
'(x+y) - z',
'g(x-0+2, y**2 - 0**0, z*y + x/1)',
'sqrt(x+y-sqrt(z/x))',
]
for expr in cases:
TeXed = ExprManip.expr2TeX(expr)
line = r'{\tt %s} & $ %s $ \\' % (expr, TeXed)
lines.append(line)
lines.append(r'\end{longtable}')
def doKwargsSubstitution(self, kwargs):
oldStoichiometry = self.stoichiometry
self.stoichiometry = {}
for base in oldStoichiometry:
self.stoichiometry[kwargs[base]] = oldStoichiometry[base]
self.kineticLaw = ExprManip.sub_for_vars(self.kineticLaw, kwargs)
def test_var_args_subs(self):
subbed = ExprManip.sub_for_func('or_func(x,y,z)', 'or_func', '*',
'a or b')
x, y, z = True, False, False
assert eval(subbed)
x, y, z = False, False, False
assert not eval(subbed)
self.assertRaises(ValueError, ExprManip.sub_for_func, 'or_func(x,y,z)',
'or_func', '*', 'a + b')
def test_extract_comps(self):
cases = [('x == 3', ['x == 3']),
('x == 3 and y == 4', ['x == 3', 'y == 4']),
('x < 3 and not y > 4', ['x < 3', 'y > 4']),
('x < 3 + (y > 4)', ['x < (3 + (y > 4))', 'y > 4']),
]
for expr, comps in cases:
result = ExprManip.extract_comps(expr)
assert result == sets.Set(comps)
def __init__(self, id, stoichiometry, kineticLaw = '', name = '',
reactant_stoichiometry = None, product_stoichiometry = None):
self.id = id
self.stoichiometry = stoichiometry
# self.reactant_stoichiometry and self.product_stoichiometry
# are defined to help repserve the stoichiometry defined in an
# SBML model
self.reactant_stoichiometry = reactant_stoichiometry
self.product_stoichiometry = product_stoichiometry
self.kineticLaw = kineticLaw
self.name = name
variables = ExprManip.extract_vars(kineticLaw)
self.parameters = variables.difference(sets.Set(stoichiometry.keys()))
def get_Ex_str(net):
"""
"""
Ex = []
for rxnid in net.rxnids:
ratelaw = net.rxns[rxnid].kineticLaw
Ex_rxn = []
for xid in net.xids:
Ex_rxn.append(expr.diff_expr(ratelaw, xid)) # diff also simplifies
Ex.append(Ex_rxn)
Ex_str = str(Ex).replace("'", "")
Ex_code = compile(Ex_str, '', 'eval') # compile to code object
net.Ex_str, net.Ex_code = Ex_str, Ex_code
return Ex_str, Ex_code
def get_Ep_str(net):
"""
"""
Ep = []
for rxnid in net.rxnids:
ratelaw = net.rxns[rxnid].kineticLaw
Ep_rxn = []
for pid in net.pids:
Ep_rxn.append(expr.diff_expr(ratelaw, pid)) # diff also simplifies
Ep.append(Ep_rxn)
Ep_str = str(Ep).replace("'", "")
Ep_code = compile(Ep_str, '', 'eval') # compile to code object
net.Ep_str, net.Ep_code = Ep_str, Ep_code
return Ep_str, Ep_code
def test_sub_for_var(self):
cases = [
('x', 'x', 'y', 'y'),
('x + 1', 'x', 'y', 'y + 1'),
('f(x)**2 - y + z', 'x', 'y*z/(x-2)', 'f(y*z/(x-2))**2 - y + z'),
('x**2', 'x', 'y+2', '(y+2)**2'),
('p[0]**x', 'x', 'y+2', 'p[0]**(y+2)'),
('g(x, y, f(z)) != y+2 and z == y', 'z', 'y',
'(g(x, y, f(y)) != (y + 2)) and (y == y)'),
]
for expr, out_var, in_expr, answer in cases:
subbed = ExprManip.sub_for_var(expr, out_var, in_expr)
assert eval(answer) == eval(subbed)
def test_name_dict(self):
name_dict = {'alpha': r'\alpha',
'beta': r'\beta',
'betarho': r'\beta\rho',
'chi': r'\lambda',
'tau': r'\tau'
}
cases = ['alpha',
'alpha**beta',
'chi(betarho, tau)',
'sqrt(4+sqrt(alpha))',
]
for expr in cases:
TeXed = ExprManip.expr2TeX(expr, name_dict)
def str2predict(s, pids, uids, us, c=None, p0=None, yids=None):
"""
Input:
us: a list of u's where each u has the same length as uids and has the
same order
c: if given, a mapping from convarid to convarval
"""
if c is not None:
s = exprmanip.sub_for_vars(s, c)
ystr = str([exprmanip.sub_for_vars(s, dict(zip(uids, u))) for u in us]).\
replace("'", "")
ycode = compile(ystr, '', 'eval')
def f(p):
return np.array(eval(ycode, dict(zip(pids, p)), mathsubs))
jaclist = []
for u in us:
s_u = exprmanip.sub_for_vars(s, dict(zip(uids, u)))
jacrow = [exprmanip.simplify_expr(exprmanip.diff_expr(s_u, pid))
for pid in pids]
jaclist.append(jacrow)
jacstr = str(jaclist).replace("'", "")
jaccode = compile(jacstr, '', 'eval')
def Df(p):
return np.array(eval(jaccode, dict(zip(pids, p)), mathsubs))
if p0 is None:
p0 = [1] * len(pids)
if yids is None:
yids = ['u=%s'%str(list(u)) for u in us]
return Predict(f=f, Df=Df, p0=p0, pids=pids, yids=yids)
def test_sub_for_func(self):
cases = [
('f(x)', 'f', 'y', 'y+1', 'x+1'),
('f(x)**2', 'f', 'y', 'y+1', '(x+1)**2'),
('f(g(x, y, z))**2', 'f', 'y', 'y+1', '(g(x,y,z)+1)**2'),
('g(f(x), y, z)**2', 'f', 'y', 'y+1', 'g(x+1,y,z)**2'),
('g(f(x), p[0], z)**2', 'f', 'y', 'y+1', 'g(x+1,p[0],z)**2'),
('g(z, y, f(x)) == y+2 and f(x) + f(y) != f(x)', 'g',
('x', 'y', 'z'), 'f(x + y/z)',
'(f(z + y/f(x)) == (y + 2)) and (f(x) + f(y) != f(x))'),
]
for expr, func_name, func_vars, func_expr, answer in cases:
subbed = ExprManip.sub_for_func(expr, func_name, func_vars,
func_expr)
assert eval(answer) == eval(subbed)
def test_extract_funcs(self):
cases = [('g(x)', [('g', 1)]), ('f(g(x))', [('f', 1), ('g', 1)]),
('f(g(x)/2, a, b(x, y))', [('f', 3), ('g', 1), ('b', 2)]),
('a + g(x)', [('g', 1)]),
('a + g(x) + (a + f(x))', [('f', 1), ('g', 1)]),
('f(g(1 + h(a))/2) + j(q**k(x)) + q.r[1] + s[1]', [('f', 1),
('g', 1),
('h', 1),
('j', 1),
('k', 1)]),
('(g(x) + 2)**f(y)', [('f', 1), ('g', 1)]),
('g(x)**f(y)', [('f', 1), ('g', 1)]),
('g(x) > f(y)', [('f', 1), ('g', 1)]),
('g(x) and f(y)', [('f', 1), ('g', 1)]),
('g(x) and not f(y)', [('f', 1), ('g', 1)])]
for expr, funcs in cases:
assert ExprManip.extract_funcs(expr) == set(funcs)
def test_simplify_expr(self):
cases = [
'x',
'x+y',
'x-y',
'x*y',
'x/y',
'x**y',
'-x',
'x**-y',
'x**(-y + z)',
'f(x)',
'g(x,y,z)',
'x**(y**z)',
'(x**y)**z',
'x**y**z',
'x - (x+y)',
'(x+y) - z',
'g(x-0+2, y**2 - 0**0, z*y + x/1)',
'x/x',
'x/y',
'(x-x)/z',
'x**2 - y/z',
'x+1-1+2-3-x',
'0+1*1',
'x-x+y',
'(-2)**2',
'-2**2',
'x/y == x/y',
'not True',
'x/x + y/y == 2',
'3 + 4 > 6',
'3 + (4 > 6)',
]
cases1 = ['x**(-y + z)']
# cases = ['-y + z']
for expr in cases:
simplified = ExprManip.simplify_expr(expr)
orig = eval(expr)
simp = eval(simplified)
if orig != 0:
assert old_div(abs(orig - simp), (0.5 * (orig + simp))) < 1e-6
else:
assert simp == 0
def __init__(self,
id,
stoichiometry,
kineticLaw='',
name='',
reactant_stoichiometry=None,
product_stoichiometry=None):
self.id = id
self.stoichiometry = stoichiometry
# self.reactant_stoichiometry and self.product_stoichiometry
# are defined to help repserve the stoichiometry defined in an
# SBML model
self.reactant_stoichiometry = reactant_stoichiometry
self.product_stoichiometry = product_stoichiometry
self.kineticLaw = kineticLaw
self.name = name
variables = ExprManip.extract_vars(kineticLaw)
self.parameters = variables.difference(sets.Set(stoichiometry.keys()))
def test_extract_vars(self):
cases = [('x', ['x']),
('x + y', ['x', 'y']),
('x * y', ['x', 'y']),
('x / y', ['x', 'y']),
('x**2', ['x']),
('x**y', ['x', 'y']),
('f(x)', ['x']),
('f(x, y)', ['x', 'y']),
('f(x + z/x, y)', ['x', 'y', 'z']),
('x**2 + f(y)', ['x', 'y']),
('x + y**2 + z**(a + b) + z**f.g.h(a + b + sqrt(c))',
['x', 'y', 'z', 'a', 'b', 'c']),
('x < y', ['x', 'y']),
('(x < y) and (x == 2)', ['x', 'y']),
]
for expr, vars in cases:
assert ExprManip.extract_vars(expr) == sets.Set(vars)
def solve_path2(s1, s2):
"""
Input:
s1 and s2: strs of ratelaws; variable is 'X'
solve_for: 'X' or 'J'
#idx_root: 0 or 1, since there can be two roots (if v1 - v2 == 0
# is a quadratic equation)
Output:
A tuple of (X string, J string)
"""
if 'inf' in s1 and 'inf' in s2:
raise ValueError
elif 'inf' in s1:
Xstr = str(sympy.solve(s1.replace('inf', '1'), 'X', simplify=True)[0])
Jstr = exprmanip.simplify_expr(exprmanip.sub_for_var(s2, 'X', Xstr))
elif 'inf' in s2:
Xstr = str(sympy.solve(s2.replace('inf', '1'), 'X', simplify=True)[0])
Jstr = exprmanip.simplify_expr(exprmanip.sub_for_var(s1, 'X', Xstr))
else:
eqn = '(%s) - (%s)' % (s1, s2)
roots = sympy.solve(eqn, 'X', simplify=True)
if len(roots) == 2:
# choose the positive root (can be the 1st or the 2nd of the two)
bools = ['+ sqrt' in str(sympy.expand(root)) for root in roots]
idx = bools.index(True)
Xstr = str(roots[idx])
else:
Xstr = str(roots[0])
Jstr = exprmanip.simplify_expr(exprmanip.sub_for_var(s1, 'X', Xstr))
"""
try:
xsol = str(roots[1])
varids = list(exprmanip.extract_vars(xsol))
tests = []
for i in range(10):
subs = dict(zip(varids, np.random.lognormal(size=len(varids))))
subs['sqrt'] = np.sqrt
tests.append(eval(xsol, subs) > 0)
if not all(tests):
raise ValueError
except (IndexError, ValueError):
xsol = str(roots[0])
"""
return Xstr, Jstr
def test_sub_for_comps(self):
cases = [
('not x < 3 and True', {
'x < 3': 'True'
}, False),
('not x < 3 and x < 3', {
'x < 3': 'True'
}, False),
('x < 3 and x < 3', {
'x < 3': 'True'
}, True),
('x < 3 and y > 4', {
'x < 3': 'True',
'y > 4': 'False'
}, False),
('x < 3 and not y > 4', {
'x < 3': 'True',
'y > 4': 'False'
}, True),
]
for expr, mapping, result in cases:
subbed = ExprManip.sub_for_comps(expr, mapping)
assert eval(subbed) == result
def replace_varid(self, varid_old, varid_new, only_expr=False):
"""Change id of reaction, species, or parameter.
:param only_expr: bool; if True, only replace varid in expressions
such as reaction ratelaws or assignment rules but not variable ids;
useful when varid_new == 'varid_old * r'
"""
if only_expr:
f = lambda varid: varid
else:
f = lambda varid: varid_new if varid == varid_old else varid
netid_new = f(self.id)
net_new = self.__class__(netid_new)
for var in self.variables:
var_new = copy.deepcopy(var)
var_new.id = f(var.id)
net_new.variables.set(var_new.id, var_new)
for rxn in self.reactions:
rxn_new = copy.deepcopy(rxn)
rxn_new.id = f(rxn.id)
rxn_new.stoichiometry = OD(
zip(map(f, rxn.stoichiometry.keys()),
rxn.stoichiometry.values()))
try:
rxn_new.reactant_stoichiometry =\
OD(zip(map(f, rxn.reactant_stoichiometry.keys()),
rxn.reactant_stoichiometry.values()))
rxn_new.product_stoichiometry =\
OD(zip(map(f, rxn.product_stoichiometry.keys()),
rxn.product_stoichiometry.values()))
except AttributeError: # some rxns have no reactant/product stoich
pass
rxn_new.parameters = set(map(f, rxn.parameters))
rxn_new.kineticLaw = exprmanip.sub_for_var(rxn.kineticLaw,
varid_old, varid_new)
net_new.reactions.set(rxn_new.id, rxn_new)
for varid, rule in self.assignmentRules.items():
net_new.assignmentRules.set(
f(varid), exprmanip.sub_for_var(rule, varid_old, varid_new))
for varid, rule in self.algebraicRules.items():
net_new.algebraicRules.set(
exprmanip.sub_for_var(varid, varid_old, varid_new),
exprmanip.sub_for_var(rule, varid_old, varid_new))
for varid, rule in self.rateRules.items():
net_new.rateRules.set(
f(varid), exprmanip.sub_for_var(rule, varid_old, varid_new))
for eid, event in self.events.items():
eid_new = f(eid)
trigger_new = exprmanip.sub_for_var(event.trigger, varid_old,
varid_new)
assignments_new = OD(
zip(map(f, event.event_assignments.keys()),
event.event_assignments.values()))
net_new.add_event(eid_new, trigger_new, assignments_new)
net_new.functionDefinitions = self.functionDefinitions.copy()
for fid, f in net_new.functionDefinitions.items():
fstr = 'lambda %s: %s' % (','.join(f.variables), f.math)
net_new.namespace[fid] = eval(fstr, net_new.namespace)
# _makeCrossReferences will take care of at least the following
# attributes:
# assignedVars, constantVars, optimizableVars, dynamicVars,
# algebraicVars
net_new._makeCrossReferences()
return net_new
def fromSBMLString(sbmlStr, id=None, duplicate_rxn_params=False):
r = libsbml.SBMLReader()
d = r.readSBMLFromString(sbmlStr)
if d.getNumErrors():
message = 'libSBML reported errors in SBML file. Try running file '\
'through the online validator: '\
'http://www.sbml.org/Facilities/Validator . Specific errors '\
'noted are: '
errors = []
for ii in range(d.getNumErrors()):
pm = d.getError(ii)
errors.append(pm.getMessage())
print(message + '; '.join(errors))
m = d.getModel()
modelId = m.getId()
if (id is None) and (modelId == ''):
raise ValueError('Network id not specified in SBML or passed in.')
elif id is not None:
modelId = id
rn = Network_mod.Network(id=modelId, name=m.getName())
for f in m.getListOfFunctionDefinitions():
id, name = f.getId(), f.getName()
math = f.getMath()
variables = []
for ii in range(math.getNumChildren() - 1):
variables.append(formula_to_py(math.getChild(ii)))
math = formula_to_py(math.getRightChild())
rn.addFunctionDefinition(id, variables, math)
for c in m.getListOfCompartments():
id, name = c.getId(), c.getName()
size = c.getSize()
isConstant = c.getConstant()
rn.addCompartment(id=id, size=size, isConstant=isConstant, name=name)
for s in m.getListOfSpecies():
id, name = s.getId(), s.getName()
compartment = s.getCompartment()
if s.isSetInitialConcentration():
iC = s.getInitialConcentration()
elif s.isSetInitialAmount():
iC = s.getInitialAmount()
else:
iC = 1
isBC, isConstant = s.getBoundaryCondition(), s.getConstant()
xml_text = s.toSBML()
uniprot_ids = set([
entry[1:].split('"')[0] for entry in xml_text.split('uniprot')[1:]
])
rn.addSpecies(id=id,
compartment=compartment,
initialConcentration=iC,
isConstant=isConstant,
is_boundary_condition=isBC,
name=name,
uniprot_ids=uniprot_ids)
for p in m.getListOfParameters():
parameter = createNetworkParameter(p)
rn.addVariable(parameter)
for rxn in m.getListOfReactions():
id, name = rxn.getId(), rxn.getName()
kL = rxn.getKineticLaw()
kLFormula = kL.getFormula()
substitution_dict = {}
# Deal with parameters defined within reactions
for p in kL.getListOfParameters():
parameter = createNetworkParameter(p)
# If a parameter with this name already exists, **and it has a
# different value than this parameter** we rename this parameter
# instance by prefixing it with the rxn name so there isn't a
# clash.
if parameter.id in list(rn.variables.keys()):
logger.warn('Parameter %s appears in two different reactions '
'in SBML file.' % parameter.id)
if parameter.value != rn.variables.get(parameter.id).value or\
duplicate_rxn_params:
oldId = parameter.id
parameter.id = id + '_' + parameter.id
substitution_dict[oldId] = parameter.id
logger.warn('It has different values in the two positions '
'so we are creating a new parameter %s.' %
(parameter.id))
else:
logger.warn('It has the same value in the two positions '
'so we are only defining one parameter %s. '
'This behavior can be changed with the option '
'duplicate_rxn_params = True' % (parameter.id))
if parameter.id not in list(rn.variables.keys()):
rn.addVariable(parameter)
kLFormula = ExprManip.sub_for_vars(kLFormula, substitution_dict)
# Assemble the stoichiometry. SBML has the annoying trait that
# species can appear as both products and reactants and 'cancel out'
# For each species appearing in the reaction, we build up a string
# representing the stoichiometry. Then we'll simplify that string and
# see whether we ended up with a float value in the end.
stoichiometry = {}
reactant_stoichiometry = {}
product_stoichiometry = {}
for reactant in rxn.getListOfReactants():
species = reactant.getSpecies()
stoichiometry.setdefault(species, '0')
stoich = reactant.getStoichiometryMath()
stoich = stoichToString(reactant, stoich)
stoichiometry[species] += '-(%s)' % stoich
if species in reactant_stoichiometry:
reactant_stoichiometry[species].append(stoich)
else:
reactant_stoichiometry[species] = [stoich]
for product in rxn.getListOfProducts():
species = product.getSpecies()
stoichiometry.setdefault(species, '0')
stoich = product.getStoichiometryMath()
stoich = stoichToString(product, stoich)
stoichiometry[species] += '+(%s)' % stoich
if species in product_stoichiometry:
product_stoichiometry[species].append(stoich)
else:
product_stoichiometry[species] = [stoich]
for species, stoich in list(stoichiometry.items()):
stoich = ExprManip.simplify_expr(stoich)
try:
# Try converting the string to a float.
stoich = float(stoich)
except ValueError:
pass
stoichiometry[species] = stoich
for modifier in rxn.getListOfModifiers():
stoichiometry.setdefault(modifier.getSpecies(), 0)
rn.addReaction(id=id,
stoichiometry=stoichiometry,
kineticLaw=kLFormula,
reactant_stoichiometry=reactant_stoichiometry,
product_stoichiometry=product_stoichiometry)
for ii, r in enumerate(m.getListOfRules()):
if r.getTypeCode() == libsbml.SBML_ALGEBRAIC_RULE:
math = formula_to_py(r.getMath())
rn.add_algebraic_rule(math)
else:
variable = r.getVariable()
math = formula_to_py(r.getMath())
if r.getTypeCode() == libsbml.SBML_ASSIGNMENT_RULE:
rn.addAssignmentRule(variable, math)
elif r.getTypeCode() == libsbml.SBML_RATE_RULE:
rn.addRateRule(variable, math)
for ii, e in enumerate(m.getListOfEvents()):
id, name = e.getId(), e.getName()
if id == '':
id = 'event%i' % ii
try:
# For libSBML 3.0
trigger_math = e.getTrigger().getMath()
except AttributeError:
# For older versions
trigger_math = e.getTrigger()
trigger = formula_to_py(trigger_math)
if e.getDelay() is not None:
try:
# For libSBML 3.0
delay_math = e.getDelay().getMath()
except AttributeError:
# For older versions
delay_math = e.getDelay()
delay = formula_to_py(delay_math)
else:
delay = 0
timeUnits = e.getTimeUnits()
eaDict = KeyedList()
for ea in e.getListOfEventAssignments():
ea_formula = formula_to_py(ea.getMath())
ea_formula = ea_formula.replace('or(', 'or_func(')
ea_formula = ea_formula.replace('and(', 'and_func(')
eaDict.set(ea.getVariable(), ea_formula)
rn.addEvent(id=id,
trigger=trigger,
eventAssignments=eaDict,
delay=delay,
name=name)
for ii, con in enumerate(m.getListOfConstraints()):
id, name = con.getId(), con.getName()
if id == '':
id = 'constraint%i' % ii
trigger_math = con.getMath()
trigger = formula_to_py(trigger_math)
if con.isSetMessage():
message = con.getMessage()
else:
message = None
rn.addConstraint(id=id, trigger=trigger, message=message, name=name)
return rn
def toSBMLString(net):
metaId = 0
try:
m = libsbml.Model(net.id)
except NotImplementedError:
m = libsbml.Model(sbml_level, sbml_version)
m.setId(net.id)
m.setName(net.name)
m.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
for id, fd in list(net.functionDefinitions.items()):
try:
sfd = libsbml.FunctionDefinition(id)
except:
sfd = libsbml.FunctionDefinition(sbml_level, sbml_version)
sfd.setId(id)
sfd.setName(fd.name)
formula = fd.math
formula = formula.replace('**', '^')
formula = 'lambda(%s, %s)' % (','.join(fd.variables), formula)
sfd.setMath(libsbml.parseFormula(formula))
sfd.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addFunctionDefinition(sfd)
for id, c in list(net.compartments.items()):
try:
sc = libsbml.Compartment(id)
except NotImplementedError:
sc = libsbml.Compartment(sbml_level, sbml_version)
sc.setId(id)
sc.setName(c.name)
sc.setConstant(c.is_constant)
sc.setSize(c.initialValue)
sc.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addCompartment(sc)
for id, s in list(net.species.items()):
try:
ss = libsbml.Species(id)
except NotImplementedError:
ss = libsbml.Species(sbml_level, sbml_version)
ss.setId(id)
ss.setName(s.name)
ss.setCompartment(s.compartment)
if s.initialValue is not None and not isinstance(s.initialValue, str):
ss.setInitialConcentration(s.initialValue)
ss.setBoundaryCondition(s.is_boundary_condition)
ss.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addSpecies(ss)
for id, p in list(net.parameters.items()):
try:
sp = libsbml.Parameter(id)
except NotImplementedError:
sp = libsbml.Parameter(sbml_level, sbml_version)
sp.setId(id)
sp.setName(p.name)
if p.initialValue is not None:
sp.setValue(p.initialValue)
sp.setConstant(p.is_constant)
sp.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addParameter(sp)
for id, r in list(net.rateRules.items()):
try:
sr = libsbml.RateRule()
except NotImplementedError:
sr = libsbml.RateRule(sbml_level, sbml_version)
sr.setVariable(id)
formula = r.replace('**', '^')
sr.setMath(libsbml.parseFormula(formula))
sr.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addRule(sr)
for id, r in list(net.assignmentRules.items()):
try:
sr = libsbml.AssignmentRule()
except NotImplementedError:
sr = libsbml.AssignmentRule(sbml_level, sbml_version)
sr.setVariable(id)
formula = r.replace('**', '^')
sr.setMath(libsbml.parseFormula(formula))
sr.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addRule(sr)
for r, r in list(net.algebraicRules.items()):
try:
sr = libsbml.AlgebraicRule()
except NotImplementedError:
sr = libsbml.AlgebraicRule(sbml_level, sbml_version)
formula = r.replace('**', '^')
sr.setMath(libsbml.parseFormula(formula))
sr.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addRule(sr)
for id, rxn in list(net.reactions.items()):
# Need to identify modifiers in kinetic law and add them to
# stoichiometry
kl_vars = ExprManip.extract_vars(rxn.kineticLaw)
species_in_kl = kl_vars.intersection(list(net.species.keys()))
for s in species_in_kl:
if s not in rxn.stoichiometry:
rxn.stoichiometry[s] = 0
try:
srxn = libsbml.Reaction(id)
except NotImplementedError:
srxn = libsbml.Reaction(sbml_level, sbml_version)
srxn.setId(id)
srxn.setName(rxn.name)
# Handle the case where the model was originally read in from an
# SBML file, so that the reactants and products of the Reaction
# object are explicitly set.
if rxn.reactant_stoichiometry != None and \
rxn.product_stoichiometry != None:
for rid, stoich_list in list(rxn.reactant_stoichiometry.items()):
for stoich in stoich_list:
rxn_add_stoich(srxn, rid, -float(stoich), is_product=False)
for rid, stoich_list in list(rxn.product_stoichiometry.items()):
for stoich in stoich_list:
rxn_add_stoich(srxn, rid, stoich, is_product=True)
# Handle the case where the model was created using the SloppyCell
# API, in which case reactants and products are inferred from their
# stoichiometries
else:
for rid, stoich in list(rxn.stoichiometry.items()):
rxn_add_stoich(srxn, rid, stoich)
formula = rxn.kineticLaw.replace('**', '^')
try:
kl = libsbml.KineticLaw(formula)
except NotImplementedError:
kl = libsbml.KineticLaw(sbml_level, sbml_version)
kl.setFormula(formula)
srxn.setKineticLaw(kl)
srxn.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addReaction(srxn)
for id, e in list(net.events.items()):
try:
se = libsbml.Event(id)
except NotImplementedError:
se = libsbml.Event(sbml_level, sbml_version)
se.setId(id)
se.setName(e.name)
formula = e.trigger.replace('**', '^')
formula = formula.replace('and_func(', 'and(')
formula = formula.replace('or_func(', 'or(')
ast = libsbml.parseFormula(formula)
if ast is None:
raise ValueError('Problem parsing event trigger: %s. Problem may '
'be use of relational operators (< and >) rather '
'than libsbml-friendly functions lt and gt.' %
formula)
try:
se.setTrigger(ast)
except TypeError:
try:
trigger = libsbml.Trigger(ast)
except NotImplementedError:
trigger = libsbml.Trigger(sbml_level, sbml_version)
trigger.setMath(ast)
se.setTrigger(trigger)
formula = str(e.delay).replace('**', '^')
try:
se.setDelay(libsbml.parseFormula(formula))
except TypeError:
try:
se.setDelay(libsbml.Delay(libsbml.parseFormula(formula)))
except NotImplementedError:
delay = libsbml.Delay(sbml_level, sbml_version)
delay.setMath(libsbml.parseFormula(formula))
se.setDelay(delay)
for varId, formula in list(e.event_assignments.items()):
try:
sea = libsbml.EventAssignment()
except NotImplementedError:
sea = libsbml.EventAssignment(sbml_level, sbml_version)
sea.setVariable(varId)
formula = str(formula).replace('**', '^')
formula = formula.replace('and_func(', 'and(')
formula = formula.replace('or_func(', 'or(')
ast = libsbml.parseFormula(formula)
replaceTime(ast)
sea.setMath(ast)
se.addEventAssignment(sea)
se.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addEvent(se)
for id, con in list(net.constraints.items()):
try:
scon = libsbml.Constraint()
except NotImplementedError:
scon = libsbml.Constraint(sbml_level, sbml_version)
scon.setId(con.id)
scon.setName(con.name)
formula = con.trigger.replace('**', '^')
ast = libsbml.parseFormula(formula)
if ast is None:
raise ValueError(
'Problem parsing constraint math: %s. Problem may '
'be use of relational operators (< and >) rather '
'than libsbml-friendly functions lt and gt.' % formula)
scon.setMath(ast)
se.setcon('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addConstraint(scon)
d = libsbml.SBMLDocument(sbml_level, sbml_version)
d.setModel(m)
sbmlStr = libsbml.writeSBMLToString(d)
return sbmlStr
def to_tex(self, d_tex=None, eqn=True,
filepath='', landscape=True, margin=2):
"""
Input:
d_tex: a mapping...
"""
_repl = exprmanip.sub_for_vars
_raisepower = lambda tu: tu[0] ** tu[1]
def _2tex_pid(pid):
if pid.startswith('Vf_') or pid.startswith('Vb_'):
pid = '%s^{%s}' % tuple(pid.split('_'))
if pid.count('_') == 2:
pid = '%s^{%s}_{%s}' % tuple(pid.split('_'))
return pid
d_tex = dict(zip(self.pids, [_2tex_pid(pid) for pid in self.pids]) +\
d_tex.items())
_2tex = lambda sympyexpr:\
sympy.latex(sympyexpr, mode='plain', long_frac_ratio=10, mul_symbol='dot',
symbol_names=butil.chkeys(d_tex, lambda k: sympy.symbols(k)))
_rm1pt0 = lambda expr: re.sub('(?<![0-9])1.0\s*\\\cdot', '', expr)
lines = []
lines.append(r'\documentclass{article}')
lines.append(r'\usepackage{amsmath,fullpage,longtable,array,calc,mathastext,breqn,xcolor}')
if landscape == True:
lines.append(r'\usepackage[a4paper,landscape,margin=1in]{geometry}')
else:
lines.append(r'\usepackage[a4paper,margin=%fin]{geometry}'%margin)
lines.append(r'\begin{document}')
coefs_r = []
yids = []
for poly in self:
termstrs = []
leadingcoef_r = sympy.Poly(poly.coeffs()[0], r).coeffs()[0]
for monom_X, coef_X in poly.terms():
coef_X = sympy.simplify(coef_X, ratio=1)
poly_r = sympy.Poly(coef_X, r)
coefs_r.extend([coef_r/leadingcoef_r for coef_r in poly_r.coeffs()])
monom_X = sympy.prod(map(_raisepower, zip(X, monom_X)))
monomstr_X = _2tex(monom_X)
if monomstr_X == '1':
monomstr_X = ''
monomstr_X = '\\textcolor{red}{%s}' % monomstr_X
termstrs_r = []
for monom_r, coef_r in poly_r.terms():
coefstr_r = _rm1pt0(_2tex(coef_r))
if coef_r.is_Add:
coefstr_r = '\left('+ coefstr_r +'\\right)'
monom_r = sympy.prod(map(_raisepower, zip(r, monom_r)))
monomstr_r = _2tex(monom_r)
if monomstr_r == '1':
monomstr_r = ''
monomstr_r = '\\textcolor{blue}{%s}' % monomstr_r
termstrs_r.append(coefstr_r + '\t' + monomstr_r)
coefstr_X = '\\left(' + '+'.join(termstrs_r) + '\\right)'
yids.append((ixid, str(monom_X), str(monom_r)))
termstrs.append(coefstr_X + '\t' + monomstr_X)
linestr = '\\begin{dmath} \n' + '+'.join(termstrs) + '=0\n\end{dmath} \n\n'
lines.append(linestr.replace('+-', '-'))
lines.append('\\end{document}')
if filepath:
fh = file(filepath, 'w')
fh.write(os.linesep.join(lines))
fh.close()
coefs_r = [_rm1pt0(str(coef)) for coef in coefs_r]
str_h = str(coefs_r).replace("'", "")
str_Dh = str([[exprmanip.diff_expr(coef, pid) for pid in self.pids]
for coef in coefs_r]).replace("'", "")
def h(p):
self.update(p=p)
return np.array(eval(str_h, self.varvals.to_dict()))
def Dh(p):
self.update(p=p)
return np.array(eval(str_Dh, self.varvals.to_dict()))
coefs = predict.Predict(f=h, Df=Dh, pids=self.pids, p0=self.p0,
yids=yids, funcform=coefs_r)
return coefs
def fromSBMLString(sbmlStr, id = None, duplicate_rxn_params=False):
r = libsbml.SBMLReader()
d = r.readSBMLFromString(sbmlStr)
if d.getNumErrors():
message = 'libSBML reported errors in SBML file. Try running file '\
'through the online validator: '\
'http://www.sbml.org/Facilities/Validator . Specific errors '\
'noted are: '
errors = []
for ii in range(d.getNumErrors()):
pm = d.getError(ii)
errors.append(pm.getMessage())
raise ValueError(message + '; '.join(errors))
m = d.getModel()
modelId = m.getId()
if (id == None) and (modelId == ''):
raise ValueError('Network id not specified in SBML or passed in.')
elif id is not None:
modelId = id
rn = Network_mod.Network(id = modelId, name = m.getName())
for f in m.getListOfFunctionDefinitions():
id, name = f.getId(), f.getName()
math = f.getMath()
variables = []
for ii in range(math.getNumChildren() - 1):
variables.append(libsbml.formulaToString(math.getChild(ii)))
math = libsbml.formulaToString(math.getRightChild())
rn.addFunctionDefinition(id, variables, math)
for c in m.getListOfCompartments():
id, name = c.getId(), c.getName()
size = c.getSize()
isConstant = c.getConstant()
rn.addCompartment(id = id, size = size,
isConstant = isConstant,
name = name)
for s in m.getListOfSpecies():
id, name = s.getId(), s.getName()
compartment = s.getCompartment()
if s.isSetInitialConcentration():
iC = s.getInitialConcentration()
elif s.isSetInitialAmount():
iC = s.getInitialAmount()
else:
iC = 1
isBC, isConstant = s.getBoundaryCondition(), s.getConstant()
xml_text = s.toSBML()
uniprot_ids = set([entry[1:].split('"')[0]
for entry in xml_text.split('uniprot')[1:]])
rn.addSpecies(id = id, compartment = compartment,
initialConcentration = iC,
isConstant = isConstant,
is_boundary_condition = isBC,
name = name, uniprot_ids = uniprot_ids)
for p in m.getListOfParameters():
parameter = createNetworkParameter(p)
rn.addVariable(parameter)
for rxn in m.getListOfReactions():
id, name = rxn.getId(), rxn.getName()
kL = rxn.getKineticLaw()
kLFormula = kL.getFormula()
substitution_dict = {}
# Deal with parameters defined within reactions
for p in kL.getListOfParameters():
parameter = createNetworkParameter(p)
# If a parameter with this name already exists, **and it has a
# different value than this parameter** we rename this parameter
# instance by prefixing it with the rxn name so there isn't a
# clash.
if parameter.id in rn.variables.keys():
logger.warn('Parameter %s appears in two different reactions '
'in SBML file.' % parameter.id)
if parameter.value != rn.variables.get(parameter.id).value or\
duplicate_rxn_params:
oldId = parameter.id
parameter.id = id + '_' + parameter.id
substitution_dict[oldId] = parameter.id
logger.warn('It has different values in the two positions '
'so we are creating a new parameter %s.'
% (parameter.id))
else:
logger.warn('It has the same value in the two positions '
'so we are only defining one parameter %s. '
'This behavior can be changed with the option '
'duplicate_rxn_params = True' % (parameter.id))
if parameter.id not in rn.variables.keys():
rn.addVariable(parameter)
kLFormula = ExprManip.sub_for_vars(kLFormula, substitution_dict)
# Assemble the stoichiometry. SBML has the annoying trait that
# species can appear as both products and reactants and 'cancel out'
# For each species appearing in the reaction, we build up a string
# representing the stoichiometry. Then we'll simplify that string and
# see whether we ended up with a float value in the end.
stoichiometry = {}
reactant_stoichiometry = {}
product_stoichiometry = {}
for reactant in rxn.getListOfReactants():
species = reactant.getSpecies()
stoichiometry.setdefault(species, '0')
stoich = reactant.getStoichiometryMath()
stoich = stoichToString(reactant, stoich)
stoichiometry[species] += '-(%s)' % stoich
if species in reactant_stoichiometry:
reactant_stoichiometry[species].append(stoich)
else:
reactant_stoichiometry[species] = [stoich]
for product in rxn.getListOfProducts():
species = product.getSpecies()
stoichiometry.setdefault(species, '0')
stoich = product.getStoichiometryMath()
stoich = stoichToString(product, stoich)
stoichiometry[species] += '+(%s)' % stoich
if species in product_stoichiometry:
product_stoichiometry[species].append(stoich)
else:
product_stoichiometry[species] = [stoich]
for species, stoich in stoichiometry.items():
stoich = ExprManip.simplify_expr(stoich)
try:
# Try converting the string to a float.
stoich = float(stoich)
except ValueError:
pass
stoichiometry[species] = stoich
for modifier in rxn.getListOfModifiers():
stoichiometry.setdefault(modifier.getSpecies(), 0)
rn.addReaction(id = id, stoichiometry = stoichiometry,
kineticLaw = kLFormula,
reactant_stoichiometry = reactant_stoichiometry,
product_stoichiometry = product_stoichiometry)
for ii, r in enumerate(m.getListOfRules()):
if r.getTypeCode() == libsbml.SBML_ALGEBRAIC_RULE:
math = libsbml.formulaToString(r.getMath())
rn.add_algebraic_rule(math)
else:
variable = r.getVariable()
math = libsbml.formulaToString(r.getMath())
if r.getTypeCode() == libsbml.SBML_ASSIGNMENT_RULE:
rn.addAssignmentRule(variable, math)
elif r.getTypeCode() == libsbml.SBML_RATE_RULE:
rn.addRateRule(variable, math)
for ii, e in enumerate(m.getListOfEvents()):
id, name = e.getId(), e.getName()
if id == '':
id = 'event%i' % ii
try:
# For libSBML 3.0
trigger_math = e.getTrigger().getMath()
except AttributeError:
# For older versions
trigger_math = e.getTrigger()
trigger = libsbml.formulaToString(trigger_math)
trigger = trigger.replace('or(','or_func(')
trigger = trigger.replace('and(','and_func(')
if e.getDelay() is not None:
try:
# For libSBML 3.0
delay_math = e.getDelay().getMath()
except AttributeError:
# For older versions
delay_math = e.getDelay()
delay = libsbml.formulaToString(delay_math)
else:
delay = 0
timeUnits = e.getTimeUnits()
eaDict = KeyedList()
for ea in e.getListOfEventAssignments():
ea_formula = libsbml.formulaToString(ea.getMath())
ea_formula = ea_formula.replace('or(','or_func(')
ea_formula = ea_formula.replace('and(','and_func(')
eaDict.set(ea.getVariable(), ea_formula)
rn.addEvent(id = id, trigger = trigger, eventAssignments = eaDict,
delay = delay, name = name)
for ii, con in enumerate(m.getListOfConstraints()):
id, name = con.getId(), con.getName()
if id == '':
id = 'constraint%i' % ii
trigger_math = con.getMath()
trigger = libsbml.formulaToString(trigger_math)
if con.isSetMessage():
message = con.getMessage()
else:
message = None
rn.addConstraint(id = id, trigger = trigger, message = message,
name = name)
return rn
