我正在使用PySB图书馆进行毕业设计。最初的目标是使用模型类提供的接口SBML在 GPU 上模拟一个。我写了一个简单的 Python 脚本pysb/cupSODACupSodaSimulatorpysb.simulator.cupsoda
from pysb.importers.sbml import model_from_sbml
from pysb.simulator.cupsoda import CupSodaSimulator
filename="BIOMD0000000005_url.xml"
model = model_from_sbml(filename=filename)
simulator = CupSodaSimulator(model=model)
但我收到以下错误
AttributeError Traceback (most recent call last)
<ipython-input-5-b1ba6e155a18> in <module>
----> 1 simulator = CupSodaSimulator(model=model)
~/anaconda3/lib/python3.8/site-packages/pysb/simulator/cupsoda.py in __init__(self, model, tspan, initials, param_values, verbose, **kwargs)
197
198 # generate the equations for the model
--> 199 pysb.bng.generate_equations(self._model, self._cleanup, self.verbose)
200
201 # build integrator options list from our defaults and any kwargs
~/anaconda3/lib/python3.8/site-packages/pysb/bng.py in generate_equations(model, cleanup, verbose, **kwargs)
729 if model.reactions:
730 return
--> 731 lines = iter(generate_network(model, cleanup=cleanup,
732 verbose=verbose, **kwargs).split('\n'))
733 _parse_netfile(model, lines)
~/anaconda3/lib/python3.8/site-packages/pysb/bng.py in generate_network(model, cleanup, append_stdout, verbose, **kwargs)
670 bngfile.action('generate_network', overwrite=True,
671 verbose=bng_action_debug, **kwargs)
--> 672 bngfile.execute()
673
674 output = bngfile.read_netfile()
~/anaconda3/lib/python3.8/site-packages/pysb/bng.py in execute(self, reload_netfile, skip_file_actions)
441 output = ''
442 if self.model and not reload_netfile:
--> 443 output += self.generator.get_content()
444 if reload_netfile:
445 filename = reload_netfile if \
~/anaconda3/lib/python3.8/site-packages/pysb/generator/bng.py in get_content(self)
24 def get_content(self):
25 if self.__content == None:
---> 26 self.generate_content()
27 return self.__content
28
~/anaconda3/lib/python3.8/site-packages/pysb/generator/bng.py in generate_content(self)
29 def generate_content(self):
30 self.__content = "begin model\n"
---> 31 self.generate_parameters()
32 self.generate_compartments()
33 self.generate_molecule_types()
~/anaconda3/lib/python3.8/site-packages/pysb/generator/bng.py in generate_parameters(self)
40
41 def generate_parameters(self):
---> 42 exprs = self.model.expressions_constant()
43 if not self.model.parameters and not exprs:
44 return
~/anaconda3/lib/python3.8/site-packages/pysb/core.py in expressions_constant(self)
1974 def expressions_constant(self):
1975 """Return a ComponentSet of constant expressions."""
-> 1976 cset = ComponentSet(e for e in self.expressions
1977 if e.is_constant_expression())
1978 return cset
~/anaconda3/lib/python3.8/site-packages/pysb/core.py in __init__(self, iterable)
2253 self._index_map = {}
2254 if iterable is not None:
-> 2255 for value in iterable:
2256 self.add(value)
2257
~/anaconda3/lib/python3.8/site-packages/pysb/core.py in <genexpr>(.0)
1975 """Return a ComponentSet of constant expressions."""
1976 cset = ComponentSet(e for e in self.expressions
-> 1977 if e.is_constant_expression())
1978 return cset
1979
~/anaconda3/lib/python3.8/site-packages/pysb/core.py in is_constant_expression(self)
1642 (isinstance(a, Expression) and a.is_constant_expression()) or
1643 isinstance(a, sympy.Number)
-> 1644 for a in self.expr.atoms())
1645
1646 def get_value(self):
~/anaconda3/lib/python3.8/site-packages/sympy/core/basic.py in atoms(self, *types)
521 result = {node for node in nodes if isinstance(node, types)}
522 else:
--> 523 result = {node for node in nodes if not node.args}
524 return result
525
~/anaconda3/lib/python3.8/site-packages/sympy/core/basic.py in <setcomp>(.0)
521 result = {node for node in nodes if isinstance(node, types)}
522 else:
--> 523 result = {node for node in nodes if not node.args}
524 return result
525
AttributeError: 'str' object has no attribute 'args'
有没有人知道如何解决这个问题？