590e29dd3dca1f837ab70c67f3a628c7ee032ac9,pysb/simulator/cupsoda.py,CupSodaSimulator,_get_cmatrix,#CupSodaSimulator#,452

Before Change

            for j in range(self._len_rxns):
                rate = 1.0
                for r in rate_args[j]:
                    x = str(r)
                    if x in par_names:
                        rate *= par_vals[i][par_dict[x]]
                    else:
                        // FIXME: need to detect non-numbers and throw an error

After Change

            for j in range(self._len_rxns):
                rate = 1.0
                for r in rate_args[j]:
                    if isinstance(r, pysb.Parameter):
                        rate *= par_vals[i][par_names.index(r.name)]
                    elif isinstance(r, pysb.Expression):
                        raise ValueError("cupSODA does not currently support "
                                         "models with Expressions")
                    else:
                        rate *= r
                // volume correction
                if self.vol:
                    rate *= (N_A * self.vol) ** (rate_order[j] - 1)
                c_matrix[i][j] = rate
        self._logger.debug("100%")

Instances