Cache last values of reaction rate related functions (v 0.3.2)

xbanalysis/_version.py

 """
 Definition of version string.
 """
-__version__ = "0.3.1"
+__version__ = "0.3.2"
 program_name = 'xbanalysis'

xbanalysis/problems/gba_problem.py

@@ -110,14 +110,63 @@ class GbaProblem:
         self.model_params['mws'] = np.array([xba_model.species[sid].mw for sid in self.var_sids])
 
         # create functions
-        self.mras, self.mras_jac, self.mras_hesss = self.get_reactions(self.mr_rids, inv=False)
-        self.pstmas, self.pstmas_jac, self.pstmas_hesss = self.get_reactions(self.ps_rids, inv=True)
-        self.degradas, self.degradas_jac, self.degradas_hesss = self.get_reactions(enz_degrad_rids, inv=False)
-        self.enz_transas, self.enz_transas_jac, self.enz_transas_hesss = self.get_reactions(enz_trans_rids, inv=False)
+        self.fmras, self.fmras_jac, self.fmras_hesss = self.get_reactions(self.mr_rids, inv=False)
+        self.fpstmas, self.fpstmas_jac, self.fpstmas_hesss = self.get_reactions(self.ps_rids, inv=True)
+        self.fdegradas, self.fdegradas_jac, self.fdegradas_hesss = self.get_reactions(enz_degrad_rids, inv=False)
+        self.fenz_tras, self.fenz_tras_jac, self.fenz_tras_hesss = self.get_reactions(enz_trans_rids, inv=False)
         self.n_constraints = {'heq_mass_balance': len(self.var_metab_sids),
                               'heq_enz_trans': self.subenz_x_trans.shape[0],
                               'heq_density': 1}
 
+    # TODO implement a factory method
+    @cache_last
+    def mras(self, x):
+        return self.fmras(x)
+
+    @cache_last
+    def mras_jac(self, x):
+        return self.fmras_jac(x)
+
+    @cache_last
+    def mras_hesss(self, x):
+        return self.fmras_hesss(x)
+
+    @cache_last
+    def pstmas(self, x):
+        return self.fpstmas(x)
+
+    @cache_last
+    def pstmas_jac(self, x):
+        return self.fpstmas_jac(x)
+
+    @cache_last
+    def pstmas_hesss(self, x):
+        return self.fpstmas_hesss(x)
+
+    @cache_last
+    def degradas(self, x):
+        return self.fdegradas(x)
+
+    @cache_last
+    def degradas_jac(self, x):
+        return self.fdegradas_jac(x)
+
+    @cache_last
+    def degradas_hesss(self, x):
+        return self.fdegradas_hesss(x)
+
+    @cache_last
+    def enz_tras(self, x):
+        return self.fenz_tras(x)
+
+    @cache_last
+    def enz_tras_jac(self, x):
+        return self.fenz_tras_jac(x)
+
+    @cache_last
+    def enz_tras_hesss(self, x):
+        return self.fenz_tras_hesss(x)
+
     def get_stoic_matrix(self, sids, rids):
         """retrieve stoichiometric sub-matrix [sids x rids].
 
@@ -640,7 +689,7 @@ class GbaProblem:
         :returns: Jacobian of mass balance equations at x
         :rtype: numpy.ndarray (1D) with shape (len(subenz_x_trans.shape[1]), 1)
         """
-        return self.subenz_x_trans.dot(self.enz_transas(x))
+        return self.subenz_x_trans.dot(self.enz_tras(x))
 
     @cache_last
     def heq_enz_trans_jac(self, x):
@@ -651,7 +700,7 @@ class GbaProblem:
         :returns: Jacobian of mass balance equations at x
         :rtype: numpy.ndarray (2D)
         """
-        return self.subenz_x_trans.dot(self.enz_transas_jac(x))
+        return self.subenz_x_trans.dot(self.enz_tras_jac(x))
 
     @cache_last
     def heq_enz_trans_hess(self, x):
@@ -662,7 +711,7 @@ class GbaProblem:
         :returns: Hessians of mass balance equations at x
         :rtype: numpy.ndarray (3D) with shape [n,x,x]
         """
-        return np.array([(row.reshape((-1, 1, 1)) * self.enz_transas_hesss(x)).sum(axis=0)
+        return np.array([(row.reshape((-1, 1, 1)) * self.enz_tras_hesss(x)).sum(axis=0)
                          for row in self.subenz_x_trans])
 
     @cache_last