From 5ee09d7454e5e316b98e0536a1ddb3e8fbe08e09 Mon Sep 17 00:00:00 2001
From: Peter Schubert <Peter.Schubert@hhu.de>
Date: Sun, 12 Jun 2022 12:42:16 +0200
Subject: [PATCH] Cache last values of reaction rate related functions (v
0.3.2)
---
xbanalysis/_version.py | 2 +-
xbanalysis/problems/gba_problem.py | 63 ++++++++++++++++++++++++++----
2 files changed, 57 insertions(+), 8 deletions(-)
diff --git a/xbanalysis/_version.py b/xbanalysis/_version.py
index 88646c9..8c2bc5b 100644
--- a/xbanalysis/_version.py
+++ b/xbanalysis/_version.py
@@ -1,5 +1,5 @@
"""
Definition of version string.
"""
-__version__ = "0.3.1"
+__version__ = "0.3.2"
program_name = 'xbanalysis'
diff --git a/xbanalysis/problems/gba_problem.py b/xbanalysis/problems/gba_problem.py
index ee30540..0e5dba8 100644
--- a/xbanalysis/problems/gba_problem.py
+++ b/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
--
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