#!/usr/bin/env python
# coding: utf-8

# # Using the COBRA toolbox with cobrapy
# 
# This example demonstrates using COBRA toolbox commands in MATLAB from python through [pymatbridge](http://arokem.github.io/python-matlab-bridge/).

# In[1]:


get_ipython().run_line_magic('load_ext', 'pymatbridge')


# In[2]:


import cobra.test
m = cobra.test.create_test_model("textbook")


# The model_to_pymatbridge function will send the model to the workspace with the given variable name.

# In[3]:


from cobra.io.mat import model_to_pymatbridge
model_to_pymatbridge(m, variable_name="model")


# Now in the MATLAB workspace, the variable name 'model' holds a COBRA toolbox struct encoding the model.

# In[4]:


get_ipython().run_cell_magic('matlab', '', 'model\n')


# First, we have to initialize the COBRA toolbox in MATLAB.

# In[5]:


get_ipython().run_cell_magic('matlab', '--silent', "warning('off'); % this works around a pymatbridge bug\naddpath(genpath('~/cobratoolbox/'));\ninitCobraToolbox();\n")


# Commands from the COBRA toolbox can now be run on the model

# In[6]:


get_ipython().run_cell_magic('matlab', '', 'optimizeCbModel(model)\n')


# FBA in the COBRA toolbox should give the same result as cobrapy (but maybe just a little bit slower :))

# In[7]:


get_ipython().run_line_magic('time', '')
m.optimize().f