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

# # FAQ

# This document will address frequently asked questions not addressed in other pages of the documentation.

# ## How do I install cobrapy?

# Please see the [INSTALL.rst](https://github.com/opencobra/cobrapy/blob/stable/INSTALL.rst) file.

# ## How do I cite cobrapy?

# Please cite the 2013 publication: [10.1186/1752-0509-7-74](http://dx.doi.org/doi:10.1186/1752-0509-7-74)

# ## How do I rename reactions or metabolites?

# TL;DR Use `Model.repair` afterwards
# 
# When renaming metabolites or reactions, there are issues because cobra indexes based off of ID's, which can cause errors. For example:

# In[1]:


from cobra.io import load_model
model = load_model("iYS1720")

for metabolite in model.metabolites:
    metabolite.id = f"test_{metabolite.id}"

try:
    model.metabolites.get_by_id(model.metabolites[0].id)
except KeyError as e:
    print(repr(e))


# The Model.repair function will rebuild the necessary indexes

# In[2]:


model.repair()
model.metabolites.get_by_id(model.metabolites[0].id)


# ## How do I delete a gene?

# That depends on what precisely you mean by delete a gene.
# 
# If you want to simulate the model with a gene knockout, use the `cobra.manipulation.knock_out_model_genes` function within a context. The effects of this function are reversed when exiting a context.

# In[3]:


model = load_model("iYS1720")
PGI = model.reactions.get_by_id("PGI")
print("bounds before knockout:", (PGI.lower_bound, PGI.upper_bound))
from cobra.manipulation import knock_out_model_genes
knock_out_model_genes(model, ["STM4221"])
print("bounds after knockouts", (PGI.lower_bound, PGI.upper_bound))


# If you want to actually remove all traces of a gene from a model, this is more difficult because this will require changing all the `gene_reaction_rule` strings for reactions involving the gene.

# ## How do I change the reversibility of a Reaction?

# `Reaction.reversibility` is a property in cobra which is computed when it is requested from the lower and upper bounds.

# In[4]:


model = load_model("iYS1720")
model.reactions.get_by_id("PGI").reversibility


# Trying to set it directly will result in an error or warning: 

# In[5]:


try:
    model.reactions.get_by_id("PGI").reversibility = False
except Exception as e:
    print(repr(e))


# The way to change the reversibility is to change the bounds to make the reaction irreversible.

# In[6]:


model.reactions.get_by_id("PGI").lower_bound = 10
model.reactions.get_by_id("PGI").reversibility


# ## How do I generate an LP file from a COBRA model?

# ### For optlang based solvers

# With optlang solvers, the LP formulation of a model is obtained by its string representation. All solvers behave the same way.

# In[7]:


with open('test.lp', 'w') as out:
    out.write(str(model.solver))


# ### How do I visualize my flux solutions?

# Please browse the [visualization packages](https://opencobra.github.io/cobrapy/tags/visualization/) on our website for the most recent list of tools.