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

# Quick Start
# ======
# <img src="https://raw.githubusercontent.com/biosustain/cameo/gh-pages/cameo_logo.png" style="height:50px;text-align:left; margin-left: 0px;"/>
# 
# 
# cameo - **c**omputer **a**ssistend **m**etabolic **e**ngineering and **o**ptimization
# 
# 
# Step 1: Load a model
# -------------------
# 
# Loading a model is easy. From the cameo package you can import the *load_model* function.

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from cameo import load_model


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print(load_model.__doc__)


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model = load_model("iJO1366")


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model


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print(model.objective)


# Step 2: Optmize the mathematical problem (solve the model)
# ------------------------------------------------------
# 
# The current objective can be optmized by calling the *solve()* or *optimize()* methods.
# solve() will raise a ***SolveException*** when the problem is infeasible.
# 
# The sense of the problem (or direction) is described the objective itself.

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solution = model.solve()


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solution


# Step 3: The metabolic model
# --------------------------
# 
# The **SolverBasedModel** object allows to explore directly explore certain properties of the metabolic model:
# 
# * *reactions*: the reactions contained in the model (it supports tab-complete; with some minor limitations...)
# 

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model.reactions


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model.reactions.E4PD


# * *exchanges*: reactions that allow the exchange of metabolites between the environment and the model

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model.exchanges


# * *metabolites*: the metabolic species present in the model (also supports tab-complete)

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model.metabolites.get_by_id("12dgr140_p")


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model.metabolites.glc_dsh_D_c


# * *medium*: the current limites for exchange rates (other then 0 to 0)

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model.medium()


# * *genes*: the genes (if present) associated with the reactions in the model

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model.genes


# * *essential_reactions*: reactions that cannot be knocked-out using the current constraints to achieve current objective

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model.essential_reactions()


# * *essential_genes*: genes that cannot be knocked-out using the current constraints to achieve the current objective

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model.essential_genes()


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