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

# # Getting started with cameo 

# **cameo** reuses and extends model data structures defined by [cobrapy](https://opencobra.github.io/cobrapy/) (**CO**nstraints-**B**ased **R**econstruction and **A**nalysis tool for **Py**thon). So, in addition to following this quick start guide and other **cameo** tutorials, we encourage you to explore cobrapy's [documentation](https://cobrapy.readthedocs.org/en/latest/cobra.core.html) as well.

# Step 1: Load a model
# -------------------
# 
# Loading a model is easy. Just import the `~cameo.io.load_model` function.

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from cameo import load_model


# For example, load the most current genome-scale metabolic reconstruction of _Escherichia coli_.

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model = load_model("iJO1366")


# Models, reactions, metabolites, etc., provide return HTML when evaluated in Jupyter notebooks and can thus be easily inspected.

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model


# ## Step 2: Simulate a model
# 
# The model can be simulated by executing `~cameo.core.solver_based_model.SolverBasedModel.solve`.

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solution = model.solve()


# A quick overview of the solution can be obtained in form of a pandas [DataFrame](http://pandas.pydata.org/pandas-docs/stable/generated/pandas.DataFrame.html) (all solution objects in cameo provide access to data frames through a `data_frame` attribute).

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solution


# The data frame is accessible through `solution.data_frame`.

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solution.data_frame


# Data frames make it very easy to process results. For example, let's take a look at reactions with flux != 0

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solution.data_frame.query('fluxes != 0')


# ## Step 3: Exploring a model
# 
# Objects—models, reactions, metabolites, genes—can easily be explored in the Jupyter notebook, taking advantage of tab completion. For example, place your cursor after the period in `model.reactions.` and press the TAB key. A dialog will appear that allows you to navigate the list of reactions encoded in the model. 

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model.reactions.PGK # delete PGK, place your cursor after the period and press the TAB key.


# For example, you can access the E4PD (_Erythrose 4-phosphate dehydrogenase_) reaction in the model.

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model.reactions.E4PD


# Be aware though that due variable naming restrictions in Python dot notation access to reactions (and other objects) might not work in some cases.

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# model.reactions.12DGR120tipp  # uncommenting and running this cell will produce a syntax error


# In these cases you need to use the `model.reactions.get_by_id`.

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model.reactions.get_by_id('12DGR120tipp')


# Metabolites are accessible through `model.metabolites`. For example, D-glucose in the cytosolic compartment.

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model.metabolites.glc__D_c


# And it is easy to find the associated reactions

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model.metabolites.glc__D_c.reactions


# A list of the genes encoded in the model can be accessed via `model.genes`.

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model.genes[0:10]


# A few additional attributes have been added that are not available in a [cobrapy](https://opencobra.github.io/cobrapy/) model. For example, exchange reactions that allow certain metabolites to enter or leave the model can be accessed through `model.exchanges`.

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model.exchanges[0:10]


# Or, the current medium can be accessed through `model.medium`.

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model.medium


# It is also possible to get a list of essential reactions ...

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model.essential_reactions()[0:10]


# ... and essential genes.

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model.essential_genes()[0:10]