Merge pull request #1 from SamiralVdB/documentation

Documentation

README.md

@@ -24,7 +24,7 @@ We have extended this package with the following features:
 Note that the package has been tested with the [Gurobi](https://www.mathworks.com/products/connections/product_detail/gurobi-optimizer.html) solver.
 
 ## What can you find where in this repository?
-This repository contains not only the source code, but also examples and scripts which were used in [publication](linktopublication).
+This repository contains not only the source code, but also examples and scripts which were used in **INSERT PUBLICATION HERE**.
 - **Data**
   - *eGFP_expression_Bienick2014*: measured growth rate and eGFP expression by [Bienick et al. (2014)](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0109105)
   - *proteinAllocationModel_iML1515_EnzymaticData_py*: information about the proteinsectors of the PAM for *Escherichia coli* (*E.coli*)

docs/.gitignore

@@ -0,0 +1,23 @@
+# Dependencies
+/node_modules
+
+# Production
+/build
+
+# Generated files
+.docusaurus
+.cache-loader
+
+# Misc
+.DS_Store
+.env.local
+.env.development.local
+.env.test.local
+.env.production.local
+
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+
+# Python venv for temporary build of pydoc-markdown
+.venv

docs/README.md

@@ -0,0 +1,49 @@
+# Website
+
+This website is built using [Docusaurus](https://docusaurus.io/), a modern static website generator.
+You will need NodeJS to be able to run Docusaurus for development.
+
+### Installation
+To use Docusaurus, install NodeJS. You will find a comprehensive guide [here](https://nodejs.org/en/download/package-manager#debian-and-ubuntu-based-linux-distributions) for linux systems.
+
+```
+$ npm install
+```
+
+### Local Development
+
+```
+$ npm run start
+```
+
+This command starts a local development server and opens up a browser window. Most changes are reflected live without having to restart the server.
+
+### Build
+
+```
+$ npm run build
+```
+
+This command generates static content into the `build` directory and can be served using any static contents hosting service.
+
+### Deployment
+
+Using SSH:
+
+```
+$ USE_SSH=true npm run deploy
+```
+
+Not using SSH:
+
+```
+$ GIT_USER=<Your GitHub username> npm run deploy
+```
+
+If you are using GitHub pages for hosting, this command is a convenient way to build the website and push to the `gh-pages` branch.
+
+# Documenting your code
+
+## Setup
+
+This installation makes use of the Python module "pydoc-markdown". If you want to use it, install this module and execute it in the base directory of this repo. The provided pydoc-markdown.yml file contains all necessary configurations needed. It will generate the API reference from the docstrings in the PAModelpy package. Please note, that you have to use Google docstring format if you want to make changes to the PAModelpy project.

docs/babel.config.js

@@ -0,0 +1,3 @@
+module.exports = {
+  presets: [require.resolve('@docusaurus/core/lib/babel/preset')],
+};

docs/default.nix

@@ -0,0 +1,45 @@
+with import <nixpkgs> { };
+
+let
+  venvDir = "./.venv";
+  pythonPackages = pkgs.python310Packages;
+in pkgs.mkShell rec {
+  name = "impurePythonEnv";
+  buildInputs = [
+    pythonPackages.python
+    pythonPackages.virtualenv
+    pythonPackages.numpy
+    pkgs.zlib
+    pkgs.expat
+    nodejs_20
+  ];
+
+  # This is very close to how venvShellHook is implemented, but
+  # adapted to use 'virtualenv'
+  shellHook = ''
+    SOURCE_DATE_EPOCH=$(date +%s)
+
+    if [ -d "${venvDir}" ]; then
+      echo "Skipping venv creation, '${venvDir}' already exists"
+    else
+      echo "Creating new venv environment in path: '${venvDir}'"
+      ${pythonPackages.python.interpreter} -m venv "${venvDir}"
+    fi
+
+    source "${venvDir}/bin/activate"
+
+    pip install -r requirements.txt
+
+    LD_LIBRARY_PATH="${pkgs.lib.makeLibraryPath buildInputs}:$LD_LIBRARY_PATH"
+    LD_LIBRARY_PATH="${pkgs.stdenv.cc.cc.lib.outPath}/lib:$LD_LIBRARY_PATH"
+
+    # Add the expat library path to LD_LIBRARY_PATH
+    LD_LIBRARY_PATH=${pkgs.expat}/lib:$LD_LIBRARY_PATH
+
+    # fixes libstdc++ issues and libgl.so issues
+    LD_LIBRARY_PATH=${pkgs.stdenv.cc.cc.lib}/lib/:/run/opengl-driver/lib/:$LD_LIBRARY_PATH
+    # fixes xcb issues :
+    QT_PLUGIN_PATH=${pkgs.qt5.qtbase}/${pkgs.qt5.qtbase.qtPluginPrefix}
+    PATH="$PWD/node_modules/.bin/:$PATH"
+  '';
+}

docs/docs/api_reference/CatalyticEvent.md

@@ -0,0 +1,183 @@
+---
+sidebar_label: CatalyticEvent
+title: CatalyticEvent
+---
+
+CatalyticEvent object which relates Reaction variables to the EnzymeVariable and Enzyme objects.
+It contains multiple functions which enable easy mapping and handling of one Event of catalysis
+(e.g. one conversion of substrate to product, can be catalyzed by multiple enzymes)
+
+## CatalyticEvent Objects
+
+```python
+class CatalyticEvent(Object)
+```
+
+CatalyticEvent is a class for holding information regarding the catalysis of a Reaction in a cobra.Model object.
+It serves as an interface between the metabolic reaction and the associated enzyme constraints and variables.
+
+**Notes**:
+
+  There are three different scenarios:
+  - Enzyme complex: multiple enzymes together are associated with an EnzymeComplex object
+  - Isozymes: multiple enzymes independently associated with a single catalytic event
+  - Other: a single enzyme is associated with a single catalytic event
+
+
+**Arguments**:
+
+- `kcats2enzymes` _dict_ - A dictionary with enzyme, kcat key, value pairs to connect the enzyme with the associated reaction.
+  The kcat is another dictionary with 'f' and 'b' for the forward and backward reactions, respectively.
+- `id` _str, optional_ - The identifier to associate with this catalytic event (default None).
+- `rxn_id` _str, optional_ - The reaction with which this catalytic event is associated.
+- `name` _str, optional_ - A human-readable name for the reaction (default "").
+
+#### kcat\_values
+
+```python
+@property
+def kcat_values()
+```
+
+returns a dictionary with kcat values and enzymes
+
+#### flux
+
+```python
+@property
+def flux() -> float
+```
+
+Get the flux value in the most recent solution.
+
+Flux is the primal value of the corresponding variable in the model.
+
+**Returns**:
+
+- `flux` _float_ - Flux is the primal value of the corresponding variable in the model.
+
+
+**Warnings**:
+
+  * Accessing reaction fluxes through a `Solution` object is the safer,
+  preferred, and only guaranteed to be correct way. You can see how to
+  do so easily in the examples.
+  * Reaction flux is retrieved from the currently defined
+  `self._model.solver`. The solver status is checked but there are no
+  guarantees that the current solver state is the one you are looking
+  for.
+  * If you modify the underlying model after an optimization, you will
+  retrieve the old optimization values.
+
+
+**Raises**:
+
+- `RuntimeError` - If the underlying model was never optimized beforehand or the
+  reaction is not part of a model.
+- `OptimizationError` - If the solver status is anything other than `optimal`.
+- `AssertionError` - If the flux value is not within the bounds.
+
+
+**Examples**:
+
+    ```
+    >>> from cobra.io import load_model
+    >>> model = load_model("textbook")
+    >>> solution = model.optimize()
+    >>> model.variables.PFK.flux
+    7.477381962160283
+    >>> solution.fluxes.PFK
+    7.4773819621602833
+    ```
+
+#### concentration
+
+```python
+@property
+def concentration() -> float
+```
+
+Get the enzyme concentration value of the most recent solution.
+The enzyme concentration equals the flux value.
+
+**Returns**:
+
+- `float` - Enzyme concentration in [mmol/gDW].
+
+#### add\_enzymes
+
+```python
+def add_enzymes(enzyme_kcat_dict: dict)
+```
+
+Add enzymes to the catalytic event and create bindings to the related model.
+The enzymes in the enzyme_kcat_dict are individual isozymes. Enzyme complexes
+should be added as an EnzymeComplex object with a single kcat value.
+
+**Arguments**:
+
+- `enzyme_kcat_dict` - Dict
+  A nested dictionary with enzyme, kcat key, value pairs to connect the
+  enzyme with the associated reaction. The kcat is another dictionary with `f` and `b`
+  for the forward and backward reactions respectively.
+
+#### remove\_enzymes
+
+```python
+def remove_enzymes(enzyme_list: list)
+```
+
+Remove enzymes from the catalytic event and remove the catalytic event from the
+constraint expressions related to the enzyme.
+
+**Arguments**:
+
+- `enzyme_list` - List[Union[str, PAModelpy.Package.Enzyme]]
+  A list with PAModelpy.Package.Enzyme objects to be removed. If a list of identifiers (str)
+  is provided, the corresponding enzyme will be obtained from the CatalyticEvent.enzymes attribute.
+
+#### change\_kcat\_values
+
+```python
+def change_kcat_values(enzyme_kcat_dict: dict)
+```
+
+Change kcat values for the enzyme variable.
+
+**Arguments**:
+
+- `enzyme_kcat_dict` - Dict[str, Dict[str, float]]
+  A nested dictionary with enzyme identifiers as keys and kcat dictionaries as values.
+  The kcat dictionary should have `f` and `b` keys for the forward and backward reactions, respectively.
+
+#### \_\_copy\_\_
+
+```python
+def __copy__() -> "CatalyticEvent"
+```
+
+Copy the CatalyticEvent.
+
+**Returns**:
+
+  CatalyticEvent:
+  A new CatalyticEvent that is a copy of the original CatalyticEvent.
+
+#### \_\_deepcopy\_\_
+
+```python
+def __deepcopy__(memo: dict) -> "CatalyticEvent"
+```
+
+Copy the CatalyticEvent with memo.
+
+**Arguments**:
+
+- `memo` _dict_ - Automatically passed parameter.
+
+
+**Returns**:
+
+  CatalyticEvent:
+  A new CatalyticEvent that is a copy of the original CatalyticEvent with memo.
+

docs/docs/api_reference/Constraints.md

@@ -0,0 +1,21 @@
+---
+sidebar_label: Constraints
+title: Constraints
+---
+
+## Constraint Objects
+
+```python
+class Constraint(Metabolite)
+```
+
+Class for information about a Constraint in a protein Sector.
+
+Constraint is a class for holding information similar to
+a metabolite in a cobra.Reaction object.
+
+**Arguments**:
+
+- `id` _str_ - The identifier to associate with the constraint.
+- `name` _str_ - A human-readable name.
+