https://github.com/andrewtarzia/enzyme_screen

Molecular size calculations for enzyme reaction screening in metal--organic frameworks
https://github.com/andrewtarzia/enzyme_screen

enzymes mofs molecular-size screening

Last synced: 9 months ago
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Molecular size calculations for enzyme reaction screening in metal--organic frameworks

• Host: GitHub
• URL: https://github.com/andrewtarzia/enzyme_screen
• Owner: andrewtarzia
• License: mit
• Created: 2020-09-08T15:25:24.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2021-02-10T22:15:04.000Z (over 5 years ago)
• Last Synced: 2025-07-26T11:41:26.176Z (11 months ago)
• Topics: enzymes, mofs, molecular-size, screening
• Language: Jupyter Notebook
• Homepage:
• Size: 10.5 MB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

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README

          
# enzyme_screen

Scripts and functions for extracting and analysing biochemical reactions.

Author: Andrew Tarzia

Email: andrew.tarzia@gmail.com or atarzia@ic.ac.uk

This work was produced in the final year of my PhD at the University of Adelaide under the supervision of A/Prof David Huang and Prof Christian Doonan.

Previously at: https://bitbucket.org/andrewtarzia/psp_source/src/master/

A Jupyter notebook that runs through the molecular size calculation from a SMILES string is available:

[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/andrewtarzia/enzyme_screen/master?filepath=examples%2Fcalculate_molecular_size.ipynb)

The molecular size calculation code is also available in a refactored form at my GitHub and through PyPi: https://github.com/andrewtarzia/mol-ellipsize

## Installation

* Tested on Ubuntu 18.04 using conda and pip

* Install Anaconda in standard way (Python 3.7.3)

* Packages required outside of what comes with conda

 * RDKit:

   * `conda install -c conda-forge rdkit`

   * Version: 2019.09.2.0

 * chemcost:

   * Python code written by Steven Bennett for the extraction of purchasability from the ZINC15 database.

   * Follow instructions found here: https://github.com/stevenbennett96/chemcost

   * Only required for `molecule_population.py`

## Workflow

### Collecting database from KEGG

* Download br08201 JSON file from [the KEGG library](https://www.genome.jp/kegg-bin/get_htext?query=08201&htext=br08902.keg)

 * Used version as of May12_2020 of br08201: Enyzmatic reactions

* Run `util/split_KEGG.py` in working directory to produce:

    * `_ECtop.json`: A dictionary of all reactions for all ECs

    * `_EClist.txt`: A list of all ECs to iterating through

* Update `data/param_file.txt` with location of these files.

### Parameter testing

* All parameter screens in the supporting information of DOI: **awaiting** are run in `param_screening.py`

    * `data/test_molecules.txt` contains the required molecular information

    * Within `param_screening.py` are the range of parameters to test, the originals being set in `data/param_file.txt`

### Reaction collection and analysis

* `RS_collection.py`

    * Iterates through provided EC and reaction files to collect reaction systems

    * Also collects unique molecules to molecule database

    * Currently only implements API for KEGG

    * To be run in directory with reactions

* `molecule_population.py`

    * Trivial parallelisation done using `utils/molecule_splitter.py`

    * Takes _unopt.mol file of all collected molecules:

        * Optimises them using ETKDG -> _opt.mol

        * Calculates their properties -> _prop.json

        * Calculates the molecule size of N conformers -> _size.csv

    * To be run in directory with molecules

    * Produces some plots of chemical space

* `chemical_space_plot.py`

    * Iterates through all collected molecules and plots various chemical space plots

    * To be run in directory with molecules

* `RS_analysis.py`

    * `molecule_population.py` must be run before this point!

        * Unanalysed molecules result in skipped reactions

    * Populates the properties of each reaction system based on the properties of constituent molecules (in molecule database)

    * To be run in directory with reactions

    * Outputs all properties to `rs_properties.csv`

* `screening.py`

    * Produces the plots and screening of all reaction systems seen in DOI: **awaiting**

    * Multiple cases are defined within the script to look at specific EC numbers or system types

        * case = production for plots in DOI:

    * To be run in directory with reactions

## Examples

* `biomin_screening.py`

    * A script used to produce Figure **XX** in DOI:

    * Analyses a list of molecules that have been tested for enzyme@ZIF-8 reactions

* `examples/calculate_molecular_size.ipynb`

    * Jupyter notebook that runs a user through calculating the size of any molecule

* `examples/screen_new_reactions.ipynb`

    * Jupyter notebook that runs through the screening process exemplified in the paper search for new reactions

* `visualise_ellipsoid_steps.py`

    * Allows the user to visualise the step-wise calculation of the min. vol. enclosing ellipsoid

* `visualise_reaction_system.py`

    * Allows the user to print properties of a reaction system