https://github.com/brsynth/rxn_rebuild

Rebuild full reaction from reaction rule
https://github.com/brsynth/rxn_rebuild

Last synced: 2 months ago
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Rebuild full reaction from reaction rule

• Host: GitHub
• URL: https://github.com/brsynth/rxn_rebuild
• Owner: brsynth
• License: mit
• Created: 2021-04-08T12:46:46.000Z (about 5 years ago)
• Default Branch: master
• Last Pushed: 2026-02-26T11:25:01.000Z (4 months ago)
• Last Synced: 2026-02-26T17:49:55.887Z (4 months ago)
• Language: Python
• Size: 270 KB
• Stars: 2
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE
  • Authors: AUTHORS.md

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README

          
# rxn_rebuild

Rebuild full reaction from reaction rule

| Name | Downloads | Version | Platforms |

| --- | --- | --- | --- |

| [![Conda Recipe](https://img.shields.io/badge/recipe-rxn_rebuild-green.svg)](https://anaconda.org/conda-forge/rxn_rebuild) | [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/rxn_rebuild.svg)](https://anaconda.org/conda-forge/rxn_rebuild) | [![Conda Version](https://img.shields.io/conda/vn/conda-forge/rxn_rebuild.svg)](https://anaconda.org/conda-forge/rxn_rebuild) | [![Conda Platforms](https://img.shields.io/conda/pn/conda-forge/rxn_rebuild.svg)](https://anaconda.org/conda-forge/rxn_rebuild) |

## Description

*rxn_rebuild* provides a cache for RetroRules and MetaNetX compounds and reactions

# rxn_rebuild

[![Anaconda-Server Badge](https://anaconda.org/brsynth/rxn_rebuild/badges/latest_release_date.svg)](https://anaconda.org/brsynth/rxn_rebuild) [![Anaconda-Server Badge](https://anaconda.org/brsynth/rxn_rebuild/badges/version.svg)](https://anaconda.org/brsynth/rxn_rebuild)

Rebuild full reaction from a reaction rule ID and a chemical transformation by adding co-factors removed when the rule has been generated. The algorithm proceeds to the following:

- seeks for the reaction(s) rule(s) of the given reaction rule ID, in the cache

- for each reaction rule

    - seeks for the template reaction of the given reaction rule ID, in the cache

    - find compounds to add by doing the difference between the template reaction and the reaction rule

  

## Input

- reaction rule ID

- chemical transfomation as SMILES (xxx.xxx>>xxx.xxx) or IDs (CMPD_ID_1 + CMPD_ID_2 = CMPD_ID_3)

- (Optional) template reaction ID

## Output

- Prints out the full completed transformation

- Returns a dictionary with the following keys:

  - 'full_transfo': completed transformation (SMILES or IDs)

  - 'added_cmpds': sub-dictionary of compounds to add to the transformation with:

    - keys: IDs

    - values: infos (SMILES, InChI, InChIKey, formula, name)

## Install

The conda package manager is required. Fresh instructions on how to install conda are [available online](https://docs.conda.io/projects/conda/en/latest/user-guide/install/).

```shell

conda install -c conda-forge rxn_rebuild 

```

## Run

### rxn_rebuild process

**From CLI**

```sh

python -m rxn_rebuild   []

```

**From Python code**

```python

from rxn_rebuild import rebuild_rxn, build_args_parser

parser = build_args_parser()

args   = parser.parse_args()

completed_transfos = rebuild_rxn(

    rxn_rule_id=args.rxn_rule_id,

    transfo=args.trans_smi,

    tmpl_rxn_id=args.ori_rxn_id

)

```

If `cache` is not provided, it ill be automatically loaded within `rebuild_rxn` function but it could be much slower if called inside a loop.

## Tests

Test can be run with the following commands:

### Natively

```bash

cd tests

pytest -v

```

# CI/CD

For further tests and development tools, a CI toolkit is provided in `ci` folder (see [ci/README.md](ci/README.md)).