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https://github.com/brsynth/rxn_rebuild

Rebuild full reaction from reaction rule

https://github.com/brsynth/rxn_rebuild

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
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    DOI references
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    Academic publication links
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    Committers with academic emails
    1 of 1 committers (100.0%) from academic institutions
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    Institutional organization owner
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (10.9%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Rebuild full reaction from reaction rule

Basic Info
  • Host: GitHub
  • Owner: brsynth
  • License: mit
  • Language: Python
  • Default Branch: master
  • Size: 195 KB
Statistics
  • Stars: 2
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 14
Created over 5 years ago · Last pushed 12 months ago
Metadata Files
Readme Changelog License Authors

README.md

rxn_rebuild

Rebuild full reaction from reaction rule | Name | Downloads | Version | Platforms | | --- | --- | --- | --- | | Conda Recipe | Conda Downloads | Conda Version | Conda Platforms |

Description

rxn_rebuild provides a cache for RetroRules and MetaNetX compounds and reactions

rxn_rebuild

Anaconda-Server Badge Anaconda-Server Badge

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 (CMPDID1 + CMPDID2 = CMPDID3)
  • (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.

shell conda install -c conda-forge rxn_rebuild

Run

rxn_rebuild process

From CLI sh python -m rxn_rebuild <rxn_rule_id> <transfo> [<ori_rxn_id>] From Python code ```python from rxnrebuild import rebuildrxn, buildargsparser

parser = buildargsparser() args = parser.parse_args()

completedtransfos = rebuildrxn( rxnruleid=args.rxnruleid, transfo=args.transsmi, tmplrxnid=args.orirxnid ) `` Ifcacheis not provided, it ill be automatically loaded withinrebuildrxn` 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).

Owner

  • Name: BioRetroSynth
  • Login: brsynth
  • Kind: organization

Our group is interested in synthetic biology and systems metabolic engineering in whole-cell and cell-free systems.

GitHub Events

Total
  • Release event: 1
  • Push event: 8
  • Create event: 1
Last Year
  • Release event: 1
  • Push event: 8
  • Create event: 1

Committers

Last synced: about 3 years ago

All Time
  • Total Commits: 58
  • Total Committers: 1
  • Avg Commits per committer: 58.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
breakthewall j****n@u****r 58
Committer Domains (Top 20 + Academic)
univ-evry.fr: 1

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 2
  • Total dependent repositories: 2
  • Total versions: 3
conda-forge.org: rxn_rebuild
  • Versions: 3
  • Dependent Packages: 2
  • Dependent Repositories: 2
Rankings
Dependent packages count: 19.6%
Dependent repos count: 20.1%
Average: 42.7%
Stargazers count: 65.3%
Forks count: 65.9%
Last synced: 11 months ago

Dependencies

.github/workflows/check.yml actions
  • actions/checkout v2 composite
  • docker://continuumio/miniconda3 * composite
.github/workflows/tag.yml actions
  • actions/checkout v2 composite
  • actions/create-release v1 composite
  • actions/download-artifact v4 composite
  • actions/upload-artifact v4 composite
  • ad-m/github-push-action master composite
  • conda-incubator/setup-miniconda v2 composite
  • mathieudutour/github-tag-action v5.6 composite
  • ruby/setup-ruby v1 composite
.github/workflows/test.yml actions
  • actions/checkout v2 composite
  • conda-incubator/setup-miniconda v2 composite
environment.yaml pypi
setup.py pypi