rxn_rebuild

Rebuild full reaction from reaction rule

Name	Downloads	Version	Platforms

Description

rxn_rebuild provides a cache for RetroRules and MetaNetX compounds and reactions

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.

conda install -c conda-forge rxn_rebuild 

Run

rxn_rebuild process

From CLI

python -m rxn_rebuild <rxn_rule_id> <transfo> [<ori_rxn_id>]

From Python code

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

cd tests
pytest -v

CI/CD

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