https://github.com/brsynth/rpreactor
A command-line and python package to handle biochemical reaction rules.
https://github.com/brsynth/rpreactor
biochemical-reactions reaction-rules retrorules
Last synced: 5 months ago
JSON representation
A command-line and python package to handle biochemical reaction rules.
- Host: GitHub
- URL: https://github.com/brsynth/rpreactor
- Owner: brsynth
- License: mit
- Created: 2020-07-22T15:34:07.000Z (almost 6 years ago)
- Default Branch: stable
- Last Pushed: 2021-05-18T08:56:20.000Z (about 5 years ago)
- Last Synced: 2025-09-09T20:14:18.030Z (9 months ago)
- Topics: biochemical-reactions, reaction-rules, retrorules
- Language: Python
- Homepage:
- Size: 308 KB
- Stars: 5
- Watchers: 1
- Forks: 0
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://anaconda.org/brsynth/rpreactor)
[](https://anaconda.org/brsynth/rpreactor)
# rpreactor
**A command-line and python package to handle biochemical reaction rules.**
*rpreactor* is designed to use reaction rules from [RetroRules](https://retrorules.org/),
and to be at the core of more complex bioretrosynthesis tools such as [RetroPathRL](https://github.com/brsynth/RetroPathRL).
It relies extensively on [RDKit](https://rdkit.org/) to handle chemicals and reactions.
Please submit your questions or any new issue you may encounter with *rpreactor* using [GitHub's issue system](https://github.com/brsynth/RetroPathRL/issues).
If you are interested in *rpreactor* you may also be interested in:
* [Reactor](https://chemaxon.com/products/reactor): ChemAxon's "*A high performance virtual synthesis engine*"
* [ATLAS](https://lcsb-databases.epfl.ch/pathways/atlas/): "*A repository of all possible biochemical reactions for synthetic biology and metabolic engineering studies*" by our friends from the [LCSB](https://www.epfl.ch/labs/lcsb/)
* [MINE](https://github.com/tyo-nu/MINE-Database): "*Metabolic In silico Network Expansion (MINE) Database Construction and DB Logic*" by our friends from the [Tyo Lab](https://tyolab.northwestern.edu/)
## Installation
**Important**: rpreactor works with Python >=3.6 and was tested with rdkit 2020.03*.
We strongly recommend you to use [conda package manager](https://docs.conda.io/en/latest/), and to follow those steps:
```bash
# installation in a new conda environment
conda create --name -c conda-forge -c brsynth rdkit=2020.03 rpreactor
conda activate
```
```bash
# installation in an already existing environment
conda activate
conda install -c conda-forge -c brsynth rdkit=2020.03 rpreactor
```
## Usage
From command line:
```bash
conda activate
python -m rpreactor.cli --help
python -m rpreactor.cli --with_hs true inline --inchi "InChI=1/C3H6O3/c1-2(4)3(5)6/h2,4H,1H3,(H,5,6)" --rsmarts "([#8&v2:1](-[#6&v4:2](-[#6&v4:3](-[#8&v2:4]-[#1&v1:5])=[#8&v2:6])(-[#6&v4:7](-[#1&v1:8])(-[#1&v1:9])-[#1&v1:10])-[#1&v1:11])-[#1&v1:12])>>([#15&v5](=[#8&v2])(-[#8&v2]-[#1&v1])(-[#8&v2]-[#1&v1])-[#8&v2:1]-[#6&v4:2](-[#6&v4:3](-[#8&v2:4]-[#1&v1:5])=[#8&v2:6])(-[#6&v4:7](-[#1&v1:8])(-[#1&v1:9])-[#1&v1:10])-[#1&v1:11].[#7&v3](=[#6&v4]1:[#7&v3]:[#6&v4](-[#8&v2]-[#1&v1]):[#6&v4]2:[#7&v3]:[#6&v4](-[#1&v1]):[#7&v3](-[#6&v4]3(-[#1&v1])-[#8&v2]-[#6&v4](-[#6&v4](-[#8&v2]-[#15&v5](=[#8&v2])(-[#8&v2]-[#1&v1])-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1:12])(=[#8&v2])-[#8&v2]-[#1&v1])(-[#1&v1])-[#1&v1])(-[#1&v1])-[#6&v4](-[#8&v2]-[#1&v1])(-[#1&v1])-[#6&v4]-3(-[#8&v2]-[#1&v1])-[#1&v1]):[#6&v4]:2:[#7&v3]:1-[#1&v1])-[#1&v1])"
```
From within a script:
```python
import json
import rpreactor
inchi = 'InChI=1/C3H6O3/c1-2(4)3(5)6/h2,4H,1H3,(H,5,6)'
rsmarts = '([#8&v2:1](-[#6&v4:2](-[#6&v4:3](-[#8&v2:4]-[#1&v1:5])=[#8&v2:6])(-[#6&v4:7](-[#1&v1:8])(-[#1&v1:9])-[#1&v1:10])-[#1&v1:11])-[#1&v1:12])>>([#15&v5](=[#8&v2])(-[#8&v2]-[#1&v1])(-[#8&v2]-[#1&v1])-[#8&v2:1]-[#6&v4:2](-[#6&v4:3](-[#8&v2:4]-[#1&v1:5])=[#8&v2:6])(-[#6&v4:7](-[#1&v1:8])(-[#1&v1:9])-[#1&v1:10])-[#1&v1:11].[#7&v3](=[#6&v4]1:[#7&v3]:[#6&v4](-[#8&v2]-[#1&v1]):[#6&v4]2:[#7&v3]:[#6&v4](-[#1&v1]):[#7&v3](-[#6&v4]3(-[#1&v1])-[#8&v2]-[#6&v4](-[#6&v4](-[#8&v2]-[#15&v5](=[#8&v2])(-[#8&v2]-[#1&v1])-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1:12])(=[#8&v2])-[#8&v2]-[#1&v1])(-[#1&v1])-[#1&v1])(-[#1&v1])-[#6&v4](-[#8&v2]-[#1&v1])(-[#1&v1])-[#6&v4]-3(-[#8&v2]-[#1&v1])-[#1&v1]):[#6&v4]:2:[#7&v3]:1-[#1&v1])-[#1&v1])'
o = rpreactor.RuleBurner(rsmarts_list=[rsmarts], inchi_list=[inchi], with_hs=True)
o.compute()
res = json.loads('[' + ', '.join(o._json) + ']')
```
## For developers
### Development installation
After a git clone:
```bash
cd
conda env create -f environment.yml -n
conda activate
conda develop -n .
```
Warning: if you do not specify an environment name with `-n `,
then 'dev_rpreactor' will be used.
Test your installation with:
```bash
conda activate
python -m rpreactor.cli -h
```
To uninstall:
```bash
conda deactivate
conda env remove -n
```
### Test suite
```bash
cd
python -m pytest --doctest-modules
```
### Build the documentation
To build a local Sphinx HTML documentation at `/docs/_build/html/index.html`:
```
cd /docs
make html
```
### Build and deployment
The process is automated with GitHub's Action.
If you want to check the build process locally:
```bash
CONDA_BLD_PATH=/conda-bld
mkdir -p ${CONDA_BLD_PATH}
cd
conda env create -f recipe/conda_build_env.yaml -n
conda activate
conda build -c conda-forge --output-folder ${CONDA_BLD_PATH} recipe
conda convert --platform osx-64 --platform linux-64 --platform win-64 --output-dir ${CONDA_BLD_PATH} ${CONDA_BLD_PATH}/*/rpreactor-*
```