https://github.com/brsynth/chemlite
Library to define compounds, reactions, pathways
https://github.com/brsynth/chemlite
Last synced: 21 days ago
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Library to define compounds, reactions, pathways
- Host: GitHub
- URL: https://github.com/brsynth/chemlite
- Owner: brsynth
- License: mit
- Created: 2021-05-31T19:53:15.000Z (about 5 years ago)
- Default Branch: main
- Last Pushed: 2026-06-10T13:14:16.000Z (about 1 month ago)
- Last Synced: 2026-06-10T15:10:42.897Z (about 1 month ago)
- Language: Python
- Size: 502 KB
- Stars: 1
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
- Authors: AUTHORS.md
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README
# chemlite
Defines chemical compounds, reactions, pathways
| Name | Downloads | Version | Platforms |
| --- | --- | --- | --- |
| [](https://anaconda.org/conda-forge/chemlite) | [](https://anaconda.org/conda-forge/chemlite) | [](https://anaconda.org/conda-forge/chemlite) | [](https://anaconda.org/conda-forge/chemlite) |
## Description
*chemlite* provides classes to deal with chemical compounds, reactions and metabolic pathways.
## Install
### From Conda
```sh
[sudo] conda install -c conda-forge -c chemlite
```
## Use
### Compound
```python
from chemlite import Compound
c = Compound(id='test_cmpd')
```
The code above creates an empty compound. The following fields can be filled and accessed either at build time or later on:
- smiles
- inchi
- inchikey
- formula
- name
- infos
### Reaction
```python
from chemlite import Reaction
r = Reaction(id='test_rxn')
```
The code above creates an empty reaction. The following fields can be filled and accessed either at build time or later on:
- ec_numbers
- reactants
- products
- infos
The following methods are also available:
- `get_smiles()`
- `add_reactant()`
- `add_product()`
### Pathway
```python
from chemlite import Pathway
p = Pathway(id='test_path')
```
The code above creates an empty reaction. The following fields can be filled and accessed either at build time or later on:
- id
- species
- reactions
The following methods are also available:
- `add_compound()`
- `add_reaction()`
- `del_reaction()`
- `Pathway.net_reaction()`
## Tests
Please follow instructions below ti run tests:
```
cd tests
pytest -v
```
For further tests and development tools, a CI toolkit is provided in `ci` folder (see [ci/README.md](ci/README.md)).
## Authors
* **Joan Hérisson**
## Acknowledgments
* Thomas Duigou
## Licence
chemlite is released under the MIT licence. See the LICENCE file for details.