https://github.com/the-metabolic-disassembler/metadisassembler
https://github.com/the-metabolic-disassembler/metadisassembler
bioinformatics cheminformatics chemoinformatics pip python3 rdkit
Last synced: about 2 months ago
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- Host: GitHub
- URL: https://github.com/the-metabolic-disassembler/metadisassembler
- Owner: the-metabolic-disassembler
- License: mit
- Created: 2019-01-31T01:56:07.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2019-12-30T06:34:46.000Z (over 6 years ago)
- Last Synced: 2025-08-24T09:34:27.142Z (10 months ago)
- Topics: bioinformatics, cheminformatics, chemoinformatics, pip, python3, rdkit
- Language: Jupyter Notebook
- Size: 3.08 MB
- Stars: 3
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# The Metabolic Disassembler
The Metabolic Disassembler is a Python package to automatically predict a combination of biosynthetic units in a natural product. This software would help to reveal the starting materials of the target natural product.
## Installation
Install The Metabolic Disassembler with `pip`.
```bash
$ pip install metadisassembler
```
## Requirements
- Python (3.6)
- [RDKit](https://www.rdkit.org) (version 2019.09.2.0)
- [NetworkX](https://networkx.github.io/documentation/stable/) (version 2.2)
- [CairoSVG](https://cairosvg.org) (version 2.4.2)
- [Pillow (PIL)](https://pillow.readthedocs.io/en/stable/) (version 6.2.1)
- [Pandas](https://pandas.pydata.org) (version 0.25.3)
- [Matplotlib](https://matplotlib.org) (version 3.1.2)
## Command Line Usage
```bash
% metadisassembler -h
usage: metadisassembler [-h] [-t TIME] [--hide] [-c] query
positional arguments:
query MDL_Molfile, SMILES, InChI, KEGG_COMPOUND_ID,
KNApSAcK_COMPOUND_ID
optional arguments:
-h, --help show this help message and exit
-t TIME, --time TIME set a time limit [s] [default: 300]
--hide hide stereochemistry [default: False]
-c, --color output color allocation information [default: False]
```
## Basic Usage
A usage example by Jupyter Notebook can be seen [here](https://github.com/the-metabolic-disassembler/metadisassembler/blob/master/jupyter_usecase/basic_usage.ipynb).
## Google Colab
You can try the process from installation to the basic usage in Google Colab. [](https://colab.research.google.com/github/the-metabolic-disassembler/metadisassembler/blob/master/jupyter_usecase/basic_usage_in_colab.ipynb)
## Citation
Amano K, Matsumoto T, Tanaka K, Funatsu K, Kotera M. Metabolic disassembler for understanding and predicting the biosynthetic units of natural products. *BMC Bioinformatics* **20**, 728 (2019) [doi:10.1186/s12859-019-3183-9](https://doi.org/10.1186/s12859-019-3183-9)