srijitseal / dili_predictor Goto Github PK

Python 97.29% Dockerfile 2.20% Shell 0.51%

dili_predictor's Introduction

DILIPredictor Online tools and Website - Drug-Induced Liver Injury Prediction

Overview

DILI is a comprehensive repository aimed at enhancing the early detection of Drug-Induced Liver Injury (DILI) through the integration of predicted in vivo and in vitro data. This project utilizes advanced machine learning models and chemical informatics to predict the likelihood of DILI for various compounds. For code see: https://github.com/srijitseal/DILI

Using PyPI

You can install the DILI Predictor using pip: pip install dilipred. Please use Python <3.12, >=3.9

Building from Source

You can also build from source using python-poetry:

Clone the repository: git clone https://github.com/Manas02/dili-pip.git
Navigate to the project directory: cd dili-pip/
Install dependencies: poetry install
Activate the virtual environment: poetry shell
Build the project: poetry build

Usage

Running DILIPredictor as CLI

To get started with the CLI, use: dili -h

Predicting DILI for a Single Molecule

Select from the sidebar to predict DILI for a single molecule.

Running DILIPredictor as Library

Here's a basic example of how to use DILIPredictor as a Python library:

from dilipred import DILIPRedictor

if __name__ == '__main__':
    dp = DILIPRedictor()
    smiles = "CCCCCCCO"
    result = dp.predict(smiles)
    print(result)

Using local implementation

Download key files from https://github.com/srijitseal/DILI/raw/main/local_implementation.zip and run locally!

Run Online on Server #1 v4.0.0 [Recommended]

If you prefer to use the predictor online via Uppsala University SciLifeLab Serve: https://dili.serve.scilifelab.se/

Run Online on Server #2 v4.0.0

If you prefer to use the predictor online via streamlit: https://dilipredictor.streamlit.app/

Citation

If you use DILI Predictor in your work, please cite:

Improved Early Detection of Drug-Induced Liver Injury by Integrating Predicted in vivo and in vitro Data; Srijit Seal, Dominic P. Williams, Layla Hosseini-Gerami, Manas Mahale, Anne E. Carpenter, Ola Spjuth, Andreas Bender bioRxiv 2024.01.10.575128; doi: https://doi.org/10.1101/2024.01.10.575128

License

This project is licensed under the MIT License. See the LICENSE file for details.

Acknowledgements

Developed and maintained by Srijit Seal and contributors.

Contact

For any questions or issues, please open an issue on the GitHub repository.

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hamzaimran08

dili_predictor's Issues

Missing Model File in Local Implementation?

Hi, thanks for this incredible work!

I installed the software quite easily using pip, and was able to run dilipred -h without any issues. However, when I try to run predictions from the CLI using a smiles string, I get an error asking for bestlivmodel_2_model.sav which does not appear to be one of the ones included in the model files that were made available for download? Or I may just not be looking in the right place. Any help would be greatly appreciated!

Thanks,

Kiran

Error installing

Hi,

I get this error when I try installing

Installing build dependencies ... done
Getting requirements to build wheel ... error
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [33 lines of output]
Traceback (most recent call last):
File "/Users/chrisswain/miniconda3/envs/DILIpredition/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in
main()
File "/Users/chrisswain/miniconda3/envs/DILIpredition/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/chrisswain/miniconda3/envs/DILIpredition/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 112, in get_requires_for_build_wheel
backend = _build_backend()
^^^^^^^^^^^^^^^^
File "/Users/chrisswain/miniconda3/envs/DILIpredition/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 77, in _build_backend
obj = import_module(mod_path)
^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/chrisswain/miniconda3/envs/DILIpredition/lib/python3.12/importlib/init.py", line 90, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "", line 1387, in _gcd_import
File "", line 1360, in _find_and_load
File "", line 1310, in _find_and_load_unlocked
File "", line 488, in _call_with_frames_removed
File "", line 1387, in _gcd_import
File "", line 1360, in _find_and_load
File "", line 1331, in _find_and_load_unlocked
File "", line 935, in _load_unlocked
File "", line 995, in exec_module
File "", line 488, in _call_with_frames_removed
File "/private/var/folders/4h/_8pw3vdd7hvbzj3p87symg0r0000gn/T/pip-build-env-k7u_ho1o/overlay/lib/python3.12/site-packages/setuptools/init.py", line 16, in
import setuptools.version
File "/private/var/folders/4h/_8pw3vdd7hvbzj3p87symg0r0000gn/T/pip-build-env-k7u_ho1o/overlay/lib/python3.12/site-packages/setuptools/version.py", line 1, in
import pkg_resources
File "/private/var/folders/4h/_8pw3vdd7hvbzj3p87symg0r0000gn/T/pip-build-env-k7u_ho1o/overlay/lib/python3.12/site-packages/pkg_resources/init.py", line 2172, in
register_finder(pkgutil.ImpImporter, find_on_path)
^^^^^^^^^^^^^^^^^^^
AttributeError: module 'pkgutil' has no attribute 'ImpImporter'. Did you mean: 'zipimporter'?
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.