https://github.com/brendaferrari/autopadelpy
AutoPaDELPy provides an automated user interface for PaDELPy software. It was created to provide a more friendly interaction with the software for the final user.
Science Score: 10.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: zenodo.org -
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○Scientific vocabulary similarity
Low similarity (13.7%) to scientific vocabulary
Keywords
Repository
AutoPaDELPy provides an automated user interface for PaDELPy software. It was created to provide a more friendly interaction with the software for the final user.
Basic Info
Statistics
- Stars: 4
- Watchers: 1
- Forks: 1
- Open Issues: 3
- Releases: 0
Topics
Metadata Files
README.md
❗❗❗ AutoPaDELPy is running through a bugfix process ❗❗❗
AutoPaDELPy: An automating tool for PaDELPy software
AutoPaDELPy provides an automated user interface for PaDELPy software. It was created to provide a more friendly interaction with the software for the final user.
Libraries and softwares used
PaDELPy - PaDELPy provides a Python wrapper for the PaDEL-Descriptor molecular descriptor calculation software. It was created to allow direct access to the PaDEL-Descriptor command-line interface via Python.
pandas - a Python package that provides fast, flexible, and expressive data structures designed to make working with "relational" or "labeled" data both easy and intuitive.
Instalation
PaDELPy:
pip install padelpy
pandas:
pip install pandas
How to use
- Download the code and unzip it on the desirable directory
To run use the following command:
python descriptor-preparation.py resources/molecules.smi
molecules.smi is the input, you may change to use for your own datasets.
Your dataset need to have the format 'smiles,molecule_id'
First you are going to choose the fingeprint descriptor. You can choose more than one but just one at time.
- Then, you are going to choose the bidimensional descriptor. You can also choose more than one but just one at time.
- Finally, you are going to choose the tridimensional descriptor. You can also choose more than one but just one at time.
- Now, the software is going to wrap up the information. You can access it at the output_files folder.
Obervations:
This software was written as an automating tool for PaDELPy, as allowed by the MIT license for PaDELPy. Please refer to them at PaDELPy
Some of the codes used to build the functions in this software was adapted from Data Professor PaDELPy tutorial. If you want to learn more about the software please refer to PaDELPy tutorial
Authorship
- Author: Brenda Ferrari (brendaferrari)
- Review: Lucas Bertoncello (lbertoncello)
Social preview original photo by Brenda Ferrari (brendaferrari)
Owner
- Name: Brenda Ferrari
- Login: brendaferrari
- Kind: user
- Repositories: 6
- Profile: https://github.com/brendaferrari
Chemistry PhD student - Python and Machine Learning student