smilesfeaturizer 0.1.3

A Python package that automatically generates derived variables from a column with SMILES (Simplified Molecular-Input Line-Entry System).

Development Status :: 3 - Alpha

SMILES featurizer

A Python package that automatically generates derived feature variables from a column with SMILES (Simplified Molecular-Input Line-Entry System)

The python package, SMILES Featurizer helps quickly and painlessly explore the baseline and key features for many projects that use SMILES strings. It's still in the development phase, and there are some errors with certain SMILES strings due to dependencies in the package. There are no scheduled regular updates, and I welcome pull requests at any time. I intentionally did not encapsulate it highly as a class, and I maintain it in the form of functions. This is because it is based on the processing of a single data frame and because the service is highly likely to be modified.

Install

$ pip install smilesfeaturizer

$ pip install git+https://github.com/dsdanielpark/SMILES-featurizer.git

Usage

The dataset assumes the presence of SMILES strings in a column named SMILES. See tutorial notebook.

Feature generation

• Create fingerprint columns for SMILES representations based on various packages RDKit, Mol2Vec, DataMol, MolFeat, Scikit-Learn.

  from smilesfeaturizer import generate_smiles_feature
  
  df = generate_smiles_feature(df) # default method="simple"
  
  df = generate_smiles_feature(df, method="specific") 
  

Create dashboard

• Through the dashboard, you can determine which compounds exhibit what prediction performance.

  from smilesfeaturizer import create_inline_dash_dashboard
  
  # Load your DataFrame and specify the columns
  true_col = 'pIC50'
  predicted_col = 'predicted_pIC50'
  
  # Create and run the Dash dashboard
  create_inline_dash_dashboard(df, true_col, predicted_col)
  

Save reporting images

• Molecular images, basic information, and the prediction versus actual values are visually represented in bar graphs for easy viewing.

  from smilesfeaturizer import smiles_insight_plot
  
  selected_metric = 'RMSE'  # Choose the error metric you want to display
  true_col = 'pIC50'  # Replace with your true column name
  predicted_col = 'predicted_pIC50'  # Replace with your predicted column name
  smiles_insight_plot(df[:1], true_col, predicted_col, selected_metric, 'output_folder', show=True)
  

License

Apache 2.0

Bugs and Issues

Sincerely grateful for any reports on new features or bugs. Your valuable feedback on the code is highly appreciated.

Contacts

• Core maintainer: Daniel Park, South Korea
  
• E-mail: [e-mail]
  

Copyright (c) 2023 MinWoo Park, South Korea