Skip to main content

A cheminformatics package to perform Applicability Domain of molecular fingerprints based in similarity calculation.

Project description

DOI

pyADA

pyADA (Python Applicability Domain Analyzer) is a cheminformatics package to perform Applicability Domain of molecular fingerprints based in similarity calculation. In this case, the calculation of the Applicability Domain consists of a scan of similarities of the structures present in the test set in relation to the training set, the best similarity threshold is the one with the lowest error and also the lowest number of molecules with similarity below the threshold. A notebook file with an example of using this package is present in the directory 'example/example_of_use.ipynb'

Dependencies

  • numpy
  • pandas
  • tqdm
  • scikit-learn
  • Tested in python3.6 and python3.8

Install

Via pip

pip3 install pyADAqsar

Via github

git clone https://github.com/jeffrichardchemistry/pyADA
cd pyADA
python3 setup.py install

How to use

This package has three classes: Smetrics (perform some statistical parameters like Q2ext R2ext etc), Similarity (realize similarity calculations based in differents metrics ) and ApplicabilityDomain (run a scan of AD with differents thresholds). The line code bellow import all classes.

from pyADA import Smetrics, Similarity, ApplicabilityDomain

A file containing a jupyter-notebook with a few examples of use is in 'example' folder. For more information about documentation run the help function of classes.

help(Smetrics)
help(Similarity)
help(ApplicabilityDomain)

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

pyADAqsar-1.1.1.tar.gz (23.3 kB view hashes)

Uploaded Source

Built Distribution

pyADAqsar-1.1.1-py3-none-any.whl (22.5 kB view hashes)

Uploaded Python 3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page