PhaKinPro

PHArmacoKINetic PROperty calculator: Used to predict varies pharmacokinetic properties using QSAR models. If you use please cite our paper. There is a webserver that runs these models, but for large numbers of compounds, running locally using this code is much more effective

Requierments

Install the requirments from the requirements.txt file. Additionally, if you want to run the webserver, you need to install flask and qunicorn

Command line use

After downloading, PhaKinPro/phakinpro.py can be called from the command line with python pharkinpro --help

--infile is required and is the fileloc for a csv of SMILES to predict properties for. Requires that csv has header and is comma seperated --smiles_col is the name of the column containing the SMILES strings of interest. Defaults to "SMILES" --outfile is the fileloc of where the output csv file should go. Defaults to current-working-directory/phakin_output.csv --ad flag to turn on applicability domain calculation for the models

Webserver interface

This repository also contains the code to run a local webserver (or host your own). You can start the server by running qunicorn wsqi:app (or using the devolpment flask server by setting the FLASK_APP variable: $env:FLASK_APP = "main" on windows or export FLASK_ENV=main on unix). From that access 127.0.0.1:5000 to view the local server

Thanks to JSME for a free and easy to use molecule editor for webpages Bienfait, B., Ertl, P. JSME: a free molecule editor in JavaScript. J Cheminform 5, 24 (2013). https://doi.org/10.1186/1758-2946-5-24