Troldmand v1.2.1 (Danish QSAR Batch Bot)

Author: Tom Burns (github.com/tomdburns)

Date : September 12th, 2023

Troldmand is a bot written in python to automate a batch mode for the Danish QSAR models:

https://qsarmodels.food.dtu.dk/runmodel/index.html

Running the code

To run the code, add the SMILES you wish to run to a .txt file

To run (python):

python troldmand.py -i \path\to\your\smiles\file.txt -o \path\to\output\file.csv

You can see the list of options by typing:

python troldmand.py --help

To run (exe)

.\troldmand.exe -i \path\to\your\smiles\file.txt -o \path\to\output\file.csv

You can see the list of options by typing:

.\troldmand.exe --help

Alternate Use:

troldmand will default to running the SMILES.txt in the code's directory when no input file is specified. The user can simply change the SMILES in this SMILES.txt file and double click the exe to run the code without needing the command line.

Models Available

There are several models this code is compatible with run via the Danish QSAR Website:

• ER alpha binding, all (human in vitro)
• ER alpha binding, balanced (human in vitro)
• ER alpha activation (human in vitro)
• ER Activation (in vitro, CERAPP data)
• AR inhibition (human in vitro)
• AR binding (in vitro, CoMPARA data)
• AR activation (in vitro, CoMPARA data)
• AR inhibition (in vitro, CoMPARA data)
• Thyroperoxidase (TPO) inhibition QSAR1 (in vitro)
• Thyroperoxidase (TPO) inhibition QSAR2 (in vitro)
• Sodium/iodide symporter (NIS), higher sensitivity
• Sodium/iodide symporter (NIS), higher specificity

To select the models being run, change the models specified in models.ini

Python dependencies (When running Python version)

The following python modules are needed to run this code:

• numpy
• pandas
• selenium

To install python module use pip. example:

pip install numpy

Contact Information

If you have any questions, contact Tom Burns: github.com/tomdburns