Chemical Similarity Calculation Script

Overview

This script is designed to perform chemical similarity calculations between a set of molecular templates and a collection of compounds. It utilizes the Open Babel (obabel) tool for generating molecular fingerprints and computing the similarity between each template and compound pair. The results are stored in CSV format for further analysis.

Prerequisites

Before using this script, ensure you have the following prerequisites:

1. Open Babel (obabel) Tool: This script relies on the 'obabel' command-line tool to calculate chemical similarity. Make sure 'obabel' is installed and accessible from the command line.

2. Python: The script is written in Python and should be executed using a Python interpreter.

3. Input Data: Prepare a directory structure containing your molecular templates and compounds in SDF (Structure-Data File) format. The script reads SDF files from two specified directories: 'template/' for templates and 'cpds/' for compounds.

Configuration

At the beginning of the script, you can configure the following parameters:

• file_type: The file extension for your SDF files (e.g., '.sdf').

• similarity_threshold: The similarity threshold to consider two molecules as highly similar.

• fp_type: The fingerprint type to be used for similarity calculations. You can choose between 'MACCS' or 'fFP2' by commenting/uncommenting the lines accordingly.

Usage

1. Place the script in a directory where you have the 'template/' and 'cpds/' subdirectories containing your SDF files.

2. Run the script by executing it with Python. You can use the following command:

   python chemical_similarity.py

   This will initiate the similarity calculations between the templates and compounds.

3. The script generates two output files:

   • output<fp_type>.csv: A CSV file containing similarity values between templates and compounds.

   • outfile_<fp_type>.res: A text file listing combinations with high similarity.

Output

• The CSV output file (output<fp_type>.csv) contains rows and columns, with each cell representing the similarity score between a template and a compound.

• The text output file (outfile_<fp_type>.res) lists combinations where the similarity value is equal to or greater than the specified threshold.

Notes

• Ensure that the 'obabel' tool is installed and accessible from your command line. The script constructs and executes 'obabel' commands for each template-compound pair.

• If you choose to use 'fFP2' instead of 'MACCS', uncomment the corresponding line in the script.

• Please review and clean the output CSV file and text file for your specific analysis.

• If you encounter any issues or have questions, feel free to ask for assistance.

Enjoy using this script for your chemical similarity calculations!