This script automates the generation of tautomers from a CSV file containing SMILES and MoleculeID columns. It utilises the open-source Java library "ambit-tautomers-2.0.0-SNAPSHOT" for tautomer generation.
Before running this code, ensure you have the following dependencies installed:
- Java Development Kit (JDK): Ensure you have Java installed on your system.
- ambit-tautomers-2.0.0-SNAPSHOT.jar: Download the JAR file from the provided link.
- Pandas
- RDKit
- Place your input CSV file containing SMILES and MoleculeID. Ensure the CSV file follows the specified format.
- Download the ambit-tautomers-2.0.0-SNAPSHOT.jar from the provided link (https://sourceforge.net/projects/ambit/files/Ambit2/AMBIT%20applications/tautomers/ambit-tautomers-2.0.0-SNAPSHOT.jar) and ensure you have Java installed on your system.
- CSV and JAR files location: Ensure both the input CSV file and the ambit-tautomers-2.0.0-SNAPSHOT.jar file are in the same folder as the python script file.
- Input csv file name: Specify the input csv file name in the script.
- Tautomers Option: Choose between generating 'all' tautomers or selecting the 'best' tautomer for each molecule based on your requirements.
- Tautomers for each molecule in the input CSV file. The tautomers will be saved in the same directory as the input CSV file, as separate SDF files.
- Additionally, a CSV file named tautomers_output.csv will be generated, summarising the tautomers.