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Bioinformatics Programming

sdftosmi.py: Convert multiple ligands/compounds in SDF format to SMILES?

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sdftosmi.py: Convert multiple ligands/compounds in SDF format to SMILES?

You can obtain SMILES of multiple compounds or ligands in an SDF file in one go. Here, we provide a simple Python script to do that.

Let’s say, we have a file in SDF format consisting of molecular structures called ‘ligands.sdf’. In order to perform some other operations, you can convert SDF to SMILES. It will not only make it easier to process but also reduce the size of the file, especially when you are dealing with millions of compounds.

Availability

The script is available on GitHub under the package ‘tanimoto_similarities‘.

Usage

The Python script named sdftosmi.py will take the input (SDF file) filename as an argument and will provide output in the ‘smiles.txt‘ file. This file will contain SMILE corresponding to each compound in the SDF file. Therefore, you may have several duplicates because a SMILE can represent different molecules.

Run the script as shown below:

$ python3 sdftosmi.py ligands.sdf


 

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

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tanimoto_similarities_one_vs_all.py – Python script to calculate Tanimoto Similarities of multiple compounds

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tanimoto_similarities_one_vs_all.py – Python script to calculate Tanimoto Similarities of a compound with multiple compounds

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tanimoto_similarities.py: A Python script to calculate Tanimoto similarities of multiple compounds using RDKit.

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tanimoto_similarities.py: A Python script to calculate Tanimoto similarities of multiple compounds using RDKit.

RDKit [1] is a very nice cheminformatics software. It allows us to perform a wide range of operations on chemical compounds/ ligands. We have provided a Python script to perform fingerprinting using Tanimoto similarity on multiple compounds using RDKit. (more…)

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