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Bioinformatics Programming

smitostr.py: Python script to convert SMILES to structures.

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smitostr.py: Python script to convert SMILES to structures.

As mentioned in some of our previous articles, RDKit provides a wide range of functions. In this article, we are using RDKit [1] to draw a molecular structure using SMILES.

Here, we provide a simple Python script for that. Write your SMILE string in front of the smi variable and save the file.

Availability

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

Usage

Run the script as shown below:

$ python3 smitostr.py


References

  1. RDKit: Open-source cheminformatics; http://www.rdkit.org

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

Bioinformatics Programming

vs_analysis_compound.py: Python script to search for binding affinities based on compound names.

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vs_analysis_compound.py: Python script to search for binding affinities based on compound names.

Previously, we have provided the vs_analysis.py script to analyze virtual screening (VS) results obtained from Autodock Vina. In this article, we have provided another script to search for binding affinity associated with a compound. (more…)

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Bioinformatics Programming

How to download files from an FTP server using Python?

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How to download files from an FTP server using Python?

In this article, we provide a simple Python script to download files from an FTP server using Python. (more…)

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Bioinformatics Programming

How to convert the PDB file to PSF format?

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How to convert the PDB file to PSF format?

VMD allows converting PDB to PSF format but sometimes it gives multiple errors. Therefore, in this article, we are going to convert PDB into PSF format using a different method. (more…)

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