Bioinformatics Programming
tanimoto_similarities_one_vs_all.py – Python script to calculate Tanimoto Similarities of multiple compounds
We previously provided a Python script to calculate the Tanimoto similarities of multiple compounds against each other. In this article, we are providing another Python script to calculate the Tanimoto similarities of one compound with multiple compounds.
The script tanimoto_similarities_one_vs_all.py is a part of our tanimoto_similarities Python package. The similarities are calculated using RDKit [1]. This script takes multiple compounds as input in the form of sdf format. All the compounds in sdf format are merged together in a single file (here, lig.sdf). The query compound is provided in the form of SMILES.
Availability
The script is available on GitHub under the package ‘tanimoto_similarities‘.
Usage
keep the input sdf file in the same directory or provide a full path to the file in the script. Run the script as shown below:
$ python3 tanimoto_similarities_one_vs_all.py
It will create a new file named ‘sims_vs_all.txt’. This file will contain all calculated similarities.
Note: If you still get an error stating “rdkit not found”, then perhaps you have not activated the rdkit environment. Run the conda activate my-rdkit-env command again and then run the script.
References
- Landrum, G. (2013). Rdkit documentation. Release, 1 (1-79), 4.
Further Reading
Fetching SMILE strings for a given number of SDF files of chemical compounds is not such a trivial task. We can quickly obtain them using RDKit or OpenBabel. But what if you don’t have SDF files of ligands in the first place? All you have is Ligand IDs from PDB. If they are a few then you can think of downloading SDF files manually but still, it seems time-consuming, especially when you have multiple compounds to work with. Therefore, we provide a Python script that will read all Ligand IDs and fetch their SDF files, and will finally convert them into SMILE strings. (more…)
Bioinformatics Programming
How to get secondary structure of multiple PDB files using DSSP in Python?
In this article, we will obtain the secondary structure of multiple PDB files present in a directory using DSSP [1]. You need to have DSSP installed on your system. (more…)
Bioinformatics Programming
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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