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.
The script is available on GitHub under the package ‘cheminformatics‘.
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
How to create a pie chart using Python?
How to make swarm boxplot?
With the new year, we are going to start with a very simple yet complicated topic (for beginners) in bioinformatics. In this tutorial, we provide a simple code to plot swarm boxplot using matplotlib and seaborn. (more…)
How to obtain ligand structures in PDB format from PDB ligand IDs?
How to obtain SMILES of ligands using PDB ligand IDs?
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…)
How to get secondary structure of multiple PDB files using DSSP in Python?
vs_analysis_compound.py: Python script to search for binding affinities based on compound names.
How to download files from an FTP server using Python?
How to convert the PDB file to PSF format?
smitostr.py: Python script to convert SMILES to structures.
How to preprocess data for clustering in MATLAB?
Data preprocessing is a foremost and essential step in clustering based on machine learning methods. It removes noise and provides better results. In this article, we are going to discuss the steps involved in data preprocessing using MATLAB . (more…)
How to calculate drug-likeness using RDKit?
RDKit  allows performing multiple functions on chemical compounds. One is the quantitative estimation of drug-likeness also known as QED properties. These properties include molecular weight (MW), octanol-water partition coefficient (ALOGP), number of hydrogen bond donors (HBD), number of hydrogen bond acceptors (HBA), polar surface area (PSA), number of rotatable bonds (ROTB), number of aromatic rings (AROM), structural alerts (ALERTS). (more…)
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. (more…)
tanimoto_similarities.py: A Python script to calculate Tanimoto similarities of multiple compounds using RDKit.
RDKit  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…)
How to commit changes to GitHub repository using vs code?
Extracting first and last residue from helix file in DSSP format.
How to extract x,y,z coordinates of atoms from PDB file?
The x, y, and z coordinates of atoms are provided in the PDB file. One way to extract them is by using the Biopython package . In this article, we will extract coordinates of C-alpha atoms for each residue from the PDB file using Biopython. (more…)
dssp_parser: A new Python package to extract helices from DSSP files.
How to calculate center of mass of a protein structure using Python script?
How to sort binding affinities based on a cutoff using vs_analysis.py script?
Previously, we have provided a Python script (vs_analysis.py) to analyze the virtual screening (VS) results of Autodock Vina. Now, we have updated this script to sort binding affinities based on user inputted cutoff value. (more…)
sminalog_analysis.py – A new Python script to fetch top binding affinities from SMINA log file
In one of our previous posts, we provided a Python script for the virtual screening analysis of Autodock Vina. This script analyzes all log files obtained from the docking of multiple ligands to a receptor and provides the binding affinities for top poses from each file. In this article, we are publishing a new Python script for the virtual screening analysis of SMINA . (more…)