Bioinformatics Programming
How to search for a specific character in a file using Python?
In this article, a simple python script is provided that can be used to search for a specific character in a file.
If you have a file consisting of some information including name, address, email, post, and so on. You want to extract only email addresses present in that file, then use the following script/block of code. Here, this input file is named “employee_info.txt”.
#!/usr/bin/env python
value = ''
str = 'Email ID:'
file = open('employee_info.txt')
result = ''
for line in file:
if '@' in line: #looking for specific character
value = line.splitlines()
print ("Email ID:", value)
file.close()
Save this script with .py extension. Suppose, save it as ‘script.py’. Open a terminal on Ubuntu or command prompt on Windows and type:
$ python script.py
If you want to redirect the output to a file, then type:
$ python script.py > output.txt
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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.
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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
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…)
Bioinformatics Programming
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…)
In this article, we are providing a few commands that are used to commit changes to GitHub repositories using VS code terminal.
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A new Python package named ‘dssp_parser‘ is developed to parse DSSP files. This package fetches all helices including long and short ones from DSSP files. (more…)
Bioinformatics Programming
How to calculate center of mass of a protein structure using Python script?
Here is a Python script that helps you calculate the center of mass of a protein using the Pymol [1]. (more…)
Bioinformatics Programming
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