Below you will find pages that utilize the taxonomy term “open babel”
Blog
Generating 2D Images of Molecules from MOL Files using Open Babel
Open Babel is a tool to work with molecular data in any way from converting one type to another, analyzing, molecular modeling, etc. It also has a method to convert MOL files into SVG or PNG images to represent them as 2D images.
Install Open Babel in Linux as following or go to their page for different operating systems
1sudo apt-get install openbabel Open Babel uses the same command to generate SVG or PNG and recognizes the file format using the given filename to as the output option -O.
Blog
Obtaining Molecule Description using Open Babel / PyBel
Open Babel is a great tool to analyze and investigate molecular data (.MOL, .SDF files). Its Python API is particularly very nice if you are familiar with Python already. In this post, I’ll demonstrate how you can obtain molecule description such as molecular weight, HBA, HBD, logP, formula, number of chiral centers using PyBel.
Installation
1$ sudo apt-get install openbabel python-openbabel Usage for MW, HBA, HBD, logP
After reading .MOL file, we need to use calcdesc method with descnames argument for getting the descriptions.