ChemicBook

How to show atom numbers in a RdKit molecule (or how to label atoms in a rdkit molecule)

In RdKit, the method SetProp is used to set an atomic property for the atoms involved in the molecule. This method takes two arguments: the peroperty to set and its value. The idea is simple: Create an rdkit mol object from SMILES string, iterate over the atoms, and set the desired property to a custom value.

Introduction to different datasets available in Computational Chemistry

Introduction

The advances in Machine Learning field have proven useful ranging from applications in Natural Language Processing to Computer Vision. These remarkably successful demonstrations have drawn high interests from the physical and biological science communities.

Mol2 file format explained for beginners (Cheminformatics Part 2)

Welcome to the second blog in the Cheminformatics for Beginners series. In the last blog, we saw a quick introduction to the SMILES notation. This post will introduce you to the mol2 format in cheminformatics.

Introduction

One major setback from the SMILES notation was that it could not provide the positions of each atom in space, typically with X, Y, and Z cartesian coordinates. Mol2 file solves this problem. It is a plain text tabular format that represents a single or multiple chemical compounds and holds atomic coordinates, chemical bond information, and metadata of a molecule.

SMILES strings explained for beginners (Cheminformatics Part 1)

Welcome to the first article in the Cheminformatics for Beginners series. This blog will introduce you to the SMILES string notation in cheminformatics.

Introduction

SMILES (Simplified molecular-input line-entry system) is a line notation method to represent molecules as well as reactions. It is one of the most common method to represent molecules because of its simplicity and readability to the human eye.