A common requirement when working with molecules is to display their molecular structure as an image. To do this in iPython Notebook requires some simple steps. Below is a way how you can do it. Enjoy! %matplotlib inline %pylab inline from IPython.display import Image from rdkit.Chem import AllChem as Chem from rdkit.Chem.Draw import IPythonConsole Example: … Continue reading Painting molecules using rdkit and iPython Notebook
Author: Joseph D'Emanuele
Introduction to Virtual Screening
Note: The following is a summary about virtual screening from Leach and Gillet [2007], chapter 8. Virtual screening is the computational analogue of biological screening. Its aim is to filter a set of molecules by scoring and ranking these structures using computational procedures to help researchers take decisions on the tasks being carried out, … Continue reading Introduction to Virtual Screening
Tanimoto Molecular Similarity Experiment
One way to rank and filter molecules from a larger set is to use similarity coefficients. One such way is by using Tanimoto. The experiment below runs similarity tests on a number of molecules using RDKit libraries (http://www.rdkit.org) and Python. Installing RDKit To install RDKit on Ubuntu 14.04 desktop OS, do: sudo apt-get install python-rdkit … Continue reading Tanimoto Molecular Similarity Experiment
R Simulation – Monty Hall Problem
Suppose you’re on a game show, and you’re given the choice of three doors: Behind one door is a car; behind the others, goats. You pick a door, say No. 1, and the host, who knows what’s behind the doors, opens another door, say No. 3, which has a goat. He then says to you, … Continue reading R Simulation – Monty Hall Problem
HDInsight – Provision a Hadoop Cluster on Azure
Creating a Hadoop cluster on Azure is easy, yet requires some steps. In this blog entry we provide a skeleton PowerShell script to get you started. Requirements To run this script, you need to have Azure PowerShell SDK installed on your machine. To check if it is already installed on your machine run the command: … Continue reading HDInsight – Provision a Hadoop Cluster on Azure