Draw molecule with atom index in RDKit

I found interesting topics in rdkit discuss. How to draw molecule with atom index. Greg developer of RDKit answered tips to do it. It can use molAtomMapNumber. https://sourceforge.net/p/rdkit/mailman/message/31663468/ I didn’t know that! I tried that in my PC. RDKit can draw molecule easily using IPythonConsole. Test in a kinase inhibitor Draw molecule. https://github.com/iwatobipen/chemo_info/blob/master/rdkit_notebook/drawmol_with%2Bidx.ipynb

The reason of failures.

I have been working  at a pharmaceutical company as MedChem for over 10 years. The progress of science is remarkable, there are lots of technologies in these area. But Drug Discovery project is still challenging area I think. An article In nature reviews drug discovery analyzed the reason of failures in Phase II and III.

Use wolfram from python.

Wolfram alpha is a computational knowledge engine developed by Wolfram Research. It is an online service that answers factual queries directly by computing the answer from externally sourced “curated data”. You know, the service can be used from following URL. https://www.wolframalpha.com/ By the way, if there is API to use wolfram alpha from another applications,

Traveling Salesperson Problem

Some days ago, I wrote blog about knapsack problem. Next I tried to solve traveling salesperson problem(TSP). The problem is : “Given a list of cites and the distances between each pair of cities, what is the shortest possible route that visits each city exactly once and returns to the origin city ?”. It is

Knapshack problem

Drug discovery project is multi objective optimization process. It’s difficult to solve you know. There are many approaches to solve the problem and one is genetic algorithm. Recently, deap is active library of GA for python. I used deap for knapsack problem. You know…. the knapsack problem or rucksack problem is a problem in combinatorial

Call rdkit from Ruby

Recently I use web app made with ruby. The app is very useful for me, but there is not chemoinformatics library in ruby. So, I want to find way to use rdkit from ruby. I found some web page that described how to run shell script from ruby. The simplest way is using back quotation.