This morning I was writing some Python code that needed to perform lookups on a very large map. 1234mapSize = 65000 amap = {} for i in range(0,mapSize): amap[’k%d’ % (i)] = i If a key did not exist in the map I needed to take some action. My initial effort performed a […]
Automating ChemDraw
I’ve been working on a project in which I needed to generate logP values using ChemDraw 12, for thousands of molecules. Since I didn’t have access to the ChemScript module, I needed a way to automate this procedure. After fiddling around with Visual Studio and various debuggers, I came across the Windows Application Testing Using […]
Molecules & MongoDB – Numbers and Thoughts
In my previous post I had mentioned that key/value or non-relational data stores could be useful in certain cheminformatics applications. I had started playing around with MongoDB and following Rich’s example, I thought I’d put it through its paces using data from PubChem. Installing MongoDB was pretty trivial. I downloaded the 64 bit version for […]
Frequency of a Term via PubMed
A little while back, Egon posted a question on FriendFeed, asking whether there was an easy way, preferably a service, to determine and plot the usage count of a term in PubMed by year. This is simple enough using the Entrez Utilities CGI. A quick Python script to do this (with minimal error checking) is […]
Preprocessing ONS Solubility Data
With the semester winding up and preparing to move to Rockville, things have been a bit hectic. However, I’ve been trying to keep track of the ONS solubility modeling project and one of the irritating things is that each time I want to build a model (due to new data being submitted), I need to […]