Algorithms, data structures, and utilities for processing chemical information
Friday, 13 April 2018
RDKit Reaction SMARTS
There's a been some papers using the RDKit for synthesis planning. If you're writing a paper and use the term "Reaction SMARTS&...
Saturday, 6 May 2017
Sharp Tools for Java Refactoring: Byte Code Analysis
I'm currently refactoring parts of the CDK core classes. As part of this I often need to find specific patterns/idioms that need to be ...
Monday, 3 April 2017
CDK AtomContainers are Slow - Let's fix that
The core class for molecule representation in CDK is the AtomContainer . The AtomContainer uses an edge-list data structure for storing the...
Sunday, 10 July 2016
Generic Structure Depiction
Last week I attended the Seventh Joint Sheffield Conference on Chemoinformatics . It was a great meeting with some cool science and attende...
Saturday, 21 November 2015
Bringing Molfile Sgroups to the CDK - Rendering Tips
In the last but one post I gave a demonstration of S(ubstance)group rendering in the CDK. Now I want to give some implementation insights. ...
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