Efficient Bits
Algorithms, data structures, and utilities for processing chemical information
Monday, 3 April 2017
CDK AtomContainers are Slow - Let's fix that
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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
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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
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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. ...
Saturday, 17 October 2015
Java Serialization: Great power but at what cost?
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The default Java serialization framework provides a convenient mechanism for streaming in-memory Objects to another computer or storing them...
Tuesday, 8 September 2015
Bringing Molfile Sgroups to the CDK - Demo
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Despite the flaws , the molfile has been a defacto standard for chemical representation for several decades. The core format (atom and bond ...
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