Efficient Bits
Algorithms, data structures, and utilities for processing chemical information
Thursday, 25 October 2018
CDK Depict on HTTPS
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Just a quick post to say CDK Depict is now using HTTPS https://simolecule.com/cdkdepict/depict.html . The main reason for this was Blogger s...
Monday, 22 October 2018
Bit packing for fast atom type assignment
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Many cheminformatics algorithms perform some form of atom typing as their first step. The atom types you need and the granularity depend on ...
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Friday, 13 April 2018
RDKit Reaction SMARTS
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Update 19/09/22 I believe I was wrong and Daylight did allow SMIRKS to be run backwards and that the "direction" parameter control...
Saturday, 6 May 2017
Sharp Tools for Java Refactoring: Byte Code Analysis
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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
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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...
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