Efficient Bits
Algorithms, data structures, and utilities for processing chemical information
Saturday, 11 January 2014
New SMILES behaviour - generating (CDK 1.5.4)
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In the previous post I outline the changes to SMILES Parsing in the Chemistry Development Kit (CDK) . The original plan was to have severa...
Wednesday, 18 December 2013
New SMILES behaviour - parsing (CDK 1.5.4)
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It's been a while since the last CDK development release (over 4 months). The CDK 1.5.4 will be released in the next few days and has a...
Monday, 11 November 2013
Improved Substructure Matching
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Since it was written the UniversalIsomorphismTester (UIT) has been the goto class in the Chemistry Development Kit (CDK) to check structu...
Friday, 25 October 2013
All The Small Things
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The SMILES Arbitrary Target Specification (SMARTS) is a succinct way of expressing and matching structural attributes of molecules. SMARTS...
Thursday, 19 September 2013
SMILES Implicit Valence of Aromatic Atoms
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The last couple of months I've been reworking the Chemistry Development Kit (CDK) handling of Simplified molecular-input line-entry sy...
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