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Chemistry Development Kit
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The Open Source Cheminformatics and Bioinformatics Toolkit
The Open Source Cheminformatics and Bioinformatics Toolkit

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Some things are unpredictable. For example, the impact of PaDEL by Chun Wei Yap. While seemingly just providing a simple API around CDK's descriptor and fingerprint functionality, it's impact is significant. Higher than, for example, that of Bioclipse and AMBIT which also provide GUIs around that functionality.

Web-of-Science lists 71 citations of this work, while Google Scholar guestimates it at around 120. Well done!

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More information on the ECFP/FCFP implementation...

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You can also read an SDfile more efficiently by repeated calls to MDLV2000Reader. The pattern is similar to BufferedReader.readLine() in a while loop.  

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Changes in CDK 1.6 #3: Constructors that now require a builder
The advantage of the builders in the CDK  is that code can be independent of data class implementations (and we have three of them in CDK 1.6, at this moment). Over the past years more and more code started using the approach, but that does involve that mor...

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Paper where +Ola Spjuth, +Arvid Berg, Sam Adams, and me where we outline of the InChI is integrated into the CDK and used in the +Bioclipse.

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Metabolomics paper by +Steffen Neumann and others where +Rajarshi Guha's rcdk package is used to calculate tanimoto similarities.

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