17 Mar 09 Does the CDK Fingeprint works? Something went wrong.

 

In my last post, I doubted the accuracy of fingerprint based substructure search and pointed out sometimes fingerprint loosed hits. In fact, something went wrong in my code. As I was reading from SDF directly, while IteratingMDLReader does not percieve atom type or detect aromaticity automatically. This cause the incorrect matchings of UniversalIsomorphismTester, sorry for the incorrect post. I’ve run the test again, using the SMILES provided by Guha as input. The groovy script is also attached here.

#	Query	Subgraph Isomorphism	Entended CDK	Missing	Extra
1		20	24	0	4
2		7	103	0	96
3		69	100	0	31
4		6	10	0	4
5		31	41	0	10
6		23	23	0	0
7		7	75	0	68

Well, CDK fingerprint is OK.

Tags: CDK, Chemoinformatics, Fingerprint

Filed in Chemoinformatics, Uncategorized

Reader's Comments

1. Does the CDK Fingerprints Work? Substructure search » ChemHack | 17 Mar 2009 00:12

   [...] The test code used in this post has fatal error, which caused the test result to be completely correct. Please see details here. [...]

2. Egon Willighagen | 17 Mar 2009 03:31

   Phew… happy to hear you found the problem.

3. Dmitry Pavlov | 05 Nov 2009 06:25

   Hello Duan,

   My name is Dmitry Pavlov. I work for SciTouch LLC.
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   called Indigo. It consists of five software products:

   Bingo: Cartridge for Oracle database supporting a wide range of searches in molecule and reaction databases.
   Dingo: Molecule and reaction rendering library with a C# wrapper and a command-line utility.
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   Deco: R-Group deconvolution and scaffold detection library and a command-line utility.
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   From your
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4. nuTleDete | 28 May 2012 19:11

   Who and where to condense this summer on furlough, slice your information.