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CDK Performance Measurements
As part of a larger project, I’ve been doing some profiling on various aspects of the CDK, focusing on core cheminformatics operations. I’m using the excellent YourKit profiler to do the tests. They...
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Faster Fingerprinting
In my last post I had reported some timing measurements for various operations. One of them was fingerprinting using the path-based hashing Fingerprinter class in the CDK. As reported, it took nearly 4...
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Faster Substructure Search in the CDK
The CDK uses the UniversalIsomorphismTester to perform graph and subgraph isomorphism. However it’s not very efficient and this shows when performing substructure searches over large collections. A...
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Multi-threaded Database Access with Python
Pub3D contains about 17.3 million 3D structures for PubChem compounds, stored in a Postgres database. One of the things we wanted to do was 3D similarity searching and to achieve that we’ve been...
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Java Port of VFLib Works and it’s Blazing
Sometime back I described how I was porting the VFLib algorithms to Java, so that we could use it for substructure search, since the current UniversalIsomorphismTester is pretty slow for this task, in...
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Brute Force – Inelegant, But Sometimes Useful
A few days back I posted on improving query times in Pub3D by going from a monolithic database (17M rows), to a partitioned version (~ 3M rows in 6 separate databases) and then performing queries in...
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The Speedups Keep on Coming
A while back I wrote about some updates I had made to the CDK fingerprinting code to improve performance. Recently Egon and Jonathan Alvarsson (Uppsala) had made even more improvements. Some of them...
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Quick Comments on an Analysis of Antithrombotics
Joerg has made a nice blog post on the use of Open Source software and data to analyse the occurence of antithrombotics. More specifically he was trying to answer the question Which XRay ligands are...
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