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 general. While I had translated the Ullman algorithm implementation of VFLib and shown that it outperformed the CDK method, it turned out […]
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 employing the Ballester and Graham-Richards method. In this post I’m going to talk about performance – how we went from a single […]
Conformational Envelopes
Joe Leonard posted a question on the CCL mailing list today regarding “conformation envelopes”. More specifically, he asked Has there been work on creating visualizations of “conformer envelopes”, graphical representations of the conformational space occupied (or available) to molecules. Particularly when such visualizations are used to (quickly/visually) compare whether 2 molecules can adopt the same […]
Live ONS Solubility Queries
In a previous post, I described a simple web form to query and visualize the solubility data being generated as part of the ONS Challenge. The previous approach required me to manually download the data and load it into a Postgres database. While trivial from a coding point of view, it’s a pain since I […]
Solubility Queries and the Google Visualization API
There was a FriendFeed dicussion on the use of RDF triples for representing the solubilty data generated by Jean-Claude and others as part of the ONS Solubility Challenge. Part of the discussion revolved around letting RDF novices easily perform queries of the data being collected. Not knowing much about RDF, I took the raw data […]