Olivia and Tucker
He's gotten much larger since then, but here's a picture of Tucker and Olivia .
View ArticleCDK/ABCL Update
An update on using the Chemistry Development Kit (CDK) with ABCLLast year I explored using the CDK with ABCL. It was nice to see that ABCL could call out to the CDK and that I could use a Common Lisp...
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ABCL-CDK update part 2
An update on using the Chemistry Development Kit (CDK) with ABCL, Part 2Rendering Stereochemical MoleculesYou may recall that in my original blog post on using CDK with ABCL I had an example for...
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More fun with CDK and ABCL
ticagrelorThe drug ticagrelor (marketed as Brilinta by AstraZeneca) is an inhibitor of platelet activation and aggregation that has been shown to reduce the frequency of cardiovascular events in...
View ArticleCommon Lisp and Java
Tales of WoeSo... in an attempt to use preexisting wheels, rather than reinvent my own at every turn, I've been trying to get a decent Common Lisp environment working with the CDK (Chemistry...
View ArticleCDK Debugging
[Well, this is more computational chemistry than computational biology, but I didn't want this to show up on planet.lisp.org, so I'm using this category] If you want to turn on logging with CDK, the...
View Articlehunchentoot-cgi update
Well, it had been a while since hunchentoot-cgi had seen any attention. It turns out that the initial releases of hunchentoot-cgi had a pretty major limitation -- it didn't work at all with POST...
View ArticleABCL Error Handling
There's probably a better way to do this, but I have been having a difficult time trying to, from the lisp side of things, track down the cause of errors signaled from java code. It turns out that we...
View Articlewith-java-stack-trace
Following up on the java stack trace post, here's a little macro that can be used to wrap the lisp code that (eventually) triggers the java-side error: (defmacro with-java-stack-trace (&body body)...
View Articlewhoops
Elias Martenson kindly pointed out that I forgot a progn around ,@body: (defmacro with-java-stack-trace (&body body) `(handler-case (progn ,@body) (java:java-exception (e) (print (#"getMessage"...
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