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6:33:53
frgo
I just woke up. And I still have problems building my extensions. The scraper is behaving differently than two weeks ago. I don't know why yet.
6:44:48
frgo
Found the problem. 6 hours of sleep abd a fresh look onto the problem and voilĂ - solved.
7:16:00
drmeister
That is a generated molecule superimposed and then forced into the "pose" of a similar molecule in the active site of thrombin.
7:18:04
drmeister
This is for a "free energy perturbation calculation". It involves building molecules that are similar to each other but differ in two different groups that chemists can modify.
7:19:03
drmeister
The built molecules need to be positioned in the active site of the protein in the same pose as a "template" molecule that was mixed with the protein and the complex structure solved using X-ray crystallography.
7:19:38
drmeister
The trick here is to programatically build different candidate molecules and superimpose them on the template molecule and force them into a similar "pose".
7:25:03
drmeister
This is neat as well - all of the candidate molecules in the correct pose - but arrayed on a grid.
10:41:08
frgo
::notify drmeister Thanks again for fixing the clbind thing. Most of it works now. I have one case where I am running into a road block - I will ask you again later on that.
14:05:52
Colleen
drmeister: frgo said 3 hours, 24 minutes ago: Thanks again for fixing the clbind thing. Most of it works now. I have one case where I am running into a road block - I will ask you again later on that.
14:07:33
scymtym
beach: i'm experimenting with using CST:RECONSTRUCT in ECLECTOR.CONCRETE-SYNTAX-TREE:CST-READ to improve precision for e.g. reader macros. it seems to work ok so far. does that sound like a good idea to you?
15:02:31
beach
I had lunch guests today, so I spent all morning cooking, and all afternoon washing dishes and discussing with my guests.
15:47:21
drmeister
https://github.com/quicklisp/quicklisp-client/blob/master/dists/quicklisp/software/trivia-20170725-git/level2/impl.lisp#L370
15:47:51
drmeister
It's a workaround for an ECL bug that clasp presumably has - we could fix the bug if I had any idea what the bug was.
15:49:08
drmeister
The slot TRIVIA.LEVEL2.IMPL::TEST in the object #<TRIVIA.LEVEL2.IMPL::DEFERRED> is unbound.
15:49:35
drmeister
https://github.com/quicklisp/quicklisp-client/blob/master/dists/quicklisp/software/trivia-20170725-git/level2/impl.lisp#L331