freenode/#clasp - IRC Chatlog
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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
16:02:45
drmeister
Bike: Do you know what "error in process filter: Wrong number of arguments: nil, 46" means? We've seen this before - and I keep forgetting what it's due to.
16:06:22
drmeister
It happens when type in a function call where the function doesn't exist: (coerce-to-condition ... <- emacs reports problem)
16:13:20
Bike
you can do like, toggle-backtrace i think and it'll show an elisp backtrace whenever the error happens.
16:22:40
Bike
https://github.com/drmeister/clasp/blob/dev/src/lisp/kernel/clos/conditions.lsp#L187-L201 that's weird
16:26:22
Bike
https://gitlab.com/embeddable-common-lisp/ecl/commit/8406e1e4fc1eb88f7ef8412cce1542235207cb6f
16:29:59
drmeister
I was playing with the "infix-math" quicklisp system and this came up while compiling it.
16:30:36
drmeister
I figure any scientist who knows anything about lisp might ask about prefix vs infix equations.
16:45:27
drmeister
Hey jackdaniel - we found a bug in the Clasp source code that you had fixed a couple of years ago.
16:45:50
drmeister
https://gitlab.com/embeddable-common-lisp/ecl/blob/develop/src/clos/conditions.lsp#L182
17:49:50
Kevslinger
No :( I think the errors I keep getting are permission errors, and sudo gets me farther but not all the way. It's with the 'make' command -- I have all the proper dependencies installed, I think. I don't know if the permissions things are because of the new OS X security update or because my computer has multiple admin users or something else, but I can't seem to figure out how to fix it
17:55:36
drmeister
It's starts up jupyter notebook at the end - that's why the end looks like it does.
17:57:13
Kevslinger
Maybe if I uninstall "python-dateutil-1.5" before trying to run 'make', it'll avoid this error. I'll try that
18:01:44
drmeister
Requirement already satisfied: ipywidgets>=5.1.5 in /Users/meister/anaconda/lib/python3.6/site-packages/ipywidgets-7.0.0-py3.6.egg (from cyjs==0.1.0.dev0)
18:02:16
drmeister
Requirement already satisfied: ipywidgets>=5.1.5 in /Library/Python/2.7/site-packages/ipywidgets-7.1.0rc0-py2.7.egg (from cyjs==0.1.0.dev0)
18:06:53
drmeister
Hmm, then the question is how do you pick one or the other - or why doesn't jupyter-cytoscape pick python3
18:10:05
Kevslinger
I changed the makefile so instead of 'pip install -e', it reads 'pip3 install -e' which is how I differentiate between the two pythons
18:14:55
drmeister
When I first ran 'make' it said I didn't have igraph - so I installed it with 'pip install igraph' and after that 'make' worked.