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16:19:30
Bike
https://github.com/clasp-developers/clasp/commit/0796212eb73cd687f5c3b5793684eeb8fb1f34d6#diff-1d48355bb5acf354d528ba130ac80a5c8a45d76533b9b96eff77b81232533807
16:56:33
drmeister
yitzi: There are a few things with molviewer that are making it a bit difficult to solve my chemistry problems. Question: How much work would be involved in fixing them?
16:57:22
drmeister
1. Hovering over atoms - the names aren't displayed anymore like they used to be. I've seen them displayed sometimes but way off to the side. I suspect they are being displayed but offscreen.
16:59:19
drmeister
Regarding 2 - to get to a specific structure in an SDF file I put the mouse over the slider and I hit right-arrow repeatedly, counting to which structure I get to.
17:01:06
drmeister
If I lose count then I may be looking at the wrong structure and I may draw the wrong conclusion.
17:02:07
drmeister
I'm trying to figure out why my code DOESN'T think the local conformations on the bond I'm looking down in these two structures are the same.
17:07:07
drmeister
This is a really difficult problem to debug and I anticipated that it would be years ago.
17:20:42
drmeister
The nglview used to print the atom name in the window when I clicked on it - that doesn't happen anymore either. If that were working then I wouldn't need the mouse-over label.
17:22:02
drmeister
Oh - wait... sdf files create their own atom names - I don't know if I can use mine. I don't right now and sdf generated names are kinda useless (sigh).
17:22:23
yitzi
#2 isn't really hard. #1 is just finicky. The tooltips in html are always kind of hackish.
17:30:51
drmeister
I'm trying to debug a subtle problem where I'm matching shapes of molecules and sometimes it fails and I'm not sure if it's because I'm not searching enough or if my matching is too stringent.
17:32:44
drmeister
Once I get this solved then I can build large molecules from these shapes extracted from thousands of training molecules.
17:44:14
yitzi
I'm not sure the header is save for each mol in the sdf file. I think the ID might be
17:50:37
drmeister
I was thinking "Title line" and or "Comment line" https://en.wikipedia.org/wiki/Chemical_table_file#Molfile
17:53:09
drmeister
Printing all this info in the upper left corner under the slider would be useful.
17:55:06
yitzi
The ngl sdf parser saves the first title + comment line for the whole file...but it looks like it it ignores the rest...but it appears to save this stuff. I just gotta make sure I can find it the structure model.
17:55:24
drmeister
Yeah - that would be very helpful to print all of that. I could put a lot of information in there.
17:55:55
yitzi
They can be multiline...so technically you could put sexpr data in there for attributes, etc.
18:04:20
yitzi
I can't do Title and Stucture for each one...the parser only the save the first one...but you can make your own <Title>, <Name> ... whatever
18:05:49
drmeister
This will make life so much easier - I won't need to cross-reference as much and potentially make errors and draw incorrect conclusions.
18:38:05
drmeister
Trying now. I'll need to rebuild some more stuff to generate that information and I'll do that next.
18:38:56
yitzi
You can always try on some SDF file you have lying around. The last one sent to me had some stuff in it.
18:39:41
yitzi
Its the same in every molecule...so it isn't particularly useful...but it demonstrates the functionality.
18:41:22
drmeister
After the jupyter-labextension I reloaded the jupyterlab page I had open from zeus and there it was.
18:42:09
yitzi
Awesome. It was pretty easy. I just generated some HTML (a description list). https://github.com/yitzchak/jupyterlab-molviewer/commit/daee8580748f9a331a0c5e15a52ff4bfa1060979
19:45:31
yitzi
drmeister; pushed an update to add the overall file's title and the index of the molecule.
22:19:30
drmeister
Aaaand it helped me find a big problem. I was pushing into a list, reversing the order of entries when I wanted to vector-push-extend