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jakmaddox wukevin richardliaw naphthalene meganrm yuhangwang brettbarbaro rahmanhpu ethanzang feihln biochunan mesoscopeautopack's Issues
1. Grids are unreliable. Need to Fix BHTree
Packing for HIV 1.5 only works reliably with PandaBullet and Jordon3 combo
Need to fix:
- Panda-Jordon combo to allow partial selection of larger volumes- for example, I can no longer pack only a portion of HIV 1.5- the grid has an out of bounds error- the same type of error we see with BHTree or other combinations.
- BHTree should be fixed
- Jordon, Jordon3, and BHTree need to work reliably, with full or partial selections, for planar recipes like Figure 3 A, B, and C, and for complex nested volumes like HIV 1.5, with PandaBullet, then Jitter, then RAPID
C4D r16 can't close then reopen autoPACK
You can't close autoPACk and continue without restarting C4D.
Move all variable files out of autoPACK code
Move to the new user/username/library/AppSupport/autoPACK/ :
AP_registration
path_preferences
user_recipe_available.json
version.txt
Change version.txt to autoPACK_version.txt to make it easy to differentiate programmatically from upy and epmv version.txt files
C4D r16 Panda Windows
Panda doesn't work in the Window's installation The path isn't found or some dir are missing- I can't recall.
A .c4d representation file won't load into cache at all, even with Force Dowloading Geometries on. I have to manually place it there... may be a Google lag issue?
, e.g. rep_file="autoPACKserver/autoPACK_database_1.0.0/geometries/HIV1_capsid_Rep_Med_0_2_0"> had to be placed manually in my cache in order for it to load- probably related to the awfulness/unreliability especially on weekends of code.google.com
Can someone point me to the algorithm that packs elements in other elements?
I was reading about this tool and found the claim:
"Position different 3D objects inside a larger object with zero to minimal overlap"
However the code base is very big, can someone point me to the algorithm that does the "volume filling"?
HIV 1.5 won't download new ingredients or containers unless ForceDownloadingTheIngredientGeometries is checked
If an ingredient or recipe or geometry or anything does not exist in cache, it should be downloaded automatically. The user currently has to know to check ForceDownloadingTheIngredientGeometries if they want to avoid an error that prevents the file and GUI from loading.
Fixed? Previously, the r16 update was not displaying container (compartment/organelle) representations
Previously, the r16 update was not displaying container (compartment/organelle) representations.
I think this has been fixed in the DEV version but has an update been provided for people who have already install?
2) Close Packing is broken
Probably a problem with the grids, but Close packing has no effect and just seems to default to Random. I tested this only with HIV ENV proteins in HIV 1.5. It works well in April 2013 version, but is broken in the January 2014 version
C4D r16 Panda Mac
Panda doesn't seem to work for mac installations that have not had Panda previously installed
Points don't display properly
Likely and issue with Jordon or some other aspect of the grid with HIV1.5, but Used points only show a few, even with a very dense packing an hundreds of clearly visible grip and ogGrid point overlaps. The Freepoints, etc are similarly broken- seems to have something to do with the distance values failing the tests in Graphics.py
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