NEW structure.GetDescription

Case number:954892-994842
Topic:Developer Preview
Opened by:Bruno Kestemont
Opened on:Wednesday, March 27, 2013 - 15:00
Last modified:Wednesday, December 16, 2015 - 12:37

I suggest the following new LUA2 command in order to be able to conceive recipes that uses this information (for example info on preferred AAs):

Function: string structure.GetDescription(integer segmentIndex)
Description: Gets the Description assigned to a segment.
V1 Function Name: New to V2

Alternative: you provide this information in cc in the segment note (this we can use with structure.GetNote)

(Wed, 03/27/2013 - 15:00  |  4 comments)

Joined: 09/24/2012
Groups: Go Science

See summary of needs and alternative solutions here:

tamirh's picture
User offline. Last seen 8 years 15 weeks ago. Offline
Joined: 05/11/2012

Did you mean just the description that you get when you hit TAB?

Various filters (and other components) add in different information here, so it's kind of a place for extra information that changes. It's fairly easy to parse though (for instance, the ResidueIE data).

Joined: 09/24/2012
Groups: Go Science

Yes I did.

In draft scripts, I use descriptions (and puzzle titel) to double-check some hypothesis got from the protein (for example: is it a symmetric etc). If the information is not present, it is not very important (the recipe will have to work as "default") but if some info is found, this can enhance the velocity or the behavior of the recipe (e.g.. tvdl enhanced DRW and Ebola use this kind of info to optimize the default options).

Several ways are possible to (automatically) gather info on preferred AAs for each segment. Presently, I manually write the preferred AAs strings into the segment note before to run some mutating program able to "getNote". Other ways were suggested elsewhere, but the present proposal would add other checking possibilities.

The fundamental is that all info given by "Foldit" in the description sections (Tab on segment, and all other info that the hand-folder can see on his screen, that you "manually" write to inform us) can potentially be useful for recipes.

Even if this info change over time, this is interesting to us, because some terminologies are standard (symmetric, hydrophobic, ALA, GLU, filter, electron, clashing etc) . For example, the recipe can test hypothesis, recognize some types of puzzles etc. If the preferred AAs change over time for the same puzzle, this is even more important (my manual writing would give erroneous info).

Conclusion for this case:: My draft recipe checks if a string "ALA" is present in the segment description before to try to mutate. If not, do some other checks elsewhere and consider jumping to another AA without loosing precious CPU time.

Joined: 09/24/2012
Groups: Go Science
Status: Open » Closed

It's a part of other suggestions that can link to this one.


Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, Boehringer Ingelheim, RosettaCommons