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LociOiling's picture
User offline. Last seen 1 hour 5 min ago. Offline
Joined: 12/27/2012

With all the new Lua functions that have been added recently, some inconsistencies have cropped up. I'm reporting this here mainly for reference, but it can also be considered as feedback.

For symmetry puzzles, the symmetric chains were off limits for recipes, until these functions were added or updated:

The function structure.GetSymCount returns the number of symmetric chains, and the added chain number argument for band.AddBetweenSegments allows adding a band that ends on one the of those chains.

Two even newer functions use a different scheme:

For points on symmetric chains, these functions return just a segment number, not a segment number and chain number. The segment number may be greater than the value from structure.GetCount.

Segment numbers are also not continuous. There seems to be one pseudoresidue between each chain in a symmetry puzzle, complicating the numbering.

It's possible to convert these "long" segment numbers to segment number, chain number format using the method outlined in normalizing a segment number.

So far, band.GetResidueEnd and structure.GetHBonds have been shown to return "long" segment numbers. It's possible other functions may do the same thing.

It probably makes more sense for the new functions to return segment number and chain number separately.

jeff101's picture
User offline. Last seen 17 hours 41 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
Please return both segment and chain numbers

I agree with Loci that these new functions should return
both segment and chain numbers. I am guessing that one
end of each band and H-bond will always connect to
chain 1, but the other end could be to chain 1 or
a different chain (or to space for some bands).


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