Lua function to determine whether a segment is hydrophobic or hydrophilic

Case number:845813-987797
Topic:Game: Tools
Opened by:Tlaloc
Status:Closed
Type:Suggestion
Opened on:Thursday, June 3, 2010 - 09:40
Last modified:Tuesday, April 3, 2012 - 15:44

Can we get a lua function to determine whether a segment is hydrophobic or not? beta_helix says that rosetta has a function ispolar that does this.

(Thu, 06/03/2010 - 09:40  |  8 comments)


Joined: 09/18/2009
Groups: SETI.Germany

If the get_aa() function would work again, you could get the letter of the sidechain, and by knowing which sidechain it is, you would know if it is hydrophobic or not.

http://fold.it/portal/node/987752

Joined: 09/18/2009
Groups: SETI.Germany

@Tlaloc:
How did you do that in your contract script, that it applies bands at hydrophobic parts?

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get_segment_score_part("reference", i) < 0

But it is not reliable. It always seems to find hydrophobic bands, but it doesn't find *every* hydrophobic band.

Joined: 09/18/2009
Groups: SETI.Germany

@Tlaloc:
So we need the get_aa() function back again.

What does reference in this case mean?
I still didn't get all meanings of the score parts.

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Topic: Biochem » Game: Tools

Example:

for i=1,get_segment_count() do
if get_segment_score_part("reference", i) < 0 then
select_index(i)
end
end
do_freeze(true, false)

This will freeze the backbone of the hydrophobic segments.

It mostly gets the hydrophobics, but isn't reliable. I think it's kind of a coincidence. I'm not even sure what "reference" means, since I could not find documentation on the scoring function anywhere on the web. (But the lack of documentation is a completely different issue.) I know what the various words allowed in the first parameter to get_segment_score_part(), but I am not sure what they mean!

Joined: 09/18/2009
Groups: SETI.Germany

I also think that it is coincidence, but as far as we don't have other possibilities, your script works as best as it can ;)

"I'm not even sure what "reference" means, since I could not find documentation on the scoring function anywhere on the web. (But the lack of documentation is a completely different issue.) I know what the various words allowed in the first parameter to get_segment_score_part(), but I am not sure what they mean!"

That's right, only information I found was here:
http://foldit.wikia.com/wiki/Get_segment_score_part

It lists all attributes, but dosen't explain what they mean.
I can imagine some meanings, but I'm not sure.

If get_aa() would work, resulting one-letters of the sidechains with A,C,F,I,L,M,P,V,W,Y are hydrophopic.
Special Case is G.

Joined: 06/17/2010
Status: Open » Closed

bool is_hydrophobic(sn) works. Done.

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Status: Closed » Closed

closed

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