Lua function to determine whether a segment is hydrophobic or hydrophilic

Started by Tlaloc

Tlaloc Lv 1

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.

Tlaloc Lv 1

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.

Crashguard303 Lv 1

@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.

Tlaloc Lv 1

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!

Crashguard303 Lv 1

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.