Re: [PyMOL] Is there a way to "count" hydrogen bond interactions?

[Thomas H. <tho...@sc...>]

Hi Ahmad,

Unfortunately there is no proper API for this. But I can think of two approaches. Note that the results can differ because the two method do slightly different h-bond detection!

1) Use "cmd.find_pairs" with mode=1 on "donors" and "acceptors" selection. Example:

sele1 = "chain A & (donors | acceptors)"
sele2 = "chain B & (donors | acceptors)"
radius = 3.5
D = cmd.find_pairs(sele1, sele2, mode=1, cutoff=radius)
print("number of h-bonds:", len(D))

1) Use "cmd.distance" and the "get_raw_distances" script. Example:

run https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/get_raw_distances.py

sele1 = "chain A"
sele2 = "chain B"
radius = 3.5
cmd.distance("distname", sele1, sele2, mode=2, cutoff=radius)
D = get_raw_distances("distname")
print("number of h-bonds:", len(D))

See also:
https://pymolwiki.org/index.php/Get_raw_distances
https://pymolwiki.org/index.php/Distance
https://pymolwiki.org/index.php/Find_pairs

Hope that helps.

Cheers,
  Thomas

> On May 5, 2017, at 5:08 AM, Ahmad Abdelzaher <und...@gm...> wrote:
> 
> I know I can can find the hydrogen bond interactions between a
> selection and surrounding residues within a certain radius. I would
> like to find a way to retrieve the actual count of those interactions
> per residue. How can I do it in the API?
> 
> Regards.

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.