On Apr 26, 2016, at 11:30 AM, Jérémie KNOOPS [531802] <Jeremie.KNOOPS@umons.ac.be> wrote:

Hi Eric,

Thank you very much, I didn't expect an (almost) ready to use script.
I only change the loop, the one with enumerate didn't work. But now it works perfectly. This is the script I use :

# the script assumes you've already opened the trajectory in Chimera 
from chimera import openModels, Molecule 
 
# we assume the trajectory is the only open model 
traj = openModels.list(modelTypes=[Molecule])[0] 
 
# load all the frames 
traj.loadAllFrames() 
 
# open the output file (change as desired) 
import os.path 
f = open(os.path.expanduser('~/Documents/hbonds.txt'), "w") 
 
# get the functions and parameters we need for finding H-bonds 
from FindHBond import findHBonds, recDistSlop, recAngleSlop 
 
# loop through the coordinate sets (frames) 
c = traj.coordSets 
for frame in range(len(c)): 
    traj.activeCoordSet = c[frame+1] 
    # find and print the number of H-bonds, and cache which atoms 
    # are donors/acceptors, so they're not computed each frame 
    print>>f, "Frame", frame+1, len(findHBonds([traj], distSlop=recDistSlop, angleSlop=recAngleSlop, cacheDA=True)) 
 
# close/flush the output file 
f.close()

I have an additional question : what's the way to restrict the residues to search for hbond donors & acceptors with python commands?

Jérémie

---

De : Eric Pettersen [pett@cgl.ucsf.edu]
Envoyé : samedi 23 avril 2016 2:29
À : Jérémie KNOOPS [531802]
Cc : chimera-users@cgl.ucsf.edu
Objet : Re: [Chimera-users] HBond on every frames of a large trajectory

On Apr 22, 2016, at 9:30 AM, Jérémie KNOOPS [531802] wrote:

Hi,

What is the easiest and fastest way to get the number of H bonds on every frame of a large trajectory (>10 000 frames) and print it to a file? 
The hbonds command does not seem to work with the perframe command and displaying the whole trajectory to run a per-frame script is quite slow.

Hi Jérémie,

To do this efficiently, we need to use a Python script.  In the script the important things to avoid are: 1) a redraw for every trajectory frame, and 2) creating and destroying graphics objects representing the H-bonds every frame.  This means we are going to avoid using the handy-but-non-efficient runCommand() Python call, which typically causes a redraw, and we are going to call the functions underlying the FindHBonds tool, in order to find the h-bonded pairs without creating pseudobonds and so on.  We will also step through the coordinate sets (frames) in Python.

Here's a script:

# the script assumes you've already opened the trajectory in Chimera

from chimera import openModels, Molecule

# we assume the trajectory is the only open model

traj = openModels.list(modelTypes=[Molecule])[0]

# load all the frames

traj.loadAllFrames()

# open the output file (change as desired)

import os.path

f = open(os.path.expanduser("~/hbonds.out"), "w")

# get the functions and parameters we need for finding H-bonds

from FindHBond import findHBonds, recDistSlop, recAngleSlop

# loop through the coordinate sets (frames)

for i, cs in enumerate(traj.coordSets):

traj.activeCoordSet = cs

# find and print the number of H-bonds, and cache which atoms

# are donors/acceptors, so they're not computed each frame

print>>f, "Frame", i+1, len(findHBonds([traj], distSlop=recDistSlop,

angleSlop=recAngleSlop, cacheDA=True))

# close/flush the output file

f.close()

Put the above in a file whose name ends in ".py" and open it in Chimera (after opening your trajectory) and it should write the number of hydrogens bonds for each frame to a file named "hbonds.out" in your home directory.  I didn't test it but I'm fairly certain the logic is correct.    I'm also pretty sure the syntax is correct, thought it's more possible I missed a parenthesis or quote somewhere.  If you know Python it should be easy to fix any such errors .  Otherwise, let me know the error and I'll provide a fix.

--Eric

Eric Pettersen

UCSF Computer Graphics Lab