[Chimera-users] Loop through hundreds of files and find HBonds

[Samuel Kyobe]

Hi Elaine

Thank you so much for your responses.
I have modified the recommended example as seen below:

		1	import chimera
		2	import os
		3	import glob
		4	
		5	from chimera import runCommand as rc 
		6	from chimera import replyobj 
		7	
		8	# change to folder with data files
		9	os.chdir("/Volumes/Auto_chimera")
		10	
		11	# absolute path to search all .pdb files of ligands
		12	path = r'./*_out_*.pdb’ # several files with output name specified as *_out_*.pdb
		13	files = glob.glob(path)
		14	print(files)
		15	
		16	file_names = files
		17	
		18	for files in file_names:
		19		my_mod=chimera.openModels.open('./HLA_5w6a_model_4.pdb',type="PDB")
		20		replyobj.status("Processing " + files)
		21		rc("open " + files)
		22		rc("addh")
		23		rc("findhbond intermodel  true intramodel  false relax  false reveal  true saveFile")
		24		rc("close all")
		25	rc("stop now”)

My current challenge is how to save the different resultant files with unique file_names (line 25).

Is there an alternative way I can call the files names after saveFile (line 25)? Your example doesn’t not work with my modified code.

Thank you

Samuel



> On 13 Apr 2022, at 19:04, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Samuel,
> Although the first link I sent you shows Chimera commands, the second link shows how to put those commands together with Python for looping.
> Elaine
> 
>> On Apr 13, 2022, at 9:00 AM, Samuel Kyobe via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>> 
>> Dear Elaine
>> 
>> The challenge I have is that the Command Index is not written for Python which I would prefer to use for looping in several files.
>> 
>> I am using only Chimera I have no access to ChimeraX.
>> 
>> Thank you
>> 
>> Samuel
>