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

[Eric Pettersen]

Hi Samuel,
	You know the ligand file name, so you could just modify that to make a corresponding unique output file name.  So between lines 22 and 23 you could do:

	hbonds_output = files[:-4] + “.hbonds.txt” # change “.pdb” to “.hbonds.txt”

and your findhbond command would be rc("findhbond intermodel  true intramodel  false relax  false reveal  true saveFile “ + hbonds_output)

—Eric

> On Apr 14, 2022, at 6:10 AM, Samuel Kyobe via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> 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
>> 
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
>