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

[Eric Pettersen]

You need a space between saveFile and the quote that follows it.

> On Apr 15, 2022, at 6:39 AM, Samuel Kyobe <samuelkyobe at gmail.com> wrote:
> 
> Hi Eric
> 
> I have modified the code:
> 
> 	hbonds_output = files[:-4] + "hbonds.txt" # change ".pdb" to "hbonds.txt"
> 	rc("findhbond intermodel  true intramodel  false relax  false reveal  true saveFile" + hbonds_output)
> 
> But, the code returns the error below:
> 
> File "/private/var/folders/y2/p069gv9n6lsf1x8w08bym32w0000gn/T/AppTranslocation/AF4918BD-D759-418D-AA97-756E6B1D941C/d/Chimera.app/Contents/Resources/share/Midas/midas_text.py", line 3396, in _parseTyped
>    % typed
> MidasError: No value provided for keyword 'saveFile247_CnA1_pol_frag_1_conf_36_out_01hbonds.txt'
> 
> Not sure what could be causing the error.
> 
> Thank you
> 
> Samuel
> 
> 
> 
> 
>> On 15 Apr 2022, at 04:02, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>> 
>> 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
>>>> 
>>> 
>>> 
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>>> 
>> 
> 
>