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

19 Apr 2022

      Hi Eric

I now have a new challenge. My files are in several folders as shown below:
		.
		├── 8_C_pol
		│   ├── 247_CnA1_pol_frag_1_conf_36_out_01.pdb
		│   ├── 247_CnA1_pol_frag_1_conf_62_out_07.pdb
		│   └── HLA_5w6a_model_4.pdb
		└── 94_C_vif
		    ├── 247_CnA1_pol_frag_1_conf_36_out_01.pdb
		    ├── 247_CnA1_pol_frag_1_conf_62_out_07.pdb
		    └── HLA_5w6a_model_4.pdb

I would like to iterate through the folders and execute the commands with the original script below (only works inside one folder):

	1	import chimera
	2	import os
	3	import glob
	4
	5	from chimera import runCommand as rc # use 'rc' as shorthand for runCommand
	6	from chimera import replyobj # for emitting status messages
	7
	8	# change to folder with data files
	9	os.chdir("/Volumes/Sammy/Grants/H3Africa/CAfGEN/CAfGEN_PhD_Work/Allele_mechanisms/Mini_ligands_All/Auto_chimera”)
	10
	11	# absolute path to search all .pdb files of ligands
	12	path = r'*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		hbonds_output = files[:-4] + "hbonds.txt" # change ".pdb" to "hbonds.txt"
	24		rc("findhbond intermodel  true intramodel  false relax  false reveal  true saveFile " + hbonds_output)
	25		rc("close all")
	26	# uncommenting the line below will cause Chimera to exit when the script is done
	27	rc("stop now")

But I have tried the following modification but it returns errors. 

	1	import chimera
	2	import os
	3	import glob
	4
	5	from chimera import runCommand as rc # use 'rc' as shorthand for runCommand
	6	from chimera import replyobj # for emitting status messages
	7
	8	rootdir = '/Volumes/Sammy/Grants/H3Africa/CAfGEN/CAfGEN_PhD_Work/Allele_mechanisms/Mini_ligands_All/Auto_chimera/try/'
	9	for subdir, dirs, files in os.walk(rootdir):
	10
	12		for file in files:
	13			print os.path.join(file)
	14	
	15			path = r'*out*.pdb'
	16			glob.glob('*out*.pdb')
	17			print(file)
	18
	19			my_mod=chimera.openModels.open('./HLA_5w6a_model_4.pdb',type="PDB")
	20			replyobj.status("Processing " + file)
	21			rc("open " + file)
	22			rc("addh")
	23			hbonds_output = files[:-4] + "hbonds.txt" # change ".pdb" to "hbonds.txt"
	24			rc("findhbond intermodel  true intramodel  false relax  false reveal  true saveFile " + hbonds_output)
	25			rc("close all”)
	26
	27	# uncommenting the line below will cause Chimera to exit when the script is done
	28	rc("stop now")

After hours of trying various options on stack overflow, I have to turn to your expert help.

Thank you

Samuel
...
On 15 Apr 2022, at 17:03, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
You need a space between saveFile and the quote that follows it.
...
On Apr 15, 2022, at 6:39 AM, Samuel Kyobe <samuelkyobe@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@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@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@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@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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