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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