Loop through hundreds of files and find HBonds
Dear Chimera (and ChimeraX) team I have run a large docking experiment using several ligands to determine the best binders for further analysis in Molecular Dynamics studies and possible wetlab evaluation. I need to find some python example or code snippet capable of looping over hundreds of files and find several .pdb poses from a docking run and find Hydrogen bonds in each one using one receptor. In the process of finding the H bonds, I would like to add Hydrogens, and the protonation state is unspecified. Then at FindHBond, I want to find intermodal Hbonds and write the results to a file. Thanks Samuel Dr. Samuel Kyobe Department of Medical Microbiology, 3rd floor, Pathology/Microbiology BLDG, School of Biomedical Sciences College of Health Sciences, Makerere University. Box 7072, Kampala, Uganda. Mob: +256775468605 Skype: samuelkyobe
Dear Samuel, First figure out interactively (by typing in the commands) what set of commands you need for each one. Take a look at "addh" for adding hydrogens and "findhbond" for finding H-bonds. Of course, you may also need other commands, like "open" "close" "select" etc. See the commands index and click the links to see the detailed information for each command. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> Then here is some basic information on how to use python to loop through several input files, and how to save the log. <https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> The "findhbond" command also has an option to save information to a file if you wanted a separate output file for each docked ligand file. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 13, 2022, at 5:41 AM, Samuel Kyobe via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera (and ChimeraX) team
I have run a large docking experiment using several ligands to determine the best binders for further analysis in Molecular Dynamics studies and possible wetlab evaluation.
I need to find some python example or code snippet capable of looping over hundreds of files and find several .pdb poses from a docking run and find Hydrogen bonds in each one using one receptor.
In the process of finding the H bonds, I would like to add Hydrogens, and the protonation state is unspecified. Then at FindHBond, I want to find intermodal Hbonds and write the results to a file.
Thanks
Samuel
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
On 13 Apr 2022, at 17:49, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Elaine
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
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
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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Hi Eric Problem solved. 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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Hi Samuel, The is just basic Python. The plan would be to go to the parent folder, loop over the subfolder names, and within that loop, loop over the files. So something like: os.chdir("parent_folder_path") for subfolder_name in ["folder_name1", "folder_name2", "folder_name3",...]: os.chdir(subfolder_name) # go into subfolder ... same code as before ... os.chdir("..") # go back to parent folder --Eric
On Apr 19, 2022, at 12:01 PM, Samuel Kyobe <samuelkyobe@gmail.com> wrote:
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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participants (3)
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Elaine Meng -
Eric Pettersen -
Samuel Kyobe