Hi Viswanath,
Please find the attach file which might help you,
You have to give the input folder path containing all the pdbs, for example
in terminal input:
"Please provide the input directory:/home/viswanath/pdb "and "Enter the
required files extension .pdb:.pdb" as input,
It will create a new folder "new" which will contain all the pdb files with
water removed and hydrogen added.
I hope that solves your issue.
Best wishes.
S.Sriram
Postdoctoral Research fellow,
Computational Structural Biology Team,
RIKEN Center for Computational Science(R-CCS), Kobe, Japan.
On Thu, Jun 17, 2021 at 6:16 PM Gundala Viswanath <gunda...@gmail.com>
wrote:
> Does Autodocktools provide a command line for batch processing?
>
> G.V.
>
> On Thu, Jun 17, 2021 at 9:24 PM Saurabh Gayali <saurabh.gay...@gmail.com>
> wrote:
>
>> You should use autodocktools [ADT] or openbabel for this purpose.
>> Converting PDB to PDBQT.
>>
>> ------------------------------
>>
>> *Saurabh Gayali* / Post Doctoral Fellow
>> saurabh.gay...@gmail.com / +91 8800412916
>>
>> *CSIR-IGIB*
>> <http://example.com/>New Delhi, India
>>
>>
>> On Thu, Jun 17, 2021 at 4:01 PM Gundala Viswanath <gunda...@gmail.com>
>> wrote:
>>
>>> Hi
>>>
>>> I'm trying to dock a ligand to several hundred PDB files (receptors). I
>>> thus need to prepare those files like removing water and adding hydrogen.
>>>
>>> I can do that manually using Pymol. But it's too troublesome. Is there a
>>> way to do it programmatically with Pymol command line procedure?
>>>
>>>
>>> Sincerely,
>>>
>>> G.V.
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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>>
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import os
from pymol import cmd
req_path=input("Please provide the input directory:")
new=os.path.join(req_path,"new")
os.mkdir(new)
if os.path.isfile(req_path):
print(f"the given path {req_path} is a file. Plaese pass only dir")
else:
all_f_ds=os.listdir(req_path)
if len(all_f_ds)==0:
print(f" given path {req_path}is empty")
else:
req_ex=input("Enter the required files extension .pdb:")
req_files=[]
for each_file in all_f_ds:
if each_file.endswith(req_ex):
#print(each_file)
req_files.append(each_file)
if len(req_files)==0:
print("thers is no files {req_ex} files in given loacation of {req_path}")
else:
print(f" there are {len(req_files)} pdbs in the {req_path}")
print(f" the required files are :{req_files}")
for pdbs in req_files:
#index=index+1
cmd.load(pdbs)
cmd.remove("resn hoh")
#cmd.h_add( string selection="(all)" )
cmd.h_add("all")
os.chdir(os.path.join(req_path,"new"))
cmd.save(pdbs)
os.chdir(req_path)
os._exit(0)
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