Re: [PyMOL] Programmatically adding hydrogen and remove water to multiple PDB files

[sriram raghavan]

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 
wrote:

> Does Autodocktools provide a command line for batch processing?
>
> G.V.
>
> On Thu, Jun 17, 2021 at 9:24 PM Saurabh Gayali 
> 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*
>> New Delhi, India
>>
>>
>> On Thu, Jun 17, 2021 at 4:01 PM Gundala Viswanath 
>> 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
>>> Unsubscribe:
>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
>> ___
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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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Re: [PyMOL] Programmatically adding hydrogen and remove water to multiple PDB files

[Gundala Viswanath]

Does Autodocktools provide a command line for batch processing?

G.V.

On Thu, Jun 17, 2021 at 9:24 PM Saurabh Gayali 
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*
> New Delhi, India
>
>
> On Thu, Jun 17, 2021 at 4:01 PM Gundala Viswanath 
> 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
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
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Re: [PyMOL] Programmatically adding hydrogen and remove water to multiple PDB files

[Saurabh Gayali]

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*
New Delhi, India


On Thu, Jun 17, 2021 at 4:01 PM Gundala Viswanath 
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
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
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[PyMOL] Programmatically adding hydrogen and remove water to multiple PDB files

[Gundala Viswanath]

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.
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