Hi Subha,
Probably this will get close:
for pdb in open('./out').readlines():
pdb = pdb.strip()
cmd.load(pdb,'tmp')
cmd.pseudoatom('tmp',name='pseudo')
cmd.save(pdb[:-4]+'-pseudo.pdb','pseudo')
cmd.delete('tmp')
cmd.delete('pseudo')
... Just a bit too much for a oneliner ;)
Hope it helps,
Tsjerk
On Wed, Oct 12, 2016 at 8:16 PM, Subha K <subhal...@gmail.com> wrote:
> Hi There,
>
> I am looking to automate the calculation of centre of mass and placing a
> pseudo atom on the COM and save it as a pdb file . Going through the forum [
> https://sourceforge.net/p/pymol/mailman/message/34458943/] , I found some
> useful scripts for this, but, I am having trouble getting it done for all
> files in a directory. My script does what I need for the first file alone.
> Some looping or other is not correct. Or there could be an easy and better
> way to do it. I couldn't figure that out. So, could some one please help
> me solve this?
>
> I have 100 files F01, F02, F100 ... in the directory dockout. I would like
> to calculate the COM and place a pseudo atom on the COM and save it as a
> pdb for all the 100 files.
> 'out' in the script corresponds to the list of all the 100 files.
>
> import pymol
>
> from pymol import cmd
>
> pymol.finish_launching()
>
> import numpy as np
>
> import glob
>
> import fileinput
>
> def center(selection, com=True):
>
> model = cmd.get_model(selection)
>
> xyz = np.array(model.get_coord_list())
>
> mass = [i.get_mass() for i in model.atom]
>
> xyz_m = xyz * np.array([mass]).T
>
> if com:
>
> return tuple(np.sum(xyz_m, 0)/model.get_mass())
>
> else:
>
> return tuple(np.average(xyz, 0))
>
>
> def GetListOfFiles (filename):
>
> l = []
>
> for line in fileinput.input( filename ):
>
> tokens = line.split( )
>
> l.append(tokens)
>
> return l
>
>
> def Calculate_COM (list):
>
> for i in range (len(list)):
>
> print list[i][0]
>
> X=1
>
> if (X<101):
>
> os.system("cp ./dockout/F"+ str(X).zfill(2)+ " ./lig.pdb")
>
> for pdb in glob.glob("lig.pdb"):
>
> cmd.load(pdb)
>
> COM = center('resn UNK')
>
> cmd.pseudoatom('ligCOM', pos=COM)
>
> cmd.save("complex_dummy.pdb", "all")
>
> os.system("mv complex_dummy.pdb complex_" + str(X).zfill(2)
> + "_dummy.pdb")
>
> os.system("rm lig.pdb")
>
> X=X+1
>
> else:
>
> break
>
> listofFiles = GetListOfFiles ("./out")
>
> print listofFiles
>
> Calculate_COM(listofFiles)
>
>
>
> Thanks,
> Subha
>
>
> ------------------------------------------------------------
> ------------------
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> _______________________________________________
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>
--
Tsjerk A. Wassenaar, Ph.D.
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