Every time you loop through the list of files, you set X=1 ; you do your X=X+1
in a loop that will only run once ( because glob.glob(“lig.pdb”) is only going
to return a list of length 1 that has lig.pdb) , so you set X=1 , then X=2,
then back to X=1 before you process the next entry. That is why you are only
processing the first file, probably doing so 100 times.
you probably want something like
with open(“out") as f:
for line in f:
in_pdb_file = line.strip()
// code for processing in_pdb_file here
or
for X in range(1,101):
in_pdb_file = “dockout/F"+ str(X).zfill(2)
// code for processing in_pdb_file here
Generally, I would recommend strongly against using os.system for performing
file operations. You should look into shutil.copy , shutil.move , and os.remove
> On Oct 12, 2016, at 2:16 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/
> <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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