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iterating over files
clarablanes
Silly Frenchman
Posts: 28
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Joined: Aug 2018
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#1
Aug-29-2018, 05:57 PM
Hello all, I think I need a lot of help.
I have a file named CONFIG.inp. What I need to do is to create 100 others (i.e. CONFIG1, CONFIG2, etc) replacing just one thing in CONFIG.inp.

One of my problems is: in the replace method I would like to replace 'a' with b, c, d or e one in each file but of course, it will be replaced with 'names'.
And the other problem is: how could I create the CONFIG1, CONFIG1, CONFIG3 and CONFIG4 output files?. I only manage to do it just for one file.
Thank you very much.
clara

I show you what I think I should do (only with 4):
a=['b','c','d','e']
for names in a:
    s=open('CONFIG.inp').read()
    s=s.replace('a','names')
    f=open('CONFIG.inp','w')
    f.write(s)
    f.close()
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buran

Super Moderators
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#2
Aug-29-2018, 07:05 PM
please, show what your CONFIG.inp file looks like and what the expected output is (one file)
did you check configparser module and can you use it? i.e. is your file compatible with a format that configparser can read?
names = ['b','c','d','e']
with open('CONFIG.inp') as f:
    current_config = f.read()
for i, name in enumerate(names, start=1):
    new_config = current_config.replace('a', name)
    with open(f'COFIG{i}.inp', 'w') as f:
        f.write(new_config)
untested, but should work for python 3.6+
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clarablanes
Silly Frenchman
Posts: 28
Threads: 8
Joined: Aug 2018
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#3
Aug-29-2018, 07:55 PM
Thanks for your reply.
This is the content of the config file: (what I want to change is ligand.inp, in the third line).
Once I manage to prepare the CONFIG files, then I should pass through into a binary command to make a molecular virtual screening with the following order: ../flexaid FlexAID2/FlexAID_Input/CONFIG.inp FlexAID2/FlexAID_Input/ga_inp_target.dat Output/Results_simulation.
First of all, I tried to put the ligand library 'library.inp' instead of 'ligand.inp', but it didn't work. Well, it just worked for the first ligand in the list. That's why I thought that I should do by hand one CONFIG file for each ligand... and then try to do the final flexaid with a loop iterating over all CONFIG files.

TEMPOP /home/c.blanes/FlexAID2/FlexAID_Output
PDBNAM /home/c.blanes/FlexAID2/Processed_files/receptor.inp.pdb
INPLIG /home/c.blanes/FlexAID2/Processed_files/ligand.inp
RNGOPT LOCCLF /home/c.blanes/FlexAID2/Binding_sites/binding_site.pdb
OPTIMZ 9999 - -1
OPTIMZ 9999 - 0
OPTIMZ 9999 - 1
OPTIMZ 9999 - 2
OPTIMZ 9999 - 3
OPTIMZ 9999 - 4
OPTIMZ 9999 - 5
OPTIMZ 9999 - 6

RMSDST /home/c.blanes/FlexAID2/Processed_files/ligand_ref.pdb


# Optimization method (genetic-algorithms)
METOPT GA

# The variation in degrees for the anchor angle of the ligand
# Float in interval [1.0-30.0]
VARANG 5.0

# The variation in degrees for the anchor dihedral of the ligand
# Float in interval [1.0-30.0]
VARDIH 5.0

# The variation in degrees for flexible dihedrals of the ligand
# Float in interval [1.0-30.0]
VARFLX 10.0

# Use Vcontacts in the calculations of surfaces in contact
COMPLF VCT

# Do not consider intramolecular interactions
NOINTR

# Side-chain rotamer acceptance threshold
# Float in interval [0.0-1.0]
DEECLA 0.8

# Use instances of side-chain conformers rather than using the Penultimate Rotamer Library
#ROTOBS

# Defines the grid spacing of the binding-site
# Float in interval [0.1,1.0]
SPACER 0.375

# Exclude hetero groups in the target (water,metal,modified amino acids,cofactors,ligands)
# To exclude these groups, uncomment the next line
#EXCHET

# Include water molecules in the target (always removed by default)
# Only considered if EXCHET is disabled
# To include water molecules, uncomment the next line
#INCHOH

# Permeability allowed between atoms
# Float in interval [0.0,1.0] from fully permeable to no permeability
PERMEA 0.9

# Permeability for side-chain rotamer acceptance
# Float in interval [0.0,1.0] from fully permeable to no permeability
ROTPER 0.8

# Solvent term penalty
# When the value is 0.0 the solvent interactions are derived from the interaction matrix
# Float in interval [-200.0,200.0]
SLVPEN 0.0

# Use Vcontacts indexing
VINDEX

# Vcontacts plane definition
# Value in [B,R,X] for Bissecting, Radical and Extended radical plane
# See McConkey et al. (2002) Bioinformatics. 18(10); 1365-1373
VCTPLA R

# Use normalized surfaces in contacts
NORMAR

# Define the RMSD cutoff between clusters
# Float in interval [0.5,3.0]
CLRMSD 2.0

# Number of results/docking poses to output
MAXRES 10

# Only output scored atoms in the final results
# Comment the next line if you wish to obtain the whole complex
SCOOUT

# Only calculate the CF for ligand atoms despite including flexible side-chains
#SCOLIG

# Ends reading of CONFIG file
ENDINP
And these are the outputs (for one ligand):
Sorry, the first one is very long.


1. 'results_simulation_1.rrd'

0 0 0.00000 1.91057 -428.68992 [6846.00000 30.00000 170.00000 170.00000 130.00000 160.00000 -60.00000 10.00000 -60.00000 110.00000 ]
1 0 0.04078 1.91171 -428.68904 [6846.00000 30.00000 170.00000 170.00000 100.00000 -180.00000 -60.00000 10.00000 -60.00000 110.00000 ]
2 0 0.00318 1.91089 -428.67757 [6846.00000 30.00000 170.00000 170.00000 140.00000 150.00000 -60.00000 10.00000 -60.00000 110.00000 ]
3 0 0.00499 1.91111 -428.66343 [6846.00000 30.00000 170.00000 170.00000 150.00000 140.00000 -60.00000 10.00000 -60.00000 110.00000 ]
4 0 0.00793 1.91141 -428.64546 [6846.00000 30.00000 170.00000 170.00000 160.00000 130.00000 -60.00000 10.00000 -60.00000 110.00000 ]
5 0 0.04382 1.90951 -428.63655 [6846.00000 30.00000 170.00000 170.00000 140.00000 160.00000 -60.00000 10.00000 -60.00000 110.00000 ]
6 0 0.04556 1.91297 -428.59275 [6846.00000 30.00000 170.00000 170.00000 140.00000 140.00000 -60.00000 10.00000 -60.00000 110.00000 ]
7 0 0.04799 1.91331 -428.56025 [6846.00000 30.00000 170.00000 170.00000 150.00000 130.00000 -60.00000 10.00000 -60.00000 110.00000 ]
8 0 0.05065 1.91363 -428.52731 [6846.00000 30.00000 170.00000 170.00000 160.00000 120.00000 -60.00000 10.00000 -60.00000 110.00000 ]
9 0 0.09099 1.90879 -428.47979 [6846.00000 30.00000 170.00000 170.00000 130.00000 -180.00000 -60.00000 10.00000 -60.00000 110.00000 ]
10 0 0.08731 1.90925 -428.46610 [6846.00000 30.00000 170.00000 170.00000 150.00000 160.00000 -60.00000 10.00000 -60.00000 110.00000 ]
11 0 0.08594 1.90971 -428.43369 [6846.00000 30.00000 170.00000 170.00000 170.00000 140.00000 -60.00000 10.00000 -60.00000 110.00000 ]
12 0 0.08731 1.91491 -428.36705 [6846.00000 30.00000 170.00000 170.00000 110.00000 160.00000 -60.00000 10.00000 -60.00000 110.00000 ]
13 0 0.12874 1.91021 -428.07818 [6846.00000 30.00000 170.00000 170.00000 -180.00000 140.00000 -60.00000 10.00000 -60.00000 110.00000 ]
14 0 0.13014 1.91805 -427.99922 [6846.00000 30.00000 170.00000 170.00000 100.00000 160.00000 -60.00000 10.00000 -60.00000 110.00000 ]
15 0 0.13219 1.91849 -427.96252 [6846.00000 30.00000 170.00000 170.00000 110.00000 150.00000 -60.00000 10.00000 -60.00000 110.00000 ]
16 0 0.13164 1.91871 -427.95265 [6846.00000 30.00000 170.00000 170.00000 120.00000 140.00000 -60.00000 10.00000 -60.00000 110.00000 ]
17 0 0.39006 2.01947 -427.91152 [6845.00000 30.00000 -180.00000 -180.00000 -70.00000 10.00000 -80.00000 0.00000 -70.00000 130.00000 ]
18 0 0.37480 2.01231 -427.86452 [6845.00000 30.00000 -180.00000 -180.00000 -60.00000 0.00000 -70.00000 0.00000 -70.00000 130.00000 ]
19 0 0.37697 2.01105 -427.85632 [6845.00000 30.00000 -180.00000 -180.00000 -50.00000 0.00000 -70.00000 0.00000 -70.00000 130.00000 ]
20 0 0.37539 2.01276 -427.80305 [6845.00000 30.00000 -180.00000 -180.00000 -70.00000 10.00000 -70.00000 0.00000 -70.00000 130.00000 ]
21 0 0.51757 2.04842 -427.55260 [6845.00000 30.00000 -180.00000 -180.00000 160.00000 50.00000 -80.00000 0.00000 -70.00000 130.00000 ]
22 0 0.51073 2.04583 -427.50010 [6845.00000 30.00000 -180.00000 -180.00000 50.00000 160.00000 -80.00000 0.00000 -70.00000 130.00000 ]
23 0 0.52745 2.04873 -427.44980 [6845.00000 30.00000 -180.00000 -180.00000 50.00000 150.00000 -80.00000 0.00000 -70.00000 130.00000 ]
24 0 0.18417 1.92446 -427.37457 [6846.00000 30.00000 170.00000 170.00000 -180.00000 70.00000 -60.00000 10.00000 -60.00000 110.00000 ]
25 0 0.54157 2.05105 -427.31456 [6845.00000 30.00000 -180.00000 -180.00000 50.00000 140.00000 -80.00000 0.00000 -70.00000 130.00000 ]
26 0 0.07275 1.91808 -427.17280 [6846.00000 30.00000 170.00000 170.00000 140.00000 160.00000 -70.00000 10.00000 -60.00000 110.00000 ]
27 0 0.07279 1.91835 -427.15725 [6846.00000 30.00000 170.00000 170.00000 150.00000 150.00000 -70.00000 10.00000 -60.00000 110.00000 ]
28 0 0.08688 1.91653 -427.14096 [6846.00000 30.00000 170.00000 170.00000 130.00000 -180.00000 -70.00000 10.00000 -60.00000 110.00000 ]
29 0 0.08555 1.91704 -427.11563 [6846.00000 30.00000 170.00000 170.00000 150.00000 160.00000 -70.00000 10.00000 -60.00000 110.00000 ]
30 0 0.08513 1.92018 -427.09598 [6846.00000 30.00000 170.00000 170.00000 140.00000 150.00000 -70.00000 10.00000 -60.00000 110.00000 ]
31 0 0.08703 1.92057 -427.05556 [6846.00000 30.00000 170.00000 170.00000 150.00000 140.00000 -70.00000 10.00000 -60.00000 110.00000 ]
32 0 0.08613 1.92068 -427.05525 [6846.00000 30.00000 170.00000 170.00000 160.00000 130.00000 -70.00000 10.00000 -60.00000 110.00000 ]
33 0 0.52327 2.04576 -427.00702 [6845.00000 30.00000 -180.00000 -180.00000 120.00000 70.00000 -70.00000 0.00000 -70.00000 130.00000 ]
34 0 0.11651 1.91634 -426.96617 [6846.00000 30.00000 170.00000 170.00000 140.00000 -180.00000 -70.00000 10.00000 -60.00000 110.00000 ]
35 0 0.11458 1.89911 -426.94522 [6846.00000 30.00000 170.00000 170.00000 130.00000 170.00000 -50.00000 10.00000 -60.00000 110.00000 ]
36 0 0.11129 1.90432 -426.90038 [6846.00000 30.00000 170.00000 170.00000 80.00000 -180.00000 -50.00000 10.00000 -60.00000 110.00000 ]
37 0 0.53809 2.04692 -426.85435 [6845.00000 30.00000 -180.00000 -180.00000 -180.00000 0.00000 -70.00000 0.00000 -70.00000 130.00000 ]
38 0 0.25269 1.93091 -426.76217 [6846.00000 30.00000 170.00000 170.00000 90.00000 140.00000 -60.00000 10.00000 -60.00000 110.00000 ]
39 0 0.32320 1.93922 -426.71872 [6846.00000 30.00000 170.00000 170.00000 50.00000 160.00000 -60.00000 10.00000 -60.00000 110.00000 ]
40 0 0.43923 1.95654 -426.66743 [6846.00000 30.00000 170.00000 170.00000 50.00000 120.00000 -60.00000 10.00000 -60.00000 110.00000 ]
41 0 0.15239 1.91696 -426.59101 [6846.00000 30.00000 170.00000 170.00000 150.00000 -180.00000 -70.00000 10.00000 -60.00000 110.00000 ]
42 0 0.14929 1.91755 -426.56191 [6846.00000 30.00000 170.00000 170.00000 -180.00000 150.00000 -70.00000 10.00000 -60.00000 110.00000 ]
43 0 0.16123 1.91109 -426.24571 [6846.00000 30.00000 170.00000 170.00000 -180.00000 70.00000 -50.00000 10.00000 -60.00000 110.00000 ]
44 0 0.18623 1.92916 -426.03734 [6846.00000 30.00000 170.00000 170.00000 100.00000 160.00000 -70.00000 10.00000 -60.00000 110.00000 ]
45 0 0.17195 1.91089 -425.99942 [6846.00000 30.00000 170.00000 170.00000 160.00000 170.00000 -60.00000 10.00000 -60.00000 110.00000 ]
46 0 0.37321 2.00925 -425.92746 [6845.00000 30.00000 -180.00000 -180.00000 -70.00000 10.00000 -70.00000 0.00000 -60.00000 130.00000 ]
47 0 0.22327 1.93397 -425.89101 [6846.00000 30.00000 -180.00000 -180.00000 140.00000 140.00000 -60.00000 10.00000 -60.00000 120.00000 ]
48 0 0.23569 1.93337 -425.77018 [6846.00000 30.00000 -180.00000 -180.00000 -150.00000 90.00000 -60.00000 10.00000 -60.00000 120.00000 ]
49 0 0.38713 2.00863 -425.68195 [6845.00000 30.00000 -180.00000 -180.00000 -180.00000 140.00000 -70.00000 0.00000 -60.00000 130.00000 ]
50 0 0.47197 1.96136 -425.66510 [6846.00000 30.00000 170.00000 170.00000 -180.00000 -20.00000 -60.00000 10.00000 -60.00000 110.00000 ]
51 0 0.21907 1.92731 -425.60663 [6846.00000 30.00000 -180.00000 -180.00000 40.00000 -120.00000 -60.00000 20.00000 -60.00000 110.00000 ]
52 0 0.22572 1.92657 -425.60561 [6846.00000 30.00000 -180.00000 -180.00000 50.00000 -120.00000 -60.00000 20.00000 -60.00000 110.00000 ]
53 0 0.22620 1.92677 -425.60293 [6846.00000 30.00000 -180.00000 -180.00000 60.00000 -130.00000 -60.00000 20.00000 -60.00000 110.00000 ]
54 0 0.21982 1.92751 -425.59747 [6846.00000 30.00000 -180.00000 -180.00000 50.00000 -130.00000 -60.00000 20.00000 -60.00000 110.00000 ]
55 0 0.22083 1.92769 -425.58508 [6846.00000 30.00000 -180.00000 -180.00000 60.00000 -140.00000 -60.00000 20.00000 -60.00000 110.00000 ]
56 0 0.22336 1.92883 -425.53454 [6846.00000 30.00000 -180.00000 -180.00000 100.00000 -180.00000 -60.00000 20.00000 -60.00000 110.00000 ]
57 0 0.39615 2.00753 -425.51356 [6845.00000 30.00000 -180.00000 -180.00000 150.00000 -180.00000 -70.00000 0.00000 -60.00000 130.00000 ]
58 0 0.22621 1.92962 -425.49962 [6846.00000 30.00000 -180.00000 -180.00000 -180.00000 110.00000 -60.00000 20.00000 -60.00000 110.00000 ]
59 0 0.22144 1.93071 -425.48670 [6846.00000 30.00000 -180.00000 -180.00000 -180.00000 100.00000 -60.00000 20.00000 -60.00000 110.00000 ]
60 0 0.23214 1.92628 -425.48520 [6846.00000 30.00000 -180.00000 -180.00000 0.00000 -60.00000 -60.00000 20.00000 -60.00000 110.00000 ]
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64 0 0.16682 1.90940 -425.41529 [6846.00000 30.00000 170.00000 170.00000 100.00000 -180.00000 -60.00000 20.00000 -60.00000 100.00000 ]
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66 0 0.23807 1.92911 -425.38305 [6846.00000 30.00000 -180.00000 -180.00000 -180.00000 120.00000 -60.00000 20.00000 -60.00000 110.00000 ]
67 0 0.16449 1.90631 -425.33845 [6846.00000 30.00000 170.00000 170.00000 120.00000 -180.00000 -60.00000 20.00000 -60.00000 100.00000 ]
68 0 0.30940 1.92862 -425.33166 [6846.00000 30.00000 170.00000 170.00000 140.00000 70.00000 -50.00000 10.00000 -60.00000 110.00000 ]
69 0 0.26441 1.95151 -425.31546 [6846.00000 30.00000 -180.00000 -180.00000 130.00000 -180.00000 -80.00000 10.00000 -70.00000 120.00000 ]
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74 0 0.22384 1.93234 -425.26668 [6846.00000 30.00000 -180.00000 -180.00000 -180.00000 90.00000 -60.00000 20.00000 -60.00000 110.00000 ]
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76 0 0.50629 2.03937 -425.25031 [6845.00000 30.00000 -180.00000 -180.00000 -180.00000 20.00000 -70.00000 0.00000 -60.00000 130.00000 ]
77 0 0.27607 1.95146 -425.20543 [6846.00000 30.00000 -180.00000 -180.00000 140.00000 -180.00000 -80.00000 10.00000 -70.00000 120.00000 ]
78 0 0.40381 1.95877 -425.19463 [6846.00000 30.00000 170.00000 170.00000 130.00000 70.00000 -70.00000 10.00000 -60.00000 110.00000 ]
79 0 0.22347 1.93729 -425.17876 [6846.00000 30.00000 -180.00000 -180.00000 -150.00000 50.00000 -60.00000 10.00000 -60.00000 120.00000 ]
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81 0 0.52269 2.04174 -425.14087 [6845.00000 30.00000 -180.00000 -180.00000 -180.00000 10.00000 -70.00000 0.00000 -60.00000 130.00000 ]
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97 0 0.25541 1.92677 -424.80659 [6846.00000 30.00000 -180.00000 -180.00000 60.00000 -110.00000 -60.00000 20.00000 -60.00000 110.00000 ]
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99 0 0.22972 1.93871 -424.75029 [6846.00000 30.00000 -180.00000 -180.00000 40.00000 -130.00000 -70.00000 20.00000 -60.00000 110.00000 ]
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101 0 0.24485 1.93424 -424.68800 [6846.00000 30.00000 -180.00000 -180.00000 70.00000 -180.00000 -60.00000 20.00000 -60.00000 110.00000 ]
102 0 0.83458 1.75141 -424.63656 [6846.00000 30.00000 170.00000 170.00000 -70.00000 -180.00000 120.00000 10.00000 -60.00000 110.00000 ]
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104 0 0.23394 1.94037 -424.58165 [6846.00000 30.00000 -180.00000 -180.00000 90.00000 -180.00000 -70.00000 20.00000 -60.00000 110.00000 ]
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112 0 0.43834 2.04938 -424.53884 [6853.00000 30.00000 -180.00000 -180.00000 120.00000 -180.00000 -60.00000 20.00000 -60.00000 110.00000 ]
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buran

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#4
Aug-29-2018, 08:17 PM (This post was last modified: Aug-29-2018, 08:17 PM by buran.)
something like this
names = ['ligand1.inp','ligand2.inp','ligand3.inp','ligand4.inp']
for i, name in enumerate(names, start=1):
    with open('CONFIG.inp') as cf, open(f'COFIG{i}.inp', 'w') as f:
        for j, line in enumerate(cf, start=1):
            if j == 3:
                line = line.replace('ligand.inp', name)
            f.write(line)
if you show what ligand names look like it may be possible to avoid explicit list of names. Although your approach - reading the full file in memory then replace ligand.inp is perfectly OK if you are sure there is only one occurrence of ligand.inp in the file, I preferred to make sure the replacement is only in line 3.

Also note I don't know if there is better approach from business point of view to achieve your ultimate goal. My example is what you asked for - create multiple config files
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Gribouillis

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#5
Aug-29-2018, 08:30 PM
You could simply use Python's format method
template = """\
TEMPOP /home/c.blanes/FlexAID2/FlexAID_Output
PDBNAM /home/c.blanes/FlexAID2/Processed_files/receptor.inp.pdb
INPLIG /home/c.blanes/FlexAID2/Processed_files/{ligand}.inp
RNGOPT LOCCLF /home/c.blanes/FlexAID2/Binding_sites/binding_site.pdb
OPTIMZ 9999 - -1
OPTIMZ 9999 - 0
OPTIMZ 9999 - 1
OPTIMZ 9999 - 2
OPTIMZ 9999 - 3
OPTIMZ 9999 - 4
...
"""

names = ['foo', 'bar', 'baz']

for idx, name in enumerate(names, 1):
    with open('CONFIG{}.inp'.format(idx), 'w') as outfile:
        outfile.write(template.format(ligand=name))
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clarablanes
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Posts: 28
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#6
Aug-30-2018, 08:55 AM (This post was last modified: Aug-30-2018, 09:24 AM by clarablanes.)
(Aug-29-2018, 08:17 PM)buran Wrote: something like this
names = ['ligand1.inp','ligand2.inp','ligand3.inp','ligand4.inp']
for i, name in enumerate(names, start=1):
    with open('CONFIG.inp') as cf, open(f'COFIG{i}.inp', 'w') as f:
        for j, line in enumerate(cf, start=1):
            if j == 3:
                line = line.replace('ligand.inp', name)
            f.write(line)
if you show what ligand names look like it may be possible to avoid explicit list of names. Although your approach - reading the full file in memory then replace ligand.inp is perfectly OK if you are sure there is only one occurrence of ligand.inp in the file, I preferred to make sure the replacement is only in line 3.

Also note I don't know if there is better approach from business point of view to achieve your ultimate goal. My example is what you asked for - create multiple config files

Dear buran, I'm trying this code but it keeps giving me the following error:

File "CONFIG_iterator.py", line 3
with open('CONFIG.inp') as cf, open(f'CONFIG{i}.inp', 'w') as f:
SyntaxError: invalid syntax
(Aug-29-2018, 08:30 PM)Gribouillis Wrote: You could simply use Python's format method
template = """\
TEMPOP /home/c.blanes/FlexAID2/FlexAID_Output
PDBNAM /home/c.blanes/FlexAID2/Processed_files/receptor.inp.pdb
INPLIG /home/c.blanes/FlexAID2/Processed_files/{ligand}.inp
RNGOPT LOCCLF /home/c.blanes/FlexAID2/Binding_sites/binding_site.pdb
OPTIMZ 9999 - -1
OPTIMZ 9999 - 0
OPTIMZ 9999 - 1
OPTIMZ 9999 - 2
OPTIMZ 9999 - 3
OPTIMZ 9999 - 4
...
"""

names = ['foo', 'bar', 'baz']

for idx, name in enumerate(names, 1):
    with open('CONFIG{}.inp'.format(idx), 'w') as outfile:
        outfile.write(template.format(ligand=name))

Dear Gribouillis,
I am just beginning with Python to be applied to science so I am very lost. Should I add your code to the CONFIG file?. If I do this, how can execute it?. I mean, if I write your code in a different document, I save it as a .py and I execute de CONFIG file to be able to obtain the other CONFIGS. But, if I add the code to the bottom of the CONFIG file, I don't know how to execute it.
Thank you for your patient...
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buran

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#7
Aug-30-2018, 09:25 AM
Which version of python? f-string works in 3.6+
If you can't explain it to a six year old, you don't understand it yourself, Albert Einstein
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clarablanes
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#8
Aug-30-2018, 09:32 AM
(Aug-30-2018, 09:25 AM)buran Wrote: Which version of python? f-string works in 3.6+

It is Python 2.6.6
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buran

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#9
Aug-30-2018, 09:40 AM
Change f'COFIG{i}.inp' to 'COFIG{}.inp'.format(i)
But it is recomended to switch to python 3
Official suport for python 2 ends 01.01.2020. And you are not using even latest python 2.
If you can't explain it to a six year old, you don't understand it yourself, Albert Einstein
How to Ask Questions The Smart Way: link and another link
Create MCV example
Debug small programs

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Gribouillis

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#10
Aug-30-2018, 09:51 AM
Yes, upgrade to python 3 before you do anything. Here is a complete code for python 3. You only need to save it in the same directory as CONFIG.inp and run it (you can replace the 'names' list by your own names list)

import io

with open('CONFIG.inp') as infile:
    lines = infile.readlines()
lines[2] = lines[2].replace('ligand.inp', '{ligand}.inp')

with io.StringIO() as f:
    f.writelines(lines)
    template = f.getvalue()

names = ['foo', 'bar', 'baz']

for idx, name in enumerate(names, 1):
    with open('CONFIG{}.inp'.format(idx), 'w') as outfile:
        outfile.write(template.format(ligand=name))
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