Question: How to convert file from one format to another one using script?
0
gravatar for alsalisbeth
5.3 years ago by
alsalisbeth10
United Kingdom
alsalisbeth10 wrote:

 

Hello,

I am trying to convert my files (several thousands) in one format to another format using pymol script.
I would like them to be saved in the same folder, i.e.: ~/myFolder/file.pdb --------> ~/myFolder/file.mol

My script:

import os
from pymol import cmd
myDir = '/folderWithFilesToConvert'
print(myDir)
for filename in os.listdir(myDir):
    filename = os.path.splitext(filename)[0]
    print('New file name is', filename)
    if '_' in filename:
        print filename
        cmd.h_add
        #till the line below everything works fine
        cmd.save(filename.mol)

What is wrong? Console output:

​AttributeError: 'str' object has no attribute 'mol'

Thanks)

Some update. I modified code like that (thanks to @Felix_Sim):

import os
from pymol import cmd
myDir = '/Users/AnnaLisa/Desktop/FRAG'
print(myDir)
for filename in os.listdir(myDir):
    filename = os.path.splitext(filename)[0]
    print('New file name is', filename)
    if '_' in filename:
        print filename
        cmd.h_add
        cmd.save(filename + '.mol')


If I convert file via command line, I get (inside the file)

untitled
  ChemPy            3D                             0

  0  0  0  0  1  0  0  0  0  0999 V2000
M  END

If I convert file manually in PyMol via GUI (inside the file):

 

017
  ChemPy            3D                             0

 75 78  0  0  1  0  0  0  0  0999 V2000
   21.0910   28.7350   14.0670 N   0  0  0  0  0  0  0  0  0  0  0  0
   20.5400   27.5660   14.5190 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.1880   27.3330   14.2100 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.6260   26.1600   14.6750 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.3840   25.2160   15.3450 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.7110   25.4230   15.7210 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.2630   26.6460   15.2920 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.4500   23.7990   15.9930 S   0  0  0  0  0  0  0  0  0  0  0  0
   17.2570   23.4660   15.0690 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.4810   22.6380   16.2400 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.7940   24.1570   17.5840 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.7830   24.4260   18.6320 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.4000   23.8560   20.0060 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.3680   22.3520   19.8930 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.5030   24.3350   20.9200 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.5050   24.8940   17.5640 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.3940   23.9640   18.1580 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2320   24.7640   18.4090 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.0130   22.8280   17.1770 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.1320   21.9410   17.8870 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.4880   20.6750   18.2230 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5870   20.0860   17.9550 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.4210   20.0660   18.9520 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.5050   18.6020   19.1020 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8390   18.3510   20.4850 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4120   18.4700   20.2840 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.2200   17.9780   18.9680 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2970   18.8060   18.2910 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.0420   19.4440   17.2410 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1310   18.4320   16.8180 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.4700   17.8870   18.2130 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2940   23.2850   15.8960 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5490   21.7500   14.8810 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1480   20.6610   14.0690 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1190   19.9330   13.3910 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.4710   20.2400   13.5170 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8600   21.3260   14.3140 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9020   22.1140   14.9680 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.6130   28.0420   13.6330 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.5740   25.9760   14.5120 H   0  0  0  0  0  0  0  0  0  0  0  0
   21.2720   24.7020   16.2970 H   0  0  0  0  0  0  0  0  0  0  0  0
   22.2800   26.8840   15.5680 H   0  0  0  0  0  0  0  0  0  0  0  0
   22.0490   28.7830   14.3490 H   0  0  0  0  0  0  0  0  0  0  0  0
   21.0350   28.7660   13.0690 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.4150   24.1730   20.3800 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.7770   23.5030   19.0810 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.5430   24.2180   18.7710 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.9530   22.3620   16.8450 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.2230   22.2690   18.1430 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.5380   18.2740   18.9140 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.8250   16.9550   19.0470 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.9200   16.9040   18.0070 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.8080   22.3050   15.4380 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.1040   20.4000   13.9780 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.8190   19.1140   12.7540 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.2140   19.6470   13.0050 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.9090   21.5580   14.4250 H   0  0  0  0  0  0  0  0  0  0  0  0
   19.7360   23.9690   18.3270 H   0  0  0  0  0  0  0  0  0  0  0  0
   18.8860   25.5170   18.7320 H   0  0  0  0  0  0  0  0  0  0  0  0
   18.0960   21.9160   20.8660 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.6240   22.0570   19.1380 H   0  0  0  0  0  0  0  0  0  0  0  0
   19.3610   21.9860   19.5930 H   0  0  0  0  0  0  0  0  0  0  0  0
   19.3160   23.9730   21.9420 H   0  0  0  0  0  0  0  0  0  0  0  0
   20.4690   23.9460   20.5640 H   0  0  0  0  0  0  0  0  0  0  0  0
   19.5280   25.4350   20.9190 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.5890   25.8090   18.1690 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.2480   25.1680   16.5300 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.0920   17.3470   20.8570 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.1870   19.0930   21.2190 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.3860   19.6860   16.3920 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.4990   20.3780   17.6010 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.7670   17.6610   16.1230 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.9880   18.8970   16.3090 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.3760   23.8160   16.1870 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.9690   23.9530   15.3410 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1 43  1  0  0  0  0
  1 44  1  0  0  0  0
  2  3  2  0  0  0  0
  2  7  1  0  0  0  0
  3  4  1  0  0  0  0
  3 39  1  0  0  0  0
  4  5  2  0  0  0  0
  4 40  1  0  0  0  0
  5  6  1  0  0  0  0
  5  8  1  0  0  0  0
  6  7  2  0  0  0  0
  6 41  1  0  0  0  0
  7 42  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  2  0  0  0  0
  8 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 16  1  0  0  0  0
 12 13  1  0  0  0  0
 12 58  1  0  0  0  0
 12 59  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 13 45  1  0  0  0  0
 14 60  1  0  0  0  0
 14 61  1  0  0  0  0
 14 62  1  0  0  0  0
 15 63  1  0  0  0  0
 15 64  1  0  0  0  0
 15 65  1  0  0  0  0
 16 17  1  0  0  0  0
 16 66  1  0  0  0  0
 16 67  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 17 46  1  0  0  0  0
 18 47  1  0  0  0  0
 19 20  1  0  0  0  0
 19 32  1  0  0  0  0
 19 48  1  0  0  0  0
 20 21  1  0  0  0  0
 20 49  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 31  1  0  0  0  0
 24 50  1  0  0  0  0
 25 26  1  0  0  0  0
 25 68  1  0  0  0  0
 25 69  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 31  1  0  0  0  0
 27 51  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 29 70  1  0  0  0  0
 29 71  1  0  0  0  0
 30 31  1  0  0  0  0
 30 72  1  0  0  0  0
 30 73  1  0  0  0  0
 31 52  1  0  0  0  0
 32 38  1  0  0  0  0
 32 74  1  0  0  0  0
 32 75  1  0  0  0  0
 33 34  2  0  0  0  0
 33 38  1  0  0  0  0
 33 53  1  0  0  0  0
 34 35  1  0  0  0  0
 34 54  1  0  0  0  0
 35 36  2  0  0  0  0
 35 55  1  0  0  0  0
 36 37  1  0  0  0  0
 36 56  1  0  0  0  0
 37 38  2  0  0  0  0
 37 57  1  0  0  0  0
M  END


Original file

 

 

script pymol file format python • 4.3k views
ADD COMMENTlink modified 3.0 years ago by Biostar ♦♦ 20 • written 5.3 years ago by alsalisbeth10

What happen if you add quotes?

cmd.save("filename.mol")
ADD REPLYlink modified 11 months ago by RamRS30k • written 5.3 years ago by Nicola Casiraghi450

My first guess would be that you need to define a variable with the new file name.

new_file = filename + '.mol'
cmd.save(new_file)

Or you do this in one step...

cmd.save(filename + '.mol')

I was trying to attempt this but I do not have a file that gets passed the cmd.h_add

ADD REPLYlink modified 11 months ago by RamRS30k • written 5.3 years ago by Felix_Sim250

It started working. But there is still a problem, probably because '.mol' is in ' ' it doesn't really convert the file, but adds extension to file name. I've tried already to convert one of my files manually and it worked, while in this case file is not converted (same file inside, just file name is different).

cmd.h_add simply adds hydrogens that may be lost etc. This line in not really important for the case, so you can comment it.

ADD REPLYlink modified 11 months ago by RamRS30k • written 5.3 years ago by alsalisbeth10

Could you update your question and add a sample input and output? I am unsure what I am supposed to be seeing when you say it does not convert the files?!

ADD REPLYlink written 5.3 years ago by Felix_Sim250

I've updated

ADD REPLYlink written 5.3 years ago by alsalisbeth10
1

Maybe you want to add the full code to your answer below. This will allow others in the future to quickly see the solution without trying for themselves ;)

ADD REPLYlink written 5.3 years ago by Felix_Sim250
2
gravatar for alsalisbeth
5.3 years ago by
alsalisbeth10
United Kingdom
alsalisbeth10 wrote:

I found the mistake, I needed to add cmd.load(myFile) line. After this addition everything works properly. Thanks to everyone =)

ADD COMMENTlink modified 11 months ago by RamRS30k • written 5.3 years ago by alsalisbeth10
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