[OpenBabel-scripting] [openbabel-scripting] [OpenBabel & Pybel] Atomic Types Automatically Changed

[laurent.personal <lau...@gm...>]

Hello

I am using openbabel for a project (convert molec in different formats ...).
Besides, I have to do some scripts in order to modify some molecules of my
DB. I use pybel to do this.

My problem is that pybel automatically changes some atomic types in molecule
of my DB ... and it shouldn't do it. It replaces some carbons (C2 or others)
by the type C.cat. The last is for the guanidium group but I don't have a
such group in my DB.

I did a basic script in order to verify this :

[quote]
#!/usr/bin/python
import openbabel
import pybel
for mol in pybel.readfile("mol2", "molec_test.mol2"):
	outputfile = pybel.Outputfile("mol2", "molec_pybel.mol2", overwrite=True)
	outputfile.write(mol)
	outputfile.close()
[/quote]

The input/output structure files are uploaded here.
http://www.nabble.com/file/p22574797/molec_pybel.mol2 molec_pybel.mol2 
http://www.nabble.com/file/p22574797/molec_test.mol2 molec_test.mol2 

Can we read a molecule with pybel with an option "read only the mol2 file
without changing anything" ?

TIA for your answer,

Cheers,

Laurent
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