Hi Filip,
OBMol has a Separate method, which does exactly what you'd like.
http://openbabel.org/dev-api/classOpenBabel_1_1OBMol.shtml#a1e5c6955a32c0ec2317a8de12ab7ba5a
import pybel
> mol = pybel.readfile('mol2', 'ligand.mol2').next()
> for m in mol.OBMol.Separate():
> print m
Note that m is an OBMol object, so to get pybel molecule you need to
initiate it via Molecule class:
for m in mol.OBMol.Separate():
> print pybel.Molecule(m)
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2015-11-10 16:59 GMT+01:00 Filip Stefaniak <stefan...@gmail.com>:
> Hi,
> I have a mol2 file:
> https://gist.github.com/filipsPL/0b936f4d416bdc45ebea
>
> There are three apparently separate molecules inside. But I'm not able
> to separate them. obabel -m doesn't solve the problem.
>
> I've tried to do it in python with pybel, but I don't know how to
> exactly code it (it is not the simple case as described here:
>
> https://openbabel.org/docs/dev/UseTheLibrary/PythonExamples.html#split-an-sdf-file-using-the-molecule-titles
> )
>
> In pybel I can see that the molecules are actually separated somehow:
>
> from pybel import *
> mol = readfile("mol2", "ligand.mol2").next()
> print mol
>
> result is:
> [Rh](N)(N)(N)(N)(N)N.[Rh](N)(N)(N)(N)(N)N.[Rh](N)(N)(N)(N)(N)N
>
> so my question is: how to separate this mol2 file into separate
> components? python or shell methods are acceptable.
>
> thank you for any tips,
> Filip
>
>
> --
> Filip Stefaniak
> Uptime: 13185 dni 16 godzin
> W lodówce ma 8.8stC, na działce w sadku 12.2stC
>
>
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