[Open Babel] splitting molecule file - the hard case
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
--
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] splitting molecule file - the hard case
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 :
> 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
>
>
> --
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
--
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] splitting molecule file - the hard case
Hi Maciek,
Maciek Wójcikowski pisze:
> 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)
Thanks for that tip. I will try it.
best regards,
Filip
--
Filip Stefaniak
Uptime: 13079 dni 19 godzin
W lodówce ma 10.8stC, na działce w sadku 16.7stC
--
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] splitting molecule file - the hard case
FYI The obabel -m option you've used separates molecules in multi-mol2 file
- the molecules must already be in separate molecule blocks.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2015-11-10 19:54 GMT+01:00 Filip Stefaniak :
> Hi Maciek,
>
> Maciek Wójcikowski pisze:
> > 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)
>
> Thanks for that tip. I will try it.
>
> best regards,
> Filip
>
>
> --
> Filip Stefaniak
> Uptime: 13079 dni 19 godzin
> W lodówce ma 10.8stC, na działce w sadku 16.7stC
>
>
> --
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
--
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] splitting molecule file - the hard case
On 11/10/2015 05:23 PM, Maciek Wójcikowski wrote:
> 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)
>
>
Thanks once more. Just for future reference, here is the full script for
splitting molecule and saving it to separate files:
https://gist.github.com/filipsPL/5c810a452559a7fcc99e
import pybel
from openbabel import *
mol = pybel.readfile('mol2', 'ligand.mol2').next()
separated = mol.OBMol.Separate()
def writeOut( theConformer, outputPath ):
myConversion = OBConversion()
outputFormat = myConversion.FormatFromExt( outputPath )
myConversion.SetOutFormat( outputFormat )
myConversion.WriteFile( theConformer, outputPath )
i = 0
for singlemol in separated:
i+=1
print "Writing part %i" % (i)
writeOut(singlemol, "output-%i.mol2" %(i) )
bests,
Filip
--
Filip Stefaniak
Uptime: 13187 dni 13 godzin
W lodówce ma 9.7stC, na działce w sadku 11.2stC
--
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
