Hello Fredrik,
I must admit that OBMol.Separate() usually causes a segfault for me
too, but I've never gotten around to reporting the bug. I've just
tested it a little bit. It seems that separating a methane is fine,
but separating ethane causes a segault.
>>> import pybel
>>> pybel.readstring("smi", "C").OBMol.Separate()
(<openbabel.OBMol; proxy of <Swig Object of type 'OpenBabel::OBMol *' at 0x12887
78> >,)
>>> pybel.readstring("smi", "CC").OBMol.Separate()
# It's a segger
I'll file a bug.
Noel
2008/12/9 Noel O'Boyle <bao...@gm...>:
> ---------- Forwarded message ----------
> From: <fre...@gm...>
> Date: 2008/12/9
> Subject: Bus error using OBMol.Separate
> To: Cinfony <ci...@go...>
>
> Hi!
>
> I'm trying to use pybel from cinfony in order to find the different R-
> groups on a general scaffold. I have managed to delete the scaffold,
> leaving the R-groups as disconnected fragments in the molecule.
> However, when I tried to separate the fragments I ran into a bus
> error. The error appears every time I try to do .Separate() on a OBMol
> such as in the following code:
>
> from cinfony import pybel
>
> mol = pybel.readstring("smi", "[NH3+]c1ccccc1.[Cl-]")
> print "Initial molecule: ", mol.write("smi")
> mol.OBMol.StripSalts(2)
> print "After StripSalts(2): ", mol.write("smi")
> mol = pybel.readstring("smi", "[NH3+]c1ccccc1.[Cl-]")
> print "Back again: ", mol.write("smi")
> temp = mol.OBMol.Separate()
> for tempMol in temp:
> print "Fragment: ", tempMol.write("smi")
>
> Do you know what can be the problem, or should I rather post the
> question with OpenBabel?
>
> I'm running cinfony on an Intel Mac with 10.5.5 and Python2.5 from
> fink and OpenBabel 2.2.0
>
> Kind regards,
> Fredrik Wallner
>
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