Re: [cclib-devel] makeopenbabel

[Karol M. L. <kar...@gm...>]

The problem originates from NumPy dtypes, which came with the new version in 
numpy. If you print out type(atomno) in that code, for some reason you'll get 
<type 'numpy.int32'> instead of <type 'int'>.

I see two solutions - python-openbabel needs to support dtypes (ouch) or 
convert atomno to an int just in case. I did the second in the last commit. 
It should work now (although remember that you probably want to pass 
atomcoords[0] since it is a 3D array now).

Cheers,
Karol

On Monday 07 September 2009 10:23:29 Noel O'Boyle wrote:
> I'm afraid I haven't looked at this code for a long time, and it isn't
> covered by any tests.
>
> The OB API will not have changed, so it must be due to some internal
> cclib changes. The specific problem appears to be that atomno is not a
> Python integer in the code below (or so it seems to me). I will look
> into this this evening....
>
> - Noel
>
> 2009/9/5 Adam Tenderholt <a-t...@st...>:
> > Hi Noel (and others),
> >
> > The makeopenbabel bridge function doesn't seem to be working for me.
> > I'm currently using OpenBabel version 2.2.1b3 on Fedora Core 11 with
> > cclib-0.8, but I was also having this problem in cclib-0.91.
> >
> > The error is:
> >
> >   File "qmforge.py", line 252, in fileOpen
> >     self.open(str(filename))
> >   File "qmforge.py", line 168, in open
> >     self.popWidget.setData(data)
> >   File "/home/adam/QMForge-2.1/src/popwidget.py", line 101, in setData
> >     self.glWidget.setMolecule(data.atomcoords[0],data.atomnos)
> >   File "/home/adam/QMForge-2.1/src/glwidget.py", line 140, in
> > setMolecule
> >     self.obmol = makeopenbabel(coords,aonums)
> >   File "/usr/lib/python2.6/site-packages/cclib/bridge/
> > cclib2openbabel.py", line 28, in makeopenbabel
> >     obatom.SetAtomicNum(atomno)
> > TypeError: in method 'OBAtom_SetAtomicNum', argument 2 of type 'int'
> >
> > Any thoughts? I can dig through the code, but I figured I'd write in
> > case you know what needs to be changed off the  top of your head(s).
> >
> > Thanks,
> >
> > Adam

-- 
written by Karol Langner
Mon Sep  7 10:54:26 CEST 2009