Re: [cclib-users] Problem with installation

[Noel O'B. <bao...@gm...>]

On 30/11/2007, Jean-Didier Mar=E9chal <jea...@ua...> wrote:
> Well, I see that I could have done in four lines what I managed with
> twice more.
>
> One question though, is there any possibility to collect the root from
> the gaussian output?

I'm afraid not. This seems to be true for both cclib and openbabel.

> I'd like to generate an input file recovering the optimized geometry and
> the keywords.
>
> All the best,
> JD
>
>
> On Fri, 2007-11-30 at 10:08 +0000, Noel O'Boyle wrote:
> > On 29/11/2007, Jean-Didier Mar=E9chal <jea...@ua...> wrot=
e:
> > > > Glad to hear. Let us know if you have any problems; also, we are
> > > > interested to know what you are using cclib for...
> > >
> > > I have different  projects I hope cclib to help me with (Well, once
I'll
> > > have understood how to use it (:-)). To get use to your module, the
> > > first thing I want to do is to generate gaussian inputs extracting th=
e
> > > optimized geometry from a previous gaussian output. I know that sound=
s
> > > ruin but truth is that I work on systems with a lot of conformations
and
> > > which size oblige me to optimize in gas phase. So, I want to perform
> > > post calculations separately afterward. Scripting the generation of
this
> > > inputs will be of great help for me.
> > >
> > > Thanks a lot,
> > >
> > > JD
> >
> > Although cclib can help you with this, our functionality overlaps a
> > little bit with another Python library, OpenBabel.
> >
> > Here is an example of reading the output file with cclib, and creating
> > a Gaussian input file with OpenBabel:
> > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> > import pybel
> >
> > from cclib.parser import ccopen
> > from cclib.bridge import makeopenbabel
> >
> > t =3D ccopen("dvb_gopt.out")
> > d =3D t.parse()
> >
> > obmol =3D makeopenbabel(d.atomcoords[-1], d.atomnos, d.charge, d.mult)
> > mol =3D pybel.Molecule(obmol)
> > print mol.write("gau")
> > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> >
> > However, OpenBabel can also read Gaussian output files, so in this
> > case it's easier just to do:
> > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> > import pybel
> >
> > mol =3D pybel.readfile("g03", "dvb_gopt.out").next()
> > print mol.write("gau")
> > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> >
> > cclib has the advantage of giving you access to lots of other
> > information, it can read output files from more computational
> > chemistry packages, and it provides implementations of several
> > computational chemistry algorithms. OpenBabel can read and write a
> > very large number of molecular file formats, and provides access to
> > several algorithms for manipulating chemical structures.
> >
> > It's easy to interconvert data from one to the other, so you can
> > easily use them both.
> >
> > Noel
>
>