Re: [cclib-users] z-matrix in Gaussian

[Adam T. <ate...@gm...>]

Hi Yaron,

cclib doesn't directly support parsing internal coordinates. However, you
can use openbabel to save using an internal coordinate system:

>>> from cclib.parser import ccopen
>>> import openbabel
>>> parser = ccopen("dvb_sp.log")
>>> data = parser.parse()
>>> from cclib.bridge import makeopenbabel
>>> mol = makeopenbabel(data.atomcoords[0], data.atomnos)
>>> obconv = openbabel.OBConversion()
>>> obconv.SetInAndOutFormats("XYZ", "FH")
>>> obconv.WriteFile(mol, "test.fh")

--
20
C   1
C   1 1.421
C   2 1.402  1 120.857
C   3 1.422  2 121.354  1   0.0
C   4 1.421  3 117.789  2   0.0
H   2 1.098  1 119.765  3 180.0
H   3 1.099  2 119.629  1 180.0
H   5 1.098  4 119.765  3 180.0
C   4 1.498  3 119.172  2 180.0
C   9 1.344  4 126.593  3 180.0
H  10 1.096  9 122.647  4   0.0
H   9 1.100  4 114.434  3   0.0
H  10 1.096  9 121.228  4 180.0
C   1 1.498  2 123.039  3 180.0
H  14 1.100  1 114.434  2 180.0
C  14 1.344  1 126.593  2   0.0
H  16 1.096 14 122.647  1   0.0
H  16 1.096 14 121.228  1 180.0
C   5 1.402  4 120.857  3   0.0
H  19 1.099  5 119.629  4 180.0
--

You may also want to see the list of formats supported by openbabel in case
you need something slightly different:
http://openbabel.org/docs/2.3.1/FileFormats/Overview.html

Hope this helps,

Adam



On Tue, Feb 19, 2013 at 10:48 AM, Yaron Pshetitsky <
yar...@li...> wrote:

> Dear cclib community,
> I'm trying to get the z-matrix (internal coordinates) from a Gaussian
> output file using cclib.
> I know that Gaussian do converts any internal or XYZ coordinates in the
> input to it's format so one can get internal coordinates from it, even if
> the input file was in cartesian coordinates.
> *Can cclib output the internal coordinates?*
>
> Thanks very much,
> Yaron
>
>
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