Hi,

If you're working on code to create z-matricies, then there is code in the CCP1GUI that might be of interest to you. You can find the CCP1GUI here:

http://sourceforge.net/projects/ccp1gui/

The main code to generate the zmatrix is the autoz routine here:

http://ccp1gui.cvs.sourceforge.net/viewvc/ccp1gui/ccp1gui/objects/zmatrix.py?view=markup

I know that Paul Sherwood (who wrote it) sent a lot of time sorting out various corner cases and it's pretty robust for even quite large molecules.

Hopefully this will give you some useful pointers and potentially working code if you're developing something similar yourself.

I'm sure that a zmatrix utility that could be used and shared by a variety of codes would be a really welcome addition to the community.

Best wishes,

Jens



On 7 April 2014 21:47, Rick Muller <rpmuller@gmail.com> wrote:
I have some python code that I'll start to stress test and maybe commit to the PyQuante2 repository sometime real soon. There's probably nothing valuable in the code right now, but maybe after the debugging process I'll know enough to help out with the process. 

Guess I should figure out how to build Avogadro...



On Mon, Apr 7, 2014 at 2:45 PM, Marcus D. Hanwell <marcus.hanwell@kitware.com> wrote:
Rick,

It is the former (to/from Cartesian, corner cases), it was also in
progress as I moved between positions and I never got around to it. I
would welcome input on robust implementations, and can handle the
Avogadro side. I would gladly update the Avogadro 1.1 version, and am
eager to port this to Avogadro 2.

Thanks,

Marcus

On Mon, Apr 7, 2014 at 4:36 PM, Rick Muller <rpmuller@gmail.com> wrote:
> Marcus,
>
> Thanks for the reply. What's the probably getting the zmatrix robust? Is it
> the conversion to cartesian coordinates, or the interaction with the rest of
> Avogadro? I might be able to help with the former, but probably not the
> latter.
>
> Rick
>
>
> On Mon, Apr 7, 2014 at 10:51 AM, Marcus D. Hanwell
> <marcus.hanwell@kitware.com> wrote:
>>
>> Hi Rick,
>>
>> On Mon, Apr 7, 2014 at 12:46 PM, Rick Muller <rpmuller@gmail.com> wrote:
>> > I'm interested in using the Z-matrix tool in Avogadro. I'm currently
>> > using
>> > Avogadro v1.1.1, and the tool does not appear in the toolbar or the
>> > menus.
>> > Can I enable it, or do I need to download a newer build to get it?
>> >
>> It is not enabled by default because I never got it working in a
>> robust way. It is enabled by a build flag, I could enable it in the
>> next release builds by default (and would like to revisit this as it
>> would be great to get working).
>>
>> Thanks,
>>
>> Marcus
>>
>>
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>
>
>
> --
> Rick Muller
> rpmuller@gmail.com
> 505-750-7557
>
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rpmuller@gmail.com
505-750-7557

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