Re: [OpenBabel-Devel] Perceive bonds with obabel

2013-02-13 Thread Marcus D. Hanwell
On Tue, Feb 12, 2013 at 12:06 PM, David Lonie david.lo...@kitware.com wrote: On Tue, Feb 12, 2013 at 12:00 PM, Noel O'Boyle baoille...@gmail.com wrote: Try the xyz format. That was our next guess, just wanted to make sure that I wasn't overlooking anything more straightforward. That is a

[OpenBabel-Devel] Perceive bonds with obabel

2013-02-12 Thread David Lonie
Hi list, Is there a way to perceive bonds in a collection of atoms with obabel? I looked though the documentation, but don't see an explicit operation for this. We thought maybe converting cml -- cml might trigger bond perception, but this doesn't seem to work either. Are there any

Re: [OpenBabel-Devel] Perceive bonds with obabel

2013-02-12 Thread Noel O'Boyle
See http://baoilleach.blogspot.co.uk/2010/04/plug-cclib-into-avogadro.html On 12 February 2013 16:26, David Lonie david.lo...@kitware.com wrote: Hi list, Is there a way to perceive bonds in a collection of atoms with obabel? I looked though the documentation, but don't see an explicit

Re: [OpenBabel-Devel] Perceive bonds with obabel

2013-02-12 Thread Noel O'Boyle
Apologies. The question was about obabel, not the API... On 12 February 2013 16:52, Noel O'Boyle baoille...@gmail.com wrote: See http://baoilleach.blogspot.co.uk/2010/04/plug-cclib-into-avogadro.html On 12 February 2013 16:26, David Lonie david.lo...@kitware.com wrote: Hi list, Is there a

Re: [OpenBabel-Devel] Perceive bonds with obabel

2013-02-12 Thread Noel O'Boyle
Try the xyz format. On 12 February 2013 16:26, David Lonie david.lo...@kitware.com wrote: Hi list, Is there a way to perceive bonds in a collection of atoms with obabel? I looked though the documentation, but don't see an explicit operation for this. We thought maybe converting cml -- cml

Re: [OpenBabel-Devel] Perceive bonds with obabel

2013-02-12 Thread David Lonie
On Tue, Feb 12, 2013 at 12:00 PM, Noel O'Boyle baoille...@gmail.com wrote: Try the xyz format. That was our next guess, just wanted to make sure that I wasn't overlooking anything more straightforward. -- Free Next-Gen

Re: [OpenBabel-Devel] Perceive bonds with obabel

2013-02-12 Thread Geoffrey Hutchison
That was our next guess, just wanted to make sure that I wasn't overlooking anything more straightforward. No, CML has support for bonds, so cml - cml won’t perceive new bonds. -Geoff -- Free Next-Gen Firewall