Re: [OpenBabel-Devel] [Open Babel] calculate bonding between atoms (connectivity matrix) given their Cartesian coordinates

[Tim V. <tim...@gm...>]

On Wed, Apr 30, 2008 at 1:33 AM, Rahul Nabar <rp...@gm...> wrote:
> On Tue, Apr 29, 2008 at 12:30 PM, Noel O'Boyle <bao...@gm...> wrote:
>  > The Python API *is* the OpenBabel API. However, you are probably
>  >  confused by Pybel, which is a layer on top of the Python API.
>  >  OBMol::ConnectTheDots()  needs an OBMol to begin with. You can access
>  >  the OBMol behind a Pybel Molecule as follows:
>  >
>  >  import pybel
>  >  mol = pybel.readfile("xyz", "myfile.xyz").next()
>  >  obmol = mol.OBMol
>  >  obmol.ConnectTheDots()
>  >  obmol.PerceiveBondOrders()
>
>  Thanks Noel. I did that now. But there is no apparent output. I
>  suspect the obmol data-structure already has the information I need
>  but how do I manage to query it? My purpose is pretty straightforward:
>  Find and print all bonds (and perhaps bond-lengths) in this set of
>  atoms. I'm sorry if this is elementary and I hat to bother you guys
>  for something that might be easily understood from a tutorial perhaps?
>  Are there any of this sort?
>
>  I looked up http://openbabel.org/wiki/Python but most of the examples
>  seem to be oriented towards setting up the molecules rather than
>  importing and querying a preexisting .xyz file.

Check the "Using iterators" part:

Once you have the mol, you can do

for bond in openbabel.OBMolBondIter(mol):
    print "bond ", bond.GetIdx(), ": length = ", bond.GetLength()

Tim