Re: [OpenBabel-scripting] get canonical atom ordering

[Geoffrey H. <ge...@ge...>]

On Mar 21, 2008, at 2:05 PM, TJ O'Donnell wrote:

> Is it possible to get the canonical atom re-ordering,
> say as an int vector, after conversion to canonical smiles?

As a matter of fact, yes. The current SVN trunk has this feature --  
after conversion to canonical SMILES, the ordering is available as an  
OBPairData called "Canonical Atom Order"

For a C++ example, of this, check out tools/obfragment.cpp.

This should be accessible from Python directly, although I defer to  
Noel on the Pybel syntax for this.

Cheers,
-Geoff