Re: [Open Babel] SMILES to PDB conversion

[Miguel H. <mt...@mt...>]

PeterMR wrote:
> This is a fundamental problem with formats such as SMILES and PDB -
> they
>  can only hold a limited range of information - i.e. they are
> non-extensible. Both can hold atoms and bonds, but SMILES cannot hold
> coordinates and PDB cannot hold bond orders.

While the PDB spec makes no provisions for multiple-bonds, there is a
(quasi-standard?) extension to support this that is used by RasMol/Chime
... and Jmol. Perhaps other packages support it too ... I don't know.

The extension is this:
If a CONECT record has more than one entry (consecutively) for the same
pair of atoms, then that is interpreted as multiple bond ... two entries
means double-bond, three entries means triple-bond.

For more a little more information on this you can see:
  http://www.umass.edu/microbio/rasmol/faq_em.htm#doublebonds


Miguel