[Jmol-developers] Covalent bonding radius + autobonding

[Miguel <mi...@jm...>]

This problem pertains to autobonding and the 'covalent radius' of the
noble gases.

--

Jmol must perform 'autobonding' when no bond connectivity data is present
in the file ... .xyz for example.

The algorithm that is currently used is derived from open babel.

 distance <= covalentRadius(atom1) + covalentRadius(atom2) + 0.45 // bond
tolerance
AND
 distance >= 0.4 // minimum bonding distance

I know that open babel makes other checks to determine whether or not a
bond is appropriate. But Jmol does not currently do any other checks ...
if two atoms are close enough (but not too close) then they will bond.

The table of covalent radii is taken directly from open babel.

I observe that the noble gases all have non-zero bonding radii. This means
that Jmol will bond these things together if they are close enough. That
seems like a problem to me.

Q: Why are there non-zero values for the covalent radii of the noble gases
in openbabel?

Q: Is there any reason why we should not set them to zero in Jmol?


I am reluctant to set them to zero in Jmol unless that is also done in
open babel. But, I am also somewhat reluctant to add more complexity to
the bonding algorithms in Jmol. Its job is rendering, not calculating.


Thoughts/suggestions?


Miguel