[ghemical-devel] Duplicate Coordinates

[Geoffrey Hutchison]

On Dec 15, 2006, at 4:41 PM, Donald Ephraim Curtis wrote:

> Before I add the duplicate atom coordinate "check" i wanted to make  
> sure
> we couldn't fix this problem in the libghemical tools.

I think this should ideally be fixed in the underlying libghemical.  
Basically, there's a divide by zero and that kills everything. You  
can see the same effect if you import a SMILES string (which will  
have 0.0 for all coordinates).

So I think libghemical needs a quick check for coordinates which are  
too close. (For example, sort by z-axis, and check for distances  
under 0.4Ang / 40pm.)

Cheers,
-Geoff