> Why is it that every time hydrogens added with different co-ordinates?
> That is not good for developing, especially for debugging. 
> 
> Is there any way that we can add hydrogens in a consistent way?
> Am i doing something wrong..?

The only time a random vector is created is for atom types where no clear 
connection can be determined (e.g., a lone oxygen atom -> water). Otherwise, 
bonding is used to determine the new bond vectors.

If you have a suggestion for improvement, I'm all ears.

-Geoff
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