Re: [OpenBabel-Devel] Usage of gen3D

[Tim V. <tim...@gm...>]

Hi,

Adding hydrogens before will place the hydrogens at 1.5A from it's
neighbouring atom. Adding hydrogens after will place them at 1.1A.
This is because the builder class still uses 1.5 for all non-fragment
library bond lengths. In most cases you still want to run a
minimization and possibly a rotor search which makes both methods as
useful. If not, I would add them after since 1.1A is closer to the
expected bond length.

Tim

On Tue, Mar 25, 2008 at 8:49 PM, Noel O'Boyle <bao...@gm...> wrote:
> If converting from 0D (SMILES) to 3D with gen3D, should hydrogens be
> added first if it is to be converted correctly?
>
> Noel
>
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