On Fri, May 16, 2014 at 2:22 PM, Jan Domanski <jan...@gmail.com> wrote:
> Yup, David you're correct I think the code is in but Paolo guessed the
> intentions of my question.
>
> I appreciate the point about amides (and other planar groups) in
> unconstrained minimization, that's totally fair. Let me put it on its head:
> what I would like is the constrained minimization being the default
> behavior. Take my molecule, identify amides or other special/planar groups,
> add constraints and minimize. Forget the unconstrained minimization – I'm
> lazy and want my amides planar without all the code Paolo and I exchanged
> in this thread (conformers.py scrip) ;)
>
> Is this totally outrageous? I'm happy to contribute bits from the
> conformers.py Paolo and I concocted.
>
Paolo was very careful to implement MMFF94 as it was originally defined and
published. I believe that this is a good thing.
Any changes that affect the default behavior of the force field would mean
that it's no longer the same thing at all. MMFF94-like is a different beast
entirely.
I believe that what you're asking for would mean doing exactly this.
-greg
------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.
Get unparalleled scalability from the best Selenium testing platform available
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
