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.
On 16 May 2014 19:03, David Hall <li...@cowsandmilk.net> wrote:
> I haven't tried it, but I'm assuming that once Paolo's pull request is
> accepted, this will work out of the box.
>
> https://github.com/rdkit/rdkit/pull/261
>
> -David
>
>
> On Fri, May 16, 2014 at 1:51 PM, Jan Domanski <jan...@gmail.com> wrote:
>
>> The reply from Paolo was amazing and quick. I'm looking at this after a
>> week and one questions comes to mind: Is there a reason this can't work out
>> of the box?
>>
>>
>> On 11 May 2014 23:08, Jan Domanski <jan...@gmail.com> wrote:
>>
>>> Awesome, this was lightning speed Paolo - many thanks!
>>>
>>> - Jan
>>>
>>>
>>> On 10 May 2014 20:47, Paolo Tosco <paolo.to...@unito.it> wrote:
>>>
>>>> Dear Jan,
>>>>
>>>> the reason why your restraint was seemingly not applied is that
>>>> MMFFAddTorsionConstraint() expected a range such as (170, 190). I have just
>>>> modified the code to make it more robust in this respect and I submitted a
>>>> pull request to Greg. Meanwhile, you may get the results you expect using a
>>>> (170, 190) degree range.
>>>> Please find attached a slightly modified version of your python script;
>>>> in particular, I added a call to SetDihedralDeg() before the constrained
>>>> minimization, to avoid troubles to the minimizer in case the geometry
>>>> generated by EmbedMultipleConfs() has dihedral values very far from the
>>>> desired target value.
>>>>
>>>> Thanks for your detailed report which allowed chasing down that
>>>> weakness in my code!
>>>>
>>>> Cheers,
>>>> Paolo
>>>>
>>>>
>>>> On 05/10/2014 04:28 PM, Jan Domanski wrote:
>>>>
>>>> Hi there,
>>>>
>>>> Attached is a crystal_ligand.mol2 for the ACE target from DUDE. I'd
>>>> like to generate a number of conformers for this ligand. The trick is it
>>>> has 2 amide bonds that I'd like to keep planar. As far as I can see neither
>>>> MMFF nor UFF will keep those planar by default, at least not for this input
>>>> file.
>>>>
>>>> One way around it, is to find all the amide bonds by smarts matching.
>>>> From that, find the hydrogen connected to N and add a DihedralConstraint on
>>>> the 4 atoms before running the minimization.
>>>>
>>>> That's what conformers.py is attempting to do (basing on one of the
>>>> test scripts). However, I still get non-planar amide bonds and I'm really
>>>> confused as to why. I can filter them out manually with GetDihedralDeg().
>>>>
>>>> Thanks for all the help (I'm using up all the rdkit credits this
>>>> weekend ;) )
>>>>
>>>> - Jan
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Is your legacy SCM system holding you back? Join Perforce May 7 to find
>>>> out:
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>>>>
>>>>
>>>> _______________________________________________
>>>> Rdkit-discuss mailing
>>>> listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>
>>>>
>>>>
>>>> --
>>>> ==========================================================
>>>> Paolo Tosco, Ph.D.
>>>> Department of Drug Science and Technology
>>>> Via Pietro Giuria, 9 - 10125 Torino (Italy)
>>>> Tel: +39 011 670 7680 | Mob: +39 348 5537206
>>>> Fax: +39 011 670 7687 | E-mail: paolo.tosco@unito.ithttp://open3dqsar.org
>>>> | http://open3dalign.org
>>>> ==========================================================
>>>>
>>>>
>>>
>>
>>
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