Yes, the pull request, once accepted, will fix the weakness in the code which
does not allow ranges such as -170,170 or -10,+10.
Cheers,
p.
> On 16 May 2014, at 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
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
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>>>>>
>>>>> _______________________________________________
>>>>> Rdkit-discuss mailing list
>>>>> Rdkit-discuss@lists.sourceforge.net
>>>>> https://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.to...@unito.it
>>>> http://open3dqsar.org | http://open3dalign.org
>>>> ==========================================================
>>
>>
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