Jason, I forgot to reply to half of your questions :)
yes, templates are used for for complicated ring systems and some macrocycles.
It is simple to add stuff provided that you have a way to write in the .mae
format (I don’t know if rdkit can do that at the moment…that’s a question for
Greg).
The image you shown with the template is correct and very similar to the one I
sent
thanks!
Nic
> On 2 Jun 2018, at 15:41, Jason Biggs <[email protected]> wrote:
>
> Nicola,
> Thanks for the example, I can definitely see the improvement in the diagram
> from the template. Is it mainly then these complicated bridged ring systems
> that use the templates? I do like the diagrams from Coordgen very much, even
> when it doesn't use a template.
>
> How difficult will it be to add more templates to the templates.mae file - as
> I find examples of molecules that don't do well in the default method? Can
> this be done with the rdkit, or would it need something else from the
> Schrodinger repo?
>
>
> This would be a question for both Greg and Nicola: What would be good words
> to describe the layout methods used by coordgen vs rdkit? I want to have an
> option for the user, Molecule[ <arguments>, DiagramLayout -> "MethodName"],
> but just using "RDKit" and "CoordGen" isn't right because it doesn't describe
> the underlying algorithm, just the library that implements them.
>
> Would it be wrong to call the rdkit method "DistanceGeometry"? What is the
> main distinction between the two methods?
>
> Best,
>
> Jason
>
>
> (the image from Nicola's email didn't come through to me, showing the example
> with template on the bottom, without template on the top - big improvement)
>
> <image.png>
>
>
>
> Jason Biggs
>
>
> On Sat, Jun 2, 2018 at 7:08 AM, Nicola Zonta <[email protected]
> <mailto:[email protected]>> wrote:
> Hello,
>
> yes, I don’t think we check for the existence of the directory (I got rid of
> that code when we released cause it was using a proprietary lib and never
> replaced it). It’s surprising that you get the same results though.
>
> here’s the smiles I use (or you can use any molecule in templates.mae (I am
> not sure if maeparser has been integrated with RDKit yet?) )
>
> C12CC3CC(C1)CC(C2)C3
>
> which should look something like this if the templates are used
> <PastedGraphic-2.tiff>
>
>
> weird about the unstable coordinates, I think looking at the structure it has
> to do with the minimisation but I have no quick solution for it
>
>
>> On 02 Jun 2018, at 12:35, Greg Landrum <[email protected]
>> <mailto:[email protected]>> wrote:
>>
>> Hi Jason,
>>
>> That's a great question. I can also confirm that it seems that setting the
>> parameter file location to a bogus value seems to have no effect.
>> @Nic: can you help us out here? I figure you can probably answer the
>> question quicker than I can dig through the code. :-)
>>
>> -greg
>>
>>
>> On Thu, May 31, 2018 at 10:22 PM Jason Biggs <[email protected]
>> <mailto:[email protected]>> wrote:
>> I recently switched to the 2018_03_1 release, and I am trying out the new 2D
>> coordinate generating functions. The diagrams look good, but I can't seem
>> to figure out what the role of the template file is.
>>
>> I find that I can set the templateFileDir parameter either to a real
>> directory with the templates.mae file in it, or to an almost-empty string "
>> ", and it has no effect. Is there an example SMILES where using the
>> template file changes the returned diagram?
>>
>> Another thing I notice is the conformer generated by CoordGen isn't always
>> reproducible. I find that if I run the following code multiple times, I
>> will get different results,
>>
>>
>> m =
>> Chem.MolFromSmiles('CO[C@H]1[C@]2(O)C(=O)N3C=CC(C)(C)c4c(C=C3C(=O)N2[C@@]23[C@@]1(O)c1ccccc1N3C([C@H]2C)(C)C)c1ccccc1[nH]4')
>> Chem.rdCoordGen.AddCoords(m)
>> m.GetConformer(0).GetPositions()[0]
>>
>> will sometime output
>>
>> array([-1.27959999, 1.35720001, 0. ])
>>
>> but other times outputs
>>
>> array([-1.28240005, 1.365 , 0. ])
>>
>> Obviously it's a small difference, but I would prefer to always return the
>> same values for the same input.
>>
>> Best,
>> Jason
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