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
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]> 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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