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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