Dear all,
I am working with peptides and RNA and want to convert sequences into 2D
molecules.
As we use non-natural and proprietary monomers, I cannot apply the ususal
workflows like MolFromHELM,
but have developed my own python code to build the macromolecules from their
building blocks (basically
using Chem.CombineMols and then rdDepictor.Compute2DCoords,
see
https://github.com/Boehringer-Ingelheim/pyPept/blob/master/src/pyPept/molecule.py).
While this works fine for even large peptides (>40 monomers), when doing the
same for RNA I run into a problem:
after a certain size (about 12 or 13 nucleotides), the 2D embedding returns all
coordinates as zeroes and all stereoinformation
is lost.
I tried the same using MolFromHELM, and there I do not see the same issue, I
get valid 2D coordinates up to hundreds of nucleotides
(yes, other than what the documentation says, RNA and DNA work, too!).
Only if I first generate the molecule and then pass it through either
rdCoordGen.AddCoords or Chem.rdDepictor.Compute2DCoords
I end up with coordinates as zero. So I suppose MolFromHELM knows sth about the
general structure of the building blocks and uses that information,
whereas the all-purpose embedders cannot take that into account and
subsequently fail. But then again, this MolFromHELM is not an option as I need
non-natural
monomers (unless there is a way to teach rdkit about non-canonical monomers,
but I haven't found anything on it).
Here is the relevant code snippet:
from rdkit import Chem
from rdkit.Chem import rdCoordGen
n_nucleotides = 20
polyA = ['R(A)P'] * n_nucleotides
polyA = '.'.join(polyA)
helm = f'RNA1{{{polyA}}}$$$$V2.0'
romol = Chem.MolFromHELM(helm)
#rdCoordGen.AddCoords(romol)
mb = Chem.MolToMolBlock(romol)
print(mb[1:300])
Now everything looks fine, but as soon as I uncomment the rdCoordGen line, the
coordinates are zero.
Any ideas, suggestions what I could do?
Thanks,
Th.
Thomas Fox
NCE
Boehringer Ingelheim Pharma GmbH & Co. KG
Birkendorfer Str. 65 | 88397 Biberach
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