Hi Amy,
the simplest way is probably to use Schroedinger's CoordGen to generate
coordinates::
from rdkit import Chem
from rdkit.Chem.Draw import rdDepictor
rdDepictor.SetPreferCoordGen(True)
peptide = Chem.MolFromSmiles("CC(C)C[C@H](NC(=O)OCC1=CC=CC=C1)C(=O)N[C@
@H](CC1CCNC1=O)C=O")
rdDepictor.Compute2DCoords(peptide)
0
peptide
[image: image.png]
Should this fail for other peptides, get in touch as there are alternative
ways.
Cheers,
p.
On Tue, Jul 26, 2022 at 5:13 PM He, Amy <[email protected]> wrote:
> Dear RDKit Experts,
>
>
>
> I have a question about drawing peptidomimetic compounds. I wanted to draw
> the peptides and let the backbone atoms appear in the most extended form.
> Please see the following ChemDraw picture as an example for what I was
> trying to achieve:
>
> The molecule shown above is inhibitor GC373
> <https://go.drugbank.com/drugs/DB15797>. The backbone atoms appear in the
> trans configuration. But this kind of “trans” configuration is about the
> directionality of bonds around the C-N and C-C single bonds, so I was
> unable to use the double bond configuration method (by characters ‘\’ and
> ‘/’) to enforce this type of structure by SMILES… :’(
>
> My RDKit structure from SMILES looks like this:
>
> [image: VDgAn4AAAAASUVORK5CYII=]
>
>
>
> My question is: Is it possible to adjust the drawing method so I can let
> the backbone atoms lay out in the most extended form (the trans
> configuration as shown in the ChemDraw picture)? Thank you for your time
> and kind advice in advance.
>
>
>
>
>
> Many Thanks,
>
> Amy
>
>
>
> --
>
> Amy He
>
> Chemistry Graduate Teaching Assistant
>
> Hadad Research Group
>
> Ohio State University
>
> [email protected]
> _______________________________________________
> Rdkit-discuss mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
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