Hi Paolo, Thank you so much for your kind advice. Yes that works well for my compounds as they are mostly analogs to GC373. Thanks again for your kind help!
Bests, Amy -- Amy He Chemistry Graduate Teaching Assistant Hadad Research Group Ohio State University [email protected] From: Paolo Tosco <[email protected]> Date: Tuesday, July 26, 2022 at 3:05 PM To: He, Amy <[email protected]> Cc: [email protected] <[email protected]> Subject: Re: [Rdkit-discuss] How to draw peptides and let the backbone atoms appear in the most extended form? 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") 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 [cid:ii_l62jqp9b2] 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]<mailto:[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: [cid:1823be2ebef847be2d22] The molecule shown above is inhibitor GC373<https://urldefense.com/v3/__https:/go.drugbank.com/drugs/DB15797__;!!KGKeukY!2ZFin_Fq-pYF9Ui-CxUV2gBcN_Ei7MpmB4sF7eca98u6EtGKnunDGjCKm5JB_w6J6GzPKgP7BazKPpPP7y6YCmoG_9pWszDQb2hjdf0$>. The backbone atoms appear in the trans configuration. But this kind of “trans” configuration is about the directionality of bonds around the C-N and C-C single bonds, so I was unable to use the double bond configuration method (by characters ‘\’ and ‘/’) to enforce this type of structure by SMILES… :’( My RDKit structure from SMILES looks like this: [VDgAn4AAAAASUVORK5CYII=] My question is: Is it possible to adjust the drawing method so I can let the backbone atoms lay out in the most extended form (the trans configuration as shown in the ChemDraw picture)? Thank you for your time and kind advice in advance. Many Thanks, Amy -- Amy He Chemistry Graduate Teaching Assistant Hadad Research Group Ohio State University [email protected]<mailto:[email protected]> _______________________________________________ Rdkit-discuss mailing list [email protected]<mailto:[email protected]> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss<https://urldefense.com/v3/__https:/lists.sourceforge.net/lists/listinfo/rdkit-discuss__;!!KGKeukY!2ZFin_Fq-pYF9Ui-CxUV2gBcN_Ei7MpmB4sF7eca98u6EtGKnunDGjCKm5JB_w6J6GzPKgP7BazKPpPP7y6YCmoG_9pWszDQ3bjpdx4$>
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