[Rdkit-discuss] Is there a Smiles library for common amino acids and ligands that can be used for AssignBondOrdersFromTemplate

Dear RDKit experts, I need your advice on finding a source Smiles library for reference, to build the template molecule from Smiles for AssignBondOrdersFromTemplate. I am using AssignBondOrdersFromTemplate to perceive bonds in a

Re: [Rdkit-discuss] Is there a Smiles library for common amino acids and ligands that can be used for AssignBondOrdersFromTemplate

Hi Rocco, That is exactly what I was looking for. Thanks so much for your kind suggestion! Massive Thanks, Amy From: Rocco Moretti Date: Friday, October 27, 2023 at 12:30 PM To: He, Amy Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Is there a Smiles library for common

[Rdkit-discuss] Atom indexing with AssignBondOrdersFromTemplate

Dear RDKit experts, I am new to RDKit and I have a simple question about atom indexing with RDKit. I am using RDKit in Python to process a collection of small molecule, for each I have the SMILES and a pdb file without explicit hydrogens. To draw the 2D images of the molecules, I used

Re: [Rdkit-discuss] How to draw peptides and let the backbone atoms appear in the most extended form?

Date: Tuesday, July 26, 2022 at 3:05 PM To: He, Amy Cc: rdkit-discuss@lists.sourceforge.net 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

[Rdkit-discuss] How to draw peptides and let the backbone atoms appear in the most extended form?

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:

Re: [Rdkit-discuss] Atom indexing with AssignBondOrdersFromTemplate

-- Amy He Chemistry Graduate Teaching Assistant Hadad Research Group Ohio State University he.1...@osu.edu From: Bennion, Brian Date: Sunday, July 17, 2022 at 8:20 PM To: He, Amy , rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Atom indexing with AssignBondOrdersFromTemplate I

Re: [Rdkit-discuss] Ligand conversion problem from 2D to 3D

still be helpful to consider a check even for 2D calculations. Best regards, Amy From: Greg Landrum Date: Tuesday, February 6, 2024 at 6:44 AM To: Emre Apaydın Cc: He, Amy , rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Ligand conversion problem from 2D to 3D Hi Emre, Both

Re: [Rdkit-discuss] Ligand conversion problem from 2D to 3D

Hi Emre! You can get more detailed info on failed conformer generations through rdDistGeom.EmbedFailureCauses, see: https://greglandrum.github.io/rdkit-blog/posts/2023-05-17-understanding-confgen-errors.html Bests, -- Amy He Hadad Lab @ OSU he.1...@osu.edu From: Emre Apaydın Date: