[Rdkit-discuss] Incorrect gold particle placement

Dear all, I'm new to RDKit and cheminformatics in general. I'm using the latest RDKit libraries. Any suggestions you can offer would be kindly received. Using the canonical SMILES C(C1C(C(C(C(O1)[S-])O)O)O)O.[Au+] of Aurothioglucose (Pubchem CID: 454937) I've generated a 3D structure

[Rdkit-discuss] Error whilst setting up 2D Pharmacophore distance bins

, 8)]; scaffolds: [0, [(0,), (1,), (2,)], 0, [(0, 0, 0), (0, 0, 1), (0, 1, 0), (0, 1, 1), (0, 1, 2), (0, 2, 1), (0, 2, 2), (1, 0, 0), (1, 0, 1), (1, 0, 2), (1, 1, 0), (1, 1, 1), (1, 1, 2), (1, 2, 0), (1, 2, 1), (1, 2, 2), (2, 0, 1), (2, 0, 2), (2, 1, 0), (2, 1, 1), (2, 1, 2), (2, 2, 0), (2, 2, 1),

Re: [Rdkit-discuss] Error whilst setting up 2D Pharmacophore distance bins

In answer to my own question, I found a post back in 2013. Adding trianglePruneBins=False to SigFactory solved the problem. However, I'm still unsure whether the definition file I used is fit for purpose. Thanks Anthony From: Anthony Nash Sent: 14 June 2021

[Rdkit-discuss] SMILES from sdf file

Dear all, This sounded routine enough that I thought I'd seek guidance to save myself hours of hacking and potential misunderstanding. My objective is to generate a canonical SMILES for each compound in an sdf file. The sdf file was downloaded from ChEMBL and contains some +10,000 drugs. I've

Re: [Rdkit-discuss] SMILES from sdf file

Hi Patrick, Thank you for the code and the links, both are very helpful and exactly what I needed. Many thanks Anthony Kind regards Dr Anthony Nash PhD MRSC Senior Research Scientist Nuffield Department of Clinical Neurosciences RMCR Kellogg College University of Oxford http

[Rdkit-discuss] 2D Pharmacophore fingerprints slow or stuck

Dear all, I'm afraid that I'm struggling to understand precisely how to build a 2D pharmacophore fingerprint. I thought I had it, but my code sits in a running state indefinitely. This is the code: fdefNameStr: str = "MinimalFeatures.fdef" featFactory =