[Rdkit-discuss] Problems with coordMap in EmbedMultipleConfs

The following code should produce 5 conformers of c1c1CCC” where the coordinates of the benzene ring is the same. But it doesn’t. What I am doing wrong? Best regards, Jan from rdkit import Chem from rdkit.Chem import AllChem template_smiles = "c1c1" template =

Re: [Rdkit-discuss] suggestions for comprehensive searchable database of natural products

I'd also be interested in Juptyer notebooks for this. Thanks Tyler! Curt On Tue, Nov 28, 2017 at 8:26 AM, Tyler Backman wrote: > Hi Jim, > > MiBIG is a useful database of natural product gene clusters and > structures, which you can download in JSON format here, and use

Re: [Rdkit-discuss] suggestions for comprehensive searchable database of natural products

Hi Jim, MiBIG is a useful database of natural product gene clusters and structures, which you can download in JSON format here, and use pretty easily from within Python: https://mibig.secondarymetabolites.org/repository.html This also includes pathway and organism information. Secondly, our

Re: [Rdkit-discuss] Problems with coordMap in EmbedMultipleConfs

Dear Jan, I don't think you are doing anything wrong. I tried using coordMap myself a few weeks ago and it looked like the parameter was being ignored. I'll try and understand why that happens as soon as I have a bit of time. Kind regards, Paolo On 11/28/17 10:16, Jan Halborg Jensen

Re: [Rdkit-discuss] RPM distros

Hi Tim and Francois, To fix missing dependencies use "sudo apt install -f" and use "yum install rdkit_package_file.rpm" to install package to have all the dependencies. On Debian (based systems) I prefer to install standalone packages via gdebi which does this automatically. Pozdrawiam, |