Re: [Rdkit-discuss] Is diimide cis-trans stereochemistry possible?

Hi, This has gotten a little bit easier in the most recent RDKit version. Here's a simple example: In [3]: print(rdkit.__version__) 2018.09.1 In [4]: from rdkit import Chem In [5]: m = Chem.MolFromSmiles('CN=NC') In [6]: m.GetBondWithIdx(1).SetStereoAtoms(0,3) In [7]:

Re: [Rdkit-discuss] MMFF changing molecule

Dear Jason, I think you have a very good point there, and I made the same consideration yesterday while I was replying to you. I'll look into fixing this issue. Best, p. On 02/06/19 15:20, Jason Biggs wrote: Thanks for the response Paolo. I would still think that regardless of the

Re: [Rdkit-discuss] MMFF changing molecule

Thanks for the response Paolo. I would still think that regardless of the MMFF94's aromaticity model, the only modifications it should make to the ROMol passed to it should be to the conformer. At the very least the documentation for MMFFMolProperties should mention the side effect. MolToInChI

Re: [Rdkit-discuss] Reaction SMARTS

Hi Jean-Marc, Try the reaction smarts '[C:1]([OH:2])=[N:3]>>[C:1](=[OH0:2])[NH:3]'. The only difference is the addition of "H0" to product atom :2. The problem is that the hydrogen count from the reactant atom gets copied over unless specified otherwise. Hope this helps, Ivan On Wed, Feb 6,

Re: [Rdkit-discuss] Reaction SMARTS

Hi Ivan, I tried the SMARTS you sent and it worked. Thank you! Jean-Marc Le 06/02/2019 à 15:46, Ivan Tubert-Brohman a écrit : Hi Jean-Marc, Try the reaction smarts '[C:1]([OH:2])=[N:3]>>[C:1](=[OH0:2])[NH:3]'. The only difference is the addition of "H0" to product atom :2. The problem is

[Rdkit-discuss] Reaction SMARTS

Dear All, I need to convert iminol functional groups into amides. Being new to reaction SMARTS I wrote the following code: * from rdkit import Chem from rdkit.Chem import AllChem #from rdkit.Chem.Draw import IPythonConsole sm1 = 'CNC(C)=O' m1 = Chem.MolFromSmiles(sm1) #m1

[Rdkit-discuss] SMILES -> MOL -> SMILES

Dear all, I needed to test whether RDKit-generated SMILES strings were readable again so that structures could be retrieved after storage. The following script produced unexpected results. * from rdkit import Chem #from rdkit.Chem import rdCoordGen #from rdkit.Chem.Draw import

[Rdkit-discuss] Is diimide cis-trans stereochemistry possible?

Hi, RDkit. I'm looking for a way to change cis-trans for a molecule at the diimide part. There was a case for the Alkene E-Z change. https://sourceforge.net/p/rdkit/mailman/message/35011276/ But when I apply above method, it doesn't work for the diimide case. For examples, let say Mymol be

Re: [Rdkit-discuss] The RDKit database cartridge install problem

One point to be clear about in all this too: This is not a problem with the installation of the RDKit cartridge. This is a problem with installing PostgreSQL itself. We may be able to help anyway, but this is, in the end, not really something for this mailing list. On Wed, Feb 6, 2019 at 8:46 AM

Re: [Rdkit-discuss] The RDKit database cartridge install problem

On 2019-02-05 20:38, tech tech wrote: Hi, all, I tried to install the cartridge for Postgres. I am using ubuntu 18.04 and postgres 9.6 However, when I typed this commond: /home/hat/anaconda3/envs/my-rdkit-env/bin/initdb -D /var/www/rdkit I saw following errors. I don't know how to fix it.