Re: [Rdkit-discuss] rdkit & Coordination chemistry on Mg

Hi Marco You can define dative bonds like this: C1CO->[Fe+2](O)(<-OC1)(<-O)(<-O)(<-O) Best regards, Jan On 22 Mar 2022, at 15.07, Marco Stenta mailto:marco.ste...@gmail.com>> wrote: You don't often get email from marco.ste...@gmail.com. Learn why this is

Re: [Rdkit-discuss] rdkit & Coordination chemistry on Mg

The SMILES I sent you works fine for me with the same version: https://colab.research.google.com/drive/19OZtX8IqICZQ4B2jLpr02owkSLc0FeZ6?usp=sharing However, the alkali and alkaline earth metals do not behave as I would expect (as shown in the Colab notebook). This looks like a bug to me and I

Re: [Rdkit-discuss] rdkit & Coordination chemistry on Mg

Thanks, Jan, the dative bond works in a number of cases with other metals. (rdkit 2021.9.5) This one works fine: rdmol = Chem.MolFromSmiles('[O-]->[Fe+2]<-[O-]', sanitize=True) # case 1 coordinate bonds assert rdmol is not None this one with Mg divalent does not rdmol =

[Rdkit-discuss] rdkit & Coordination chemistry on Mg

Dear RDKitters, I am struggling with working organometals and coordination complexes. with a small team, we are creating a series of recommendations to draw correctly organometals (catalyst, complexes, etc), so that we can use them in our chemoinformatics pipeline. I know it is a horrible mess

[Rdkit-discuss] Forcing depiction to match input mol block

Hello Everyone, I'm having some trouble trying to depict molecules the exact same way as the input mol block (V2000) was drawn. My main problem is that I've drawn in a wedge bond between atoms 1 and 7 (the right hand side of the cyclopropyl ring), and RDKit depicts the molecule with a wedge bond