[Rdkit-discuss] Hiding/removing specific atoms in a RDKit molecule

Hi all, I have been working on a library that computes properties for molecules where hydrogens are explicit. These properties are then saved into a dictionary where keys are indices, then I am using the dictionary to depict these properties on their corresponding hydrogens - also according to som

[Rdkit-discuss] Using EnumerateLibraryFromReaction without fragmenting reactants

Hi, I've been working with the EnumerateLibraryFromReaction function to generate some quick access molecule libraries, using standard lists of reagents. However, when I get the output back, I notice that I get results that chop up the reactants I use wherever they match the reaction rule, so for a

Re: [Rdkit-discuss] Hiding/removing specific atoms in a RDKit molecule

Hi Gianmarco, I am not aware of a method to simply hide atoms: here's a method t remove atoms given a list of indices, which should be what you need. Note that remove_selected_hs() replaces the "real" hydrogen with an implicit H on the parent atom, which I believe is what you want. from rdkit imp

Re: [Rdkit-discuss] Using EnumerateLibraryFromReaction without fragmenting reactants

Hi James, I am not quite sure I understand what you have done and what you'd like to achieve. Ideally, could you please post: * the reaction you are using * some example reactants * the desired product(s) * the undesired product(s) Thanks, cheers p. On Thu, Dec 2, 2021 at 6:03 PM James Wallace