Hi, I have a project where I would like to find similar atom environments to a specified atom in a selected molecule.
For example Suppose I have this query molecule C1CNCC(C1)c1ccccc1, and the selected atom is the nitrogen. I also have a file containing SMILES strings and ID for a list of reference molecules. I would like to identify the molecule within the references molecules that contains a nitrogen most similar to the selected atom in the query molecule even if the rest of the molecule is very different. My feeling is to start with say a 3 atom radius and if no similar atom is found above a set similarity to repeat the search using a 2 atom radius, but to be honest I suspect it will require a bit of trial and error to see what the optimum radius is? I'd then want to return the ID of the most similar molecule. I’ve had a look through the examples but not found anything that close. Cheers Chris ------------------------------------------------------------------------------ _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
