Hi Greg, Thank you, it's great to hear that it's fixed! I'll give it a try with the next release.
Best, Ivan On Mon, Sep 17, 2018 at 11:38 PM, Greg Landrum <greg.land...@gmail.com> wrote: > As an FYI: the changes to carry reactant atom indices over into reaction > products are already merged and will be in the next release. > > Here’s the issue connected to the changes: > https://github.com/rdkit/rdkit/issues/1269 > > > Best, > -greg > > > On Mon, 17 Sep 2018 at 18:23, Ivan Tubert-Brohman <ivan.tubert-brohman@ > schrodinger.com> wrote: > >> Hi Connor, >> >> Thank you for your suggestions! I think the isotope hack will work for me >> for now, but for the longer term it would be nicer to have the official >> version of RDKit provide sufficient atom mapping information, so I'll >> consider that as well. >> >> Ivan >> >> On Mon, Sep 17, 2018 at 11:52 AM, Connor Coley <cco...@mit.edu> wrote: >> >>> Hi Ivan, >>> >>> This is something I ran into a couple years ago - it's a pretty easy >>> fix. >>> >>> One approach is to update the source with a few lines to copy over the >>> atom map numbers from the reactants to the products as a new field. You can >>> see the necessary changes to the code in my forked version here: >>> https://github.com/rdkit/rdkit/commit/0a8393fbf89e486ed67f2a44f9a7ea >>> 8d9f2efd95 >>> >>> Another approach is more hacky but might be good enough for your use >>> case. If your reactions don't involve isotopic changes or require specific >>> isotopes, you can set unique isotope numbers for every reacting atom. Those >>> will be preserved in the products so you can get the atom-atom mapping >>> after running the reaction. >>> >>> Connor >>> >>> On Mon, Sep 17, 2018 at 10:36 AM Ivan Tubert-Brohman < >>> ivan.tubert-broh...@schrodinger.com> wrote: >>> >>>> I'd like to know where each atom in a reaction product came from, but >>>> as far as I can tell, RDKit doesn't provide enough information. Here's what >>>> I found out empirically so far. >>>> >>>> There are four kinds of product atoms: >>>> >>>> 1. New atoms: atoms are defined in the product template without a >>>> mapping number. These can't be mapped to reactant atoms, so there's no >>>> issue. >>>> >>>> 2. Unmatched atoms: atoms that were not matched by any atom from the >>>> reactant template but were carried over to the product because they were >>>> connected (directly or indirectly) to a mapped reactant atom. These have >>>> the "react_atom_idx" property, which holds the atom index of the atom in >>>> the reactant molecule. This is useful as long as the reactant side has only >>>> one molecule; when there are multiple molecules, it is not clear which >>>> reactant molecule a product atom came from. >>>> >>>> 3. Mapped dummy atoms: atoms which are defined as dummies in the >>>> product template and have a mapping number (e.g., [*:1]). These also get a >>>> "react_atom_idx" property, as well as an "old_mapno" property which holds >>>> the mapping number (1 for [*:1]) >>>> >>>> 4. Mapped non-dummy atoms: atoms which are NOT defined as dummies in >>>> the product template and have a mapping number (e.g., [C:1]). These >>>> have "old_mapno", but no "react_atom_idx". >>>> >>>> One thing I tried was to add my own unique atom identifier property to >>>> all reactant atoms before applying the reaction, but that didn't help >>>> because mapped atoms (types 3 and 4) don't preserve user properties (I >>>> guess these atoms are seen as "replacements" for the atoms they mapped, >>>> rather than "copies"?) >>>> >>>> I'd be willing to hack the RDKit source code if necessary and >>>> contribute my changes, but before starting such a project I'd like to hear >>>> if it's reasonable. >>>> >>>> One possibility would be to preserve user properties for mapped atoms. >>>> >>>> Alternatively we could add react_atom_idx to mapped non-dummy atoms, >>>> and also add a new "react_mol_idx" property? >>>> >>>> Best, >>>> Ivan >>>> _______________________________________________ >>>> Rdkit-discuss mailing list >>>> Rdkit-discuss@lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>>> >>> >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >
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