Hi Jennifer,
I had this same issue a while back. Here is an issue I posted about it on the
github: https://github.com/rdkit/rdkit/issues/1269
I never did make the pull request mentioned in the issue, but all the code that
does what you want should be in there. Let me know if you have any
I'm afraid that there's likely to be rather a lot of devil hiding in the
details (as is so often the case).
A simple example of one problem: let's take your [But]O case. Suppose you
do a substructure search for the molecule defined by the SMARTS "OCC". Does
that match "[But]O"? What does it
Ideally, I'd like to treat these pseudoatoms as similarly to normal atoms as
possible. I would mostly want to use them for substructure matching, running
reactions, and also display purposes. Also, basic atom queries, such as
getting a mapping number or a atom symbol.
I was thinking that
Hi Paolo,
Thanks so much for your quick response.
Hmm… would you mind sharing how you are calculating those RMSDs? I’m seeing
RMSDs with constraints of over 1.0 Angstrom, so clearly some detail is
still escaping me.
My goal here is to reproduce the strain energy calculations that are part
of
Hi Paolo,
Thanks so much for this suggestion (ages ago now). Based on Francois’
suggestion and your suggestion I have cobbled together a script that seems
like it ought to work to apply position constraints on each atom, minimize,
and then return the local minima conformations. Perhaps I’m still
There's currently no way to add to the periodic table. I'm somewhat
uncomfortable with the idea (there's a lot that can go wrong), but your use
case isn't that uncommon (using custom atom types to represent amino acids
has come up before), so it's worth thinking about how to do something like
The way i was thinking about it, the smarts of OCC would not match the O[but]
because [but] is a totally new atom that is not related to carbon at all. This
doesn't really make sense in this example, but it does (i think) for most of my
purposes (where i want to mask away a biological
Hi All,
I am working with atom mapping for reactions. How do I get the correct atom
mapping for my products?
I have tried the following:
>> rxn =
rdChemReactions.ReactionFromSmarts('[C:1](=[O:2])O.[N:3]>>[C:1](=[O:2])[N:3]')
>> rcts_lab = (Chem.MolFromSmiles('[C:1](=[O:2])[O:3]'),
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