On Wed, Oct 13, 2021 at 12:55 PM Jon Zingale <jonzing...@gmail.com> wrote:
> Thanks Roger, Marcus. I am a newbie in this area and so it might be good > for me to ask some potentially obvious questions about SMILES (since they > are used everywhere). > > 1. Is the SMILES isomorphism problem equivalent to the graph isomorphism > problem, or is there some advantage from being context free parsable? > > Equivalent to graph isomorphism with labelled vertices, having an atomic weight allows you to break some degeneracies. 2. In practice, do the edge cases that Roger mentioned effectively get > added into the rewrite rules for the grammar or are they a separate kind of > thing? > > The edge cases are yours to deal with, they're totally legit potential molecular structures, they'd be difficult to impossible to realize as material structures, you have to pick where to draw the line. And as to whether it's impossible or only difficult to make, opinions may vary, and many a chemist makes her reputation by showing a compound is only difficult to make, but it can take years, or decades. 3. How is chirality handled? > > Eric's link looks good. Having some physical models to manipulate is highly recommended. -- rec --
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