On Dec 4, 2012, at 11:56 AM, Greg Landrum wrote:
> Bonds are matched purely using bond type, with the one exception that a bond
> of unspecified type matches anything and is matched by anything.
And I forgot to ask - is there any way in SMILES to produce a
bond of unspecified type?
> hmm, not sure what you mean there. Given that no fingerprint screen is going
> to be perfect, the substructure matcher is going to have to do this anyway.
Yes. It's a matter of tradeoff. How significant is bond aromaticity in
improving the screen out ratio? I'm working to get to the point where
I can answer that question.
> ah, ok. Of course, that H could theoretically be there because the user
> wanted an H in that position... it's always tough to say.
Indeed. I was going to say that the toughness can depend on the sketcher,
where a human-sketched 'H' is kept as an independent atom, but it's also
possible that the user deliberately set the number of on-atom hydrogens
in order to specify a radical. (I'm testing out 'on-atom hydrogen' as
an alternative to the different implicit/explicit meanings.)
Cheers,
Andrew
[email protected]
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