I also like the term "FuzzyBonds" better than vague bonds if we get to
rename it :)
Cheers,
Brian
On Tue, Jun 7, 2016 at 3:21 PM, Brian Kelley wrote:
> I was also thinking that instead of protonating, we could just "and" with
> a heavy degree query with the degree equal to the current degree.
I was also thinking that instead of protonating, we could just "and" with a
heavy degree query with the degree equal to the current degree. This
should have the same effect, correct?
Cheers,
Brian
On Tue, Jun 7, 2016 at 12:37 AM, Greg Landrum
wrote:
> And while we're at it we should think abo
And while we're at it we should think about including options like what
ChemAxon calls "Vague Bond Search" (
https://docs.chemaxon.com/pages/viewpage.action?pageId=22217121#Tautomersearch/Vaguebondsearch/sp-Hybridization-vaguebond).
This would help address some of the aromaticity problems.
On Tue,
I think that here it's worth, at least initially, ignoring what is
currently possible with the RDKit (and how that's implemented) and instead
thinking about what we want to be able to do.[1]
The goal, I think, is to have some options allowing control over how a
query coming from a MOL block/CTAB a
My solution for the problem was the following:
qmol = Chem.MolFromMolBlock(molblock)
for atom in qmol.GetAtoms():
if atom.HasQuery():
continue
atom.SetNumExplicitHs(atom.GetTotalNumHs())
This gives a SMARTS like
this: [#7]1(-[#6](-[#6H2]-[#6,#8]-[#6H](-[#6H2]-1)-[*])=[#8])-[*]
This may b
An interesting conversation came up at work a few days ago regarding
MolBlocks/CTABs with queries that behave in an unexpected manner. I'm
tackling some of these issues when it comes to reaction processing .rxn
based files and plan on contributing it relatively soon. However, I hadn't
considered
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