Would it be okay to do that as part of a separate pull request? i.e.
if there are no other concerns, could you merge it as is. The easiest
way to do the pruning is to comment out relevant code one at a time,
and seeing whether the results change (for the worse). This will take
some time, but it wou
> Personally, I'd also like to remove any "patterns" that aren't
> triggered by (aromatic atoms in) molecules in any of these databases,
> on the basis that it's better to have a set of patterns that we know
> are correct (and all covered by test cases)
I’d be fine with some pruning. I’ve been mak
Ok - am getting somewhere now. I've confirmed that there is a problem
with the current codebase and the use of 'D', e.g. for protonated
imidazole (as in histidine in vivo), two different answers are found
depending on whether hydrogens are explicit or not:
C:\Users\noel>obabel -:Cc1[nH]c[nH+]c1 -o
Maybe am overthinking. If it doesn't change the final output (as
regards aromatic SMILES) on ChEMBL, maybe it's not worth worrying
about now.
- Noel
On 30 January 2017 at 18:31, Noel O'Boyle wrote:
> Great. One question I've run into is what was the intention of the D2
> etc in the SMARTS patter
Great. One question I've run into is what was the intention of the D2
etc in the SMARTS patterns. Was it the number of heavy atom neighbors?
As written, it's the number of explicit nbrs in the graph, which is
complicated by the fact that OB's SMILES parser currently adds an
explicit H for H's insid
I should mention on that note, that a collaboration with Carnegie Mellon
students produced a parallel implementation of Kekulization using the
Eigen3 matrix library. They also wrote a CUDA implementation that was
modestly faster.
It hasn't been ported back to Open Babel yet, but I'll leave the bas
I think it's a great idea. Chris Morley had recommended similar concepts in
terms of implicit valence.
Yes, many of the stranger SMARTS patterns here are for "dodgy" SMILES that
should retain aromaticity. It's possible, perhaps to set some level of "if
it was initially flagged as an aromatic atom,
Hi there,
Here's a heads-up on some work I've been prototyping.
The aromatic atom typer currently uses SMARTS patterns in aromatic.txt
to assign max/min values of pi electrons. A more efficient approach is
to simultaneously match against all the SMARTS patterns rather than
one at a time, and well