Re: [OpenBabel-Devel] Replacement of aromatic.txt SMARTS patterns with switch statement

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

Re: [OpenBabel-Devel] Replacement of aromatic.txt SMARTS patterns with switch statement

> 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

Re: [OpenBabel-Devel] Replacement of aromatic.txt SMARTS patterns with switch statement

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

Re: [OpenBabel-Devel] Replacement of aromatic.txt SMARTS patterns with switch statement

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 >

Re: [OpenBabel-Devel] Replacement of aromatic.txt SMARTS patterns with switch statement

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

Re: [OpenBabel-Devel] Replacement of aromatic.txt SMARTS patterns with switch statement

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