On 2018-01-16 22:46, Greg Landrum wrote:

It might be worth thinking about adding an option to the aromaticity perception code to maintain the original bond types and just set the "isAromatic" flag on the bonds.

This is how it's modeled in mmCIF chem. comp. It may or may not come from openeye they were using originally to process their ligands/chem comps.

From programming perspective it's pretty annoying since you have to remember to add an extra if stanza to all your code, queries, etc.

What's wrong with keeping a copy of the original molecule around? -- I'm not sure I get the "I want to sanitize and keep the original bonds too", it sounds too much like the proverbial cake.


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