What does "canonical resonance form" mean to you? I thought it meant "best resonance form", but apparently not. When I submit (CH3)2C+OH to the resonance plugin:
| resPlugin.setMolecule(molecule); |
Molecule molRes = resPlugin.getStructure(0);
it properly returns (CH3)2C=OH+. But when I submit (CH3)2C=OH+, which is itself the best canonical resonance form, it returns (CH3)2C+OH. From this behavior, it seems that you define "canonical resonance form" as "best resonance form other than the one submitted".
I would like the submitted resonance form to be included in the list of returned resonance forms. If the submitted resonance form is the best, then it should be first in the list of returned resonance forms.