mino rmrv -> mol conversion bug

I had a Molecule object that contained a positively charged N atom with a trivalent doublet radical flag. When I imported it into a MOL string, the flag was lost. It was retained when I imported it into an MRV string.

Will have a look and fix it ASAP.

I think there is no bug to fix. MDL molfiles cannot store trivalent radicals. There are four possible M RAD values and none of them is trivalent

OK, I understand. But doesn't this situation contradict your stated policy of avoiding constants that are incompatible with the MOL format? See this discussion. And if this is not your policy, would you consider adding a DOUBLE_OR_TRIPLE bond constant, even though it is not compatible with MOL, just like the trivalent radical constant is not compatible with MOL?

Are you sure you need it?


"Adding a constant" also means a lot of programming in the import/export modules and the GUI. Probably also in jchem, because the search will also have to recognize the new bond type. And there will be lot of user complaints because they do not like this bond and will want to make it optional. Moreover, MolBond.TYPE_MASK = 7 is full, there are no more free bits. It could be changed, but then users must also recompile. OK, it is not an important problem. But still there will be a lot of problems with rewriting serialization in a backward compatible way. I would avoid all these complications if possible...

Those are all good reasons not to implement the change. But, as I'm sure you recognize, there are many reasons TO implement the change, not least of which is the ability to search for DOUBLE_OR_TRIPLE bonds. Don't you think many users will want to have that ability? I doubt anyone will complain about having the option; if they don't want it, they won't have to use it.





Anyway, no, it's not absolutely necessary for us, but it would be helpful. Definitely not a high priority, but not bottom of the list, either.

Let us continue the double or triple question in its original topic. I am going to post some information there.