On Wed, Sep 3, 2008 at 8:26 AM, Evgueni Kolossov <[email protected]> wrote: > > I can accept explanation for aromaticity but for structure 11 it will be > good to have ability to read it with warning for example. All structure > editors can read it!
If you want to be able to handle molecules that are unrealistic, you can always read things in without sanitization. In order to do anything useful with the molecules, you will then need to call the individual pieces of the sanitization code by hand (from C++). Doing this will probably work, but might cause problems elsewhere in the code and I'm not going to be able to support it. The reason the RDKit is strict about valency (and making sure molecules are reasonably realistic) is the observation I have made that if you allow bogus molecules to pass with a warning, people will ignore the warnings and you will end up with bogus molecules in your databases (or in the SD files you publish). It is, in my opinion, far better to have the bad molecules generate errors so that the user is forced to fix them immediately. -greg
