Handle different charging failures appropriately

[ChayaSt]

Calculating AM1 WBOs can fail for several reasons. Some are:

1. Missing BCC parameters
2. Missing stereochemistry
3. Total charge does not equal formal charge.

The current workaround is just to continue growing the fragment until the failures stop.
Tagging all the right functional groups to avoid creating fragments with weird chemistry so this doesn't happen is probably the best solution. It might also be good to handle each kind of failure appropriately.