Correct filtering of unique atom and bond matches. The filter now uses a new predicate for each successive iterations.
Adding method for mapping atoms and bonds - this removes the need to iterate twice for the atom and bond mapping. Also added a temporary message in bold that the API doc really needs to be read. Still thinking about a fix to make it behaviour more like java developers expect (i.e. mutable beans).
Remove deprecation warning - this will likely be the best way to set the parameters for SMARTS for a while.
Point to correct usage in error message
Also initialise descriptors loaded by name.
Implicit hydrogen count should always be 0 or greater.
Ensure an exception is not thrown when a tetrahedral centre has an implicit hydrogen by the target does not. We want matching to be consistent whether the query as implicit/explicit hydrogens and so we say this is not a substructure match (with stereochemistry).