match problem with hypervalent C atoms

The structure CH5 (five explicit H atoms added to C) is coming up as an exact match to CH4 (with the four H atoms either explicit or implicit). Any reason why? I have reproduced the problem in another case, too.





If this feature is intentional, can we turn it off?

Hi Bob!





The reason is that search expects valid input molecules.





CH5 does not exist, and the valence violation may confuse the search.





I suggest to check the molecule drawn by the student for valence errors before doing the search:

Code:

Molecule m; boolean valenceError = false; m.valenceCheck(); for(int i=0; i < m.getAtomCount(); i++) {     MolAtom ma = m.getAtom(i);     if(ma.hasValenceError()) {         // VALENCE ERROR at atom i:         valenceError = true;     } }

But you have to be careful in cases where you ask for only a fragment of a molecule. (In this case the valence in the fragment may be incorrect, but it will be correct when the whole molecule is sketched.)

Thanks, Szabolcs. Your code worked great for us.