Fix depository dictionaries that have different atomLabels

... separate molecules with different atomLabels.

Hopes to fix issue https://github.com/GreenGroup/RMG-database/issues/54

Previously I had imported the reactions and labeled them by checking for isomorphisms, but this unfortunately identifies two molecules to be the same even when they have different atomLabels.  This commit intends to fix that problem by creating new labels for those species.  @pierrelb Could you please run your scripts on this to see that it's working properly?