I'm unhappy with some of the recent changes because they reduce code 
segregation. Up to now, OBConversion (and also babel and the GUI) 
didn't know anything about chemistry - mol.h was not #included. Maybe 
this is a bit of a fetish, but I do think it helps to keep large 
projects manageable if parts can be independently compiled and linked. 
Even when they cannot, it is also better to keep the dependency in one 
direction only, which is ensured by using a plugin. The price paid is 
slightly more complicated and less obvious code.

I have committed an op which has similar read-conformers functionality 
when used with (o)babel. (It handles multiple groups of conformers and 
allows conformers to have different titles.) Use with 
OBConversion::Read() etc. (a bit less convenient) is illustrated at 
the end of readconformers.cpp.

I've commented out your changes in OBConversion, but only to avoid 
incompatibilities. If you would rather do it this way, we should 
discuss it further.

Chris

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