Sorry if I’m a bit late to the discussion, this is the sort of thing I use 
Openbabel for

http://openbabel.org/wiki/Obfit <http://openbabel.org/wiki/Obfit>

Align all the molecules in "testmv.sdf" on a single molecule of "testref.sdf" 
by superimposing them on its N-methylpiperidyl portion (and outputting a new SD 
file to the standard output):

obfit '[nh]1c2c(=O)n(C)c(=O)n(C)c2cc1' testref.sdf testmv.sdf



> 
>> 
>> Thank you for your useful hints. All the compounds that I want to align
>> are supposed to belong to the same analogue series so they should shave a
>> common substructure with substantial size.

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