Have you considered using the 'through' argument for the many to many 
field?  This lets you specify your own intermediate table to which you can 
add extra data.  So you could add in a quantity field so you would know how 
many of each molecule you need.

Here is the documentation: 
http://docs.djangoproject.com/en/1.3/topics/db/models/#intermediary-manytomany

Hope this helps,

Ryan

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