Predicting enviromental conditions from configurations

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have a bunch of different configurations of a single molecule under some sort of enviromental conditions. They are not of course the same configuration because of fluctations.

I have another bunch of different configurations of the same molecule under different or the same conditions (this is unknown). How would I tell if they are under the same conditions or not?

This seems like a very general statistical question that I am sure some one has dealt with before in some form. Does anyone know? I need some good search words to google and get started...
 
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One way is, you could compute some numeric function of each molecule, intending to capture the relevant portions of the molecule's configuration with that number, and test for difference of means between the two groups.
 

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