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Is there a software package that when given two sets of 3D structures can return the isomeric relationship between them? Even if it was only able to state that they are conformational isomers that would be enough.

It appears that Jmol has the ability, but I am seeking a non-graphical solution that could be easily included in scripts that would compare many such pairs of structures - in addition, I'm not a java programmer.

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You might become interested in OpenBabel. Written in C++, it offers bindings to Python (ref). It looks like stereochemistry is covered more in detail (here, here) than the obchiral command (here).

OpenEye's Chemistry Toolkit, on the other hand, equally capable to read numerous chemical file types (ref), offers several approaches to detect stereochemistry (examples). Written in Python, it may offer an alternative starting point. Perhaps you qualify for one of their academic licenses (ref).

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