Automated Identification of Isomeric Relationship from 3D Structure?
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).