Python command line tool to get chemical structure
There are multiple approaches in Python.

My suggestion would be to use a cheminformatics library like Open Babel or RDKit to convert from SMILES (for example) to 3D coordinates.

If you want to grab from chemical databases, I can suggest two approaches:


CIRPy - Uses the NIH chemical resolver to convert from names, SMILES, etc. into 3D structures. 
Webel - This is a web-based cheminformatics tool. I've used it in the past, but I'm not sure if it's still maintained.


There are other databases, including my PQR and PubChemQC that offer QM-optimized geometries.

The catch with databases is that you might want the geometry of a molecule that's not in the database. In that case, Open Babel or RDKit is a better solution.

One other caveat. Nothing I've indicated above does a very good job with metal-containing species. If you want ferrocene, that's a trickier problem with current solutions.