Python command line tool to get chemical structure In computational chemistry, we need to provide an starting molecular structure to start our calculations. Is there any way to get that from a chemical database? Say, I want to run H2, it would call something like     

url="www.chemicaldatabase.com"
H2=(url,H2)


or it can use smile/other standard symbols for chemical representation.
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.