Would it perhaps make sense for wrappers like pdb2gmx.py to be auto-generated from a CWL tool description?
Somewhat related (but different granularity) - running cwltools from Jupyter iPython Notebook:
import cwltool.factory
f = cwltool.factory.Factory()
echo = f.make("v1.0/v1.0/echo-tool.cwl")
out = echo(in="foo")