I have a very large library (almost 1000) of similar genetic
sequences, for which I would like to generate homology models. Does
anyone know of a way to automate requests to a homology modeling
server, such as SWISS-Model through pymol, or alternatively through
I believe Modeller uses Python - never tried it myself, though. There is a server for Modeller but academic users can download the program itself.
There is in fact an API for using SWISS-Model from a Perl script (which could probably be converted to Python, or wrapped by a Python script), which I used years ago for a similar project. As far as I know this is unpublished, probably because they don't want people to trash their server, but they were happy to supply it when I contacted the site maintainer. They asked that I limit the frequency of my requests, however. I would recommend emailing them. (I have no idea how Modeller compares to SWISS-Model, but I suspect it's more rigorous, especially when sequence homology is remote.)
There are other ways to go about this - bioinformaticists have been abusing online databases and servers like this for years - but it's considered bad etiquette to do this without permission (and some groups explicitly forbid this use).