Large protein optimizations

[jacktday]

Modelling of whole proteins is problematically slow. This change allows a fairly old laptop to calculate the maps for GPCRs in seconds to minutes. It would hang for 10s of minutes before this change.

[joanimato]

@jacktday Can you provide a couple of examples for this change and the scripts to run them?

Thanks!

[jacktday]

@joanimato what sort of examples do you want? I haven't touched this code in about a year, so I've lost a lot of context.

Also are you guys interested in an OpenCL version of the force maps?

What is the plan for Vina Autodock going forward?

Thanks,
Jack

[joanimato]

@jacktday : Any examples that deal with the feature implemented here. Since this PR deals with whole proteins, something along those lines.

For now, our plan is maintenance and making sure the software works as intended. However, if you have implemented any new features, feel free to open another PR as long as it doesn't break existing functionality. We're trying to standardize this process a bit, ideally with examples and tests for every new feature added.