RESTCapableHybridTopologyFactory working with small molecules

[ijpulidos]

Description

the lambda_protocol option for the HybridRepexSampler object was being specified, forcing LambdaProtocol() (which can only be used with HybridTopologyFactory, not RESTCapableHybridTopologyFactory) to be used. lambda_protocol is now left undefined, so that the HybridRepexSampler will automatically detect and choose the appropriate lambda protocol according to the HTF.

Motivation and context

Resolves #1039

How has this been tested?

Tested locally with partial tyk2 benchmark simulation

Change log

Bug fix when trying to use the new `RESTCapableHybridTopologyFactory` in the small molecule pipeline -- fixed by not specifying a protocol, hence allowing the `HybridCompatibilityMixin` object to automatically handle it.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 52.28%. Comparing base (af66f31) to head (0a09e2e).
Report is 66 commits behind head on main.

Additional details and impacted files

[zhang-ivy]

@ijpulidos : LGTM! I just made some clarifying changes to the description.