Author: Brian Coventry (2020)
The SAP score is a property of proteins that determines how aggregation prone they are. This was originally developed for antibodies, but it has tons of uses for proteins. It comes from this paper:
Developability Index: A Rapid In Silico Tool for the Screening of Antibody Aggregation Propensity
Brian Coventry added various ways to calculate this as well as design with it to Rosetta. See below for the various options.
The radius that determines which residues are considered when calculating the SAP score of a particular residue or region is 5Å.
These metrics calculate SAP scores:
For these to work. You must enable the sap_constraint scoreterm. Ideally with weight = 1.
You can get whole-pose, per-residue, and per-atom sap scores with these functions.
core.pack.guidance_scoreterms.sap.calculate_sap()
core.pack.guidance_scoreterms.sap.calculate_per_res_sap()
core.pack.guidance_scoreterms.sap.calculate_per_atom_sap()