ScoreFunction

The ScoreFunction calculates the energies of a PoseStack using a weighted sum of EnergyTerms. Many EnergyTerms are provided, some of which represent physical forces like electrostatics and van der Waals' interactions, while others represent statistical terms like the probability of finding the torsion angles in Ramachandran space. New score terms may also be added.

Whole-Pose vs Block-Pair scoring

Two varieties of ScoreFunction are provided: whole-pose and block-pair scoring. In whole-pose scoring, energies are provided in sum for the whole of each structure in the PoseStack. In block-pair scoring, energies are provided between every pair of blocks in each of the structures as a NxN tensor. In block-pair scoring, one-body terms still return an NxN tensor with values being placed only on the diagonal.

Derivatives

Torch uses a system called autograd to automatically collect gradients. The ScoreFunction uses this to collect gradients across all the constituent sub-terms, giving you a complete gradient for the whole function.