avoid get_at when calculating surface score

Author: lucidrains

alphafold3_pytorch/alphafold3.py

@@ -5701,11 +5701,12 @@ def calc_atom_access_surface_score(
 
         max_included = include_in_free_calc.long().sum(dim = -1).amax()
 
-        include_indices = include_in_free_calc.long().topk(max_included, dim = -1).indices
+        include_in_free_calc, include_indices = include_in_free_calc.long().topk(max_included, dim = -1)
 
-        include_in_free_calc = einx.get_at('i [m], i j -> i j', include_in_free_calc, include_indices)
-        atom_rel_pos = einx.get_at('i [m] c, i j -> i j c', atom_rel_pos, include_indices)
-        target_atom_radii_sq = einx.get_at('[m], i j -> i j', atom_radii_sq, include_indices)
+        # atom_rel_pos = einx.get_at('i [m] c, i j -> i j c', atom_rel_pos, include_indices)
+
+        atom_rel_pos = atom_rel_pos.gather(1, repeat(include_indices, 'i j -> i j c', c = 3))
+        target_atom_radii_sq = atom_radii_sq[include_indices]
 
         # overall logic
 

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "alphafold3-pytorch"
-version = "0.5.52"
+version = "0.5.53"
 description = "Alphafold 3 - Pytorch"
 authors = [
     { name = "Phil Wang", email = "[email protected]" },