Add MSA, resolution parsing, and switch to hybrid-resolution confidence head and labels (#168)

Add MSA, resolution parsing, and switch to hybrid-resolution confidence head and labels

Author: amorehead

README.md

@@ -98,10 +98,7 @@ atom_pos = torch.randn(2, atom_seq_len, 3)
 molecule_atom_indices = molecule_atom_lens - 1 # last atom, as an example
 
 distance_labels = torch.randint(0, 37, (2, seq_len, seq_len))
-pae_labels = torch.randint(0, 64, (2, seq_len, seq_len))
-pde_labels = torch.randint(0, 64, (2, seq_len, seq_len))
-plddt_labels = torch.randint(0, 50, (2, seq_len))
-resolved_labels = torch.randint(0, 2, (2, seq_len))
+resolved_labels = torch.randint(0, 2, (2, atom_seq_len))
 
 # train
 
@@ -122,9 +119,6 @@ loss = alphafold3(
     atom_pos = atom_pos,
     molecule_atom_indices = molecule_atom_indices,
     distance_labels = distance_labels,
-    pae_labels = pae_labels,
-    pde_labels = pde_labels,
-    plddt_labels = plddt_labels,
     resolved_labels = resolved_labels
 )