fix some test for now for multi_chain_permutation

Author: lucidrains

alphafold3_pytorch/alphafold3.py

@@ -2753,8 +2753,8 @@ def forward(
         pairwise_trunk: Float['b n n dpt'],
         pairwise_rel_pos_feats: Float['b n n dpr'],
         molecule_atom_lens: Int['b n'],
-        molecule_atom_indices: Int['b n'],
         token_bonds: Bool['b n n'],
+        molecule_atom_indices: Int['b n'] | None = None,
         missing_atom_mask: Bool['b m'] | None = None,
         atom_parent_ids: Int['b m'] | None = None,
         return_denoised_pos = False,
@@ -2822,7 +2822,7 @@ def forward(
 
         # section 4.2 - multi-chain permutation alignment
 
-        if single_structure_input:
+        if exists(molecule_atom_indices) and single_structure_input:
             try:
                 atom_pos_aligned_ground_truth = self.multi_chain_permutation_alignment(
                     pred_coords=denoised_atom_pos,

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "alphafold3-pytorch"
-version = "0.5.1"
+version = "0.5.2"
 description = "Alphafold 3 - Pytorch"
 authors = [
     { name = "Phil Wang", email = "[email protected]" },