fix some logic with has_{embed_type}

Author: lucidrains

alphafold3_pytorch/alphafold3.py

@@ -3053,8 +3053,11 @@ def __init__(
 
         # optional atom and atom bond embeddings
 
-        has_atom_embeds = exists(num_atom_embeds)
-        has_atompair_embeds = exists(num_atompair_embeds)
+        num_atom_embeds = default(num_atom_embeds, 0)
+        num_atompair_embeds = default(num_atompair_embeds, 0)
+
+        has_atom_embeds = num_atom_embeds > 0
+        has_atompair_embeds = num_atompair_embeds > 0
 
         if has_atom_embeds:
             self.atom_embeds = nn.Embedding(num_atom_embeds, dim_atom)
@@ -3067,6 +3070,8 @@ def __init__(
 
         # residue or nucleotide modifications
 
+        num_molecule_mods = default(num_molecule_mods, 0)
+
         has_molecule_mod_embeds = num_molecule_mods > 0
         self.num_molecule_mods = num_molecule_mods
 

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "alphafold3-pytorch"
-version = "0.1.109"
+version = "0.1.110"
 description = "Alphafold 3 - Pytorch"
 authors = [
     { name = "Phil Wang", email = "[email protected]" }