move towards using residue_atom_lens for both packed and unpacked rep…

…resentations for clarity. atom mask internally derived for atom transformer

README.md

@@ -36,7 +36,7 @@ seq_len = 16
 atom_seq_len = seq_len * 27
 
 atom_inputs = torch.randn(2, atom_seq_len, 77)
-atom_mask = torch.ones((2, atom_seq_len)).bool()
+atom_lens = torch.randint(0, 27, (2, seq_len))
 atompair_feats = torch.randn(2, atom_seq_len, atom_seq_len, 16)
 additional_residue_feats = torch.randn(2, seq_len, 33)
 
@@ -61,7 +61,7 @@ resolved_labels = torch.randint(0, 2, (2, seq_len))
 loss = alphafold3(
     num_recycling_steps = 2,
     atom_inputs = atom_inputs,
-    atom_mask = atom_mask,
+    residue_atom_lens = atom_lens,
     atompair_feats = atompair_feats,
     additional_residue_feats = additional_residue_feats,
     msa = msa,

alphafold3_pytorch/alphafold3.py

@@ -55,6 +55,8 @@
 
 # constants
 
+DIM_ADDITIONAL_RESIDUE_FEATS = 10
+
 LinearNoBias = partial(Linear, bias = False)
 
 # helper functions
@@ -1435,7 +1437,8 @@ def forward(
         w = self.atoms_per_window
         is_unpacked_repr = exists(w)
 
-        assert is_unpacked_repr ^ exists(residue_atom_lens), '`residue_atom_lens` must be passed in if using packed_atom_repr (atoms_per_window is None)'
+        if not is_unpacked_repr:
+            assert exists(residue_atom_lens), '`residue_atom_lens` must be passed in if using packed_atom_repr (atoms_per_window is None)'
 
         atom_feats = self.proj(atom_feats)
 
@@ -1613,7 +1616,8 @@ def forward(
         w = self.atoms_per_window
         is_unpacked_repr = exists(w)
 
-        assert is_unpacked_repr ^ exists(residue_atom_lens)
+        if not is_unpacked_repr:
+            assert exists(residue_atom_lens)
 
         # in the paper, it seems they pack the atom feats
         # but in this impl, will just use windows for simplicity when communicating between atom and residue resolutions. bit less efficient
@@ -2350,7 +2354,6 @@ def __init__(
         self,
         *,
         dim_atom_inputs,
-        dim_additional_residue_feats = 10,
         atoms_per_window = 27,
         dim_atom = 128,
         dim_atompair = 16,
@@ -2396,9 +2399,7 @@ def __init__(
             atoms_per_window = atoms_per_window
         )
 
-        dim_single_input = dim_token + dim_additional_residue_feats
-
-        self.dim_additional_residue_feats = dim_additional_residue_feats
+        dim_single_input = dim_token + DIM_ADDITIONAL_RESIDUE_FEATS
 
         self.single_input_to_single_init = LinearNoBias(dim_single_input, dim_single)
         self.single_input_to_pairwise_init = LinearNoBiasThenOuterSum(dim_single_input, dim_pairwise)
@@ -2415,7 +2416,7 @@ def forward(
 
     ) -> EmbeddedInputs:
 
-        assert additional_residue_feats.shape[-1] == self.dim_additional_residue_feats
+        assert additional_residue_feats.shape[-1] == DIM_ADDITIONAL_RESIDUE_FEATS
 
         w = self.atoms_per_window
 
@@ -2608,7 +2609,6 @@ def __init__(
         self,
         *,
         dim_atom_inputs,
-        dim_additional_residue_feats,
         dim_template_feats,
         dim_template_model = 64,
         atoms_per_window = 27,
@@ -2713,7 +2713,6 @@ def __init__(
 
         self.input_embedder = InputFeatureEmbedder(
             dim_atom_inputs = dim_atom_inputs,
-            dim_additional_residue_feats = dim_additional_residue_feats,
             atoms_per_window = atoms_per_window,
             dim_atom = dim_atom,
             dim_atompair = dim_atompair,
@@ -2723,7 +2722,7 @@ def __init__(
             **input_embedder_kwargs
         )
 
-        dim_single_inputs = dim_input_embedder_token + dim_additional_residue_feats
+        dim_single_inputs = dim_input_embedder_token + DIM_ADDITIONAL_RESIDUE_FEATS
 
         # relative positional encoding
         # used by pairwise in main alphafold2 trunk
@@ -2866,22 +2865,28 @@ def forward(
 
         atom_seq_len = atom_inputs.shape[-2]
 
+        assert exists(residue_atom_lens) or exists(atom_mask)
+
         # determine whether using packed or unpacked atom rep
 
-        assert exists(residue_atom_lens) ^ exists(atom_mask), 'either atom_lens or atom_mask must be given depending on whether packed_atom_repr kwarg is True or False'
+        if self.packed_atom_repr:
+            assert exists(residue_atom_lens), 'residue_atom_lens must be given if using packed atom repr'
 
         if exists(residue_atom_lens):
-            assert self.packed_atom_repr, '`packed_atom_repr` kwarg on Alphafold3 must be True when passing in `atom_lens`'
 
-            # handle atom mask
+            if self.packed_atom_repr:
+                # handle atom mask
 
-            total_atoms = residue_atom_lens.sum(dim = -1)
-            atom_mask = lens_to_mask(total_atoms, max_len = atom_seq_len)
+                total_atoms = residue_atom_lens.sum(dim = -1)
+                atom_mask = lens_to_mask(total_atoms, max_len = atom_seq_len)
 
-            # handle offsets for residue atom indices
+                # handle offsets for residue atom indices
 
-            if exists(residue_atom_indices):
-                residue_atom_indices += F.pad(residue_atom_lens, (-1, 1), value = 0)
+                if exists(residue_atom_indices):
+                    residue_atom_indices += F.pad(residue_atom_lens, (-1, 1), value = 0)
+            else:
+                atom_mask = lens_to_mask(residue_atom_lens, max_len = self.atoms_per_window)
+                atom_mask = rearrange(atom_mask, 'b ... -> b (...)')
 
         # get atom sequence length and residue sequence length depending on whether using packed atomic seq
 

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "alphafold3-pytorch"
-version = "0.0.34"
+version = "0.0.36"
 description = "Alphafold 3 - Pytorch"
 authors = [
     { name = "Phil Wang", email = "[email protected]" }

tests/test_af3.py

@@ -344,7 +344,6 @@ def test_input_embedder():
 
     embedder = InputFeatureEmbedder(
         dim_atom_inputs = 77,
-        dim_additional_residue_feats = 10
     )
 
     embedder(
@@ -369,7 +368,7 @@ def test_alphafold3():
     token_bond = torch.randint(0, 2, (2, seq_len, seq_len)).bool()
 
     atom_inputs = torch.randn(2, atom_seq_len, 77)
-    atom_mask = torch.ones((2, atom_seq_len)).bool()
+    atom_lens = torch.randint(0, 27, (2, seq_len))
     atompair_feats = torch.randn(2, atom_seq_len, atom_seq_len, 16)
     additional_residue_feats = torch.randn(2, seq_len, 10)
 
@@ -389,7 +388,6 @@ def test_alphafold3():
 
     alphafold3 = Alphafold3(
         dim_atom_inputs = 77,
-        dim_additional_residue_feats = 10,
         dim_template_feats = 44,
         num_dist_bins = 38,
         confidence_head_kwargs = dict(
@@ -414,7 +412,7 @@ def test_alphafold3():
     loss, breakdown = alphafold3(
         num_recycling_steps = 2,
         atom_inputs = atom_inputs,
-        atom_mask = atom_mask,
+        residue_atom_lens = atom_lens,
         atompair_feats = atompair_feats,
         additional_residue_feats = additional_residue_feats,
         token_bond = token_bond,
@@ -437,7 +435,7 @@ def test_alphafold3():
     sampled_atom_pos = alphafold3(
         num_sample_steps = 16,
         atom_inputs = atom_inputs,
-        atom_mask = atom_mask,
+        residue_atom_lens = atom_lens,
         atompair_feats = atompair_feats,
         additional_residue_feats = additional_residue_feats,
         msa = msa,
@@ -452,7 +450,7 @@ def test_alphafold3_without_msa_and_templates():
     atom_seq_len = seq_len * 27
 
     atom_inputs = torch.randn(2, atom_seq_len, 77)
-    atom_mask = torch.ones((2, atom_seq_len)).bool()
+    atom_lens = torch.randint(0, 27, (2, seq_len))
     atompair_feats = torch.randn(2, atom_seq_len, atom_seq_len, 16)
     additional_residue_feats = torch.randn(2, seq_len, 10)
 
@@ -467,7 +465,6 @@ def test_alphafold3_without_msa_and_templates():
 
     alphafold3 = Alphafold3(
         dim_atom_inputs = 77,
-        dim_additional_residue_feats = 10,
         dim_template_feats = 44,
         num_dist_bins = 38,
         confidence_head_kwargs = dict(
@@ -492,7 +489,7 @@ def test_alphafold3_without_msa_and_templates():
     loss, breakdown = alphafold3(
         num_recycling_steps = 2,
         atom_inputs = atom_inputs,
-        atom_mask = atom_mask,
+        residue_atom_lens = atom_lens,
         atompair_feats = atompair_feats,
         additional_residue_feats = additional_residue_feats,
         atom_pos = atom_pos,
@@ -536,7 +533,6 @@ def test_alphafold3_with_packed_atom_repr():
 
     alphafold3 = Alphafold3(
         dim_atom_inputs = 77,
-        dim_additional_residue_feats = 10,
         dim_template_feats = 44,
         num_dist_bins = 38,
         packed_atom_repr = True,