Fix residue readout

compomics · May 13, 2024 · e890279 · e890279
1 parent bafbdf2
commit e890279
Showing 1 changed file with 13 additions and 17 deletions.
diff --git a/molexpress/layers/residue_readout.py b/molexpress/layers/residue_readout.py
@@ -22,8 +22,8 @@ def build(self, input_shape: dict[str, tuple[int, ...]]) -> None:
             raise ValueError("Cannot perform readout: 'residue_size' not found.")
 
     def call(self, inputs: types.MolecularGraph) -> types.Array:
-        peptide_size = keras.ops.cast(inputs['peptide_size'], 'int32')
-        residue_size = keras.ops.cast(inputs['residue_size'], 'int32')
+        peptide_size = keras.ops.cast(inputs["peptide_size"], "int32")
+        residue_size = keras.ops.cast(inputs["residue_size"], "int32")
         n_residues = keras.ops.shape(residue_size)[0]
         segment_ids = keras.ops.repeat(range(n_residues), residue_size)
         residue_state = self._readout_fn(
@@ -34,25 +34,21 @@ def call(self, inputs: types.MolecularGraph) -> types.Array:
         )
         # Make shape known
         residue_state = keras.ops.reshape(
-            residue_state, 
-            (
-                keras.ops.shape(residue_size)[0], 
-                keras.ops.shape(inputs['node_state'])[-1]
-            )
+            residue_state,
+            (keras.ops.shape(residue_size)[0], keras.ops.shape(inputs["node_state"])[-1]),
         )
-        
+
         if keras.ops.shape(peptide_size)[0] == 1:
             # Single peptide in batch
             return residue_state[None]
-        
+
         # Split and stack (with padding in the second dim)
         # Resulting shape: (n_peptides, n_residues, n_features)
-        residues = keras.ops.split(residue_state, peptide_size[:-1])
+        residues = keras.ops.split(residue_state, keras.ops.cumsum(peptide_size)[:-1])
         max_residue_size = keras.ops.max([len(r) for r in residues])
-        return keras.ops.stack([
-            keras.ops.pad(r, [(0, max_residue_size-keras.ops.shape(r)[0]), (0, 0)])
-            for r in residues
-        ])
-
-
-
+        return keras.ops.stack(
+            [
+                keras.ops.pad(r, [(0, max_residue_size - keras.ops.shape(r)[0]), (0, 0)])
+                for r in residues
+            ]
+        )