Merge pull request #3 from compomics/fixes

Various fixes

molexpress/datasets/encoders.py

@@ -1,5 +1,7 @@
 from __future__ import annotations
 
+from typing import Union
+
 import numpy as np
 
 from molexpress import types
@@ -23,27 +25,32 @@ def __call__(self, residues: list[types.Molecule | types.SMILES | types.InChI])
         for residue in residues:
             residue = chem_ops.get_molecule(residue)
             residue_graph = {
-                **self.node_encoder(residue), 
+                **self.node_encoder(residue),
                 **self.edge_encoder(residue)
             }
             residue_graphs.append(residue_graph)
             residue_sizes.append(residue.GetNumAtoms())
         disjoint_peptide_graph = self._merge_molecular_graphs(residue_graphs)
         disjoint_peptide_graph["residue_size"] = np.array(residue_sizes)
-        return disjoint_peptide_graph 
-
+        disjoint_peptide_graph["peptide_size"] = np.array([len(residues)], dtype="int32")
+        return disjoint_peptide_graph
+
     @staticmethod
-    def _collate_fn(
-        data: list[tuple[types.MolecularGraph, np.ndarray]],
+    def collate_fn(
+        data: list[Union[types.MolecularGraph, tuple[types.MolecularGraph, np.ndarray]]],
     ) -> tuple[types.MolecularGraph, np.ndarray]:
-        """TODO: Not sure where to implement this collate function.
-                 Temporarily putting it here.
-
-        Procedure:
-            Merges list of graphs into a single disjoint graph.
         """
+        Merge list of graphs into a single disjoint graph.
 
-        disjoint_peptide_graphs, y = list(zip(*data))
+        Data can be a list of MolecularGraphs or a list of tuples where the first element is a
+        MolecularGraph and the second element is a label.
+
+        """
+        if isinstance(data[0], tuple):
+            disjoint_peptide_graphs, y = list(zip(*data))
+        else:
+            disjoint_peptide_graphs = data
+            y = None
 
         disjoint_peptide_batch_graph = PeptideGraphEncoder._merge_molecular_graphs(
             disjoint_peptide_graphs
@@ -54,7 +61,11 @@ def _collate_fn(
         disjoint_peptide_batch_graph["residue_size"] = np.concatenate([
             g["residue_size"] for g in disjoint_peptide_graphs
         ]).astype("int32")
-        return disjoint_peptide_batch_graph, np.stack(y)
+
+        if y is None:
+            return disjoint_peptide_batch_graph
+        else:
+            return disjoint_peptide_batch_graph, np.stack(y)
 
     @staticmethod
     def _merge_molecular_graphs(

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
+            ]
+        )