From cd50b19257109fd7a2d2f8ab082d1c535e462dd8 Mon Sep 17 00:00:00 2001
From: Alexander Kensert <alexander.kensert@gmail.com>
Date: Mon, 15 Apr 2024 16:53:43 +0200
Subject: [PATCH] improve readability

---
 molexpress/datasets/encoders.py | 40 +++++++++++++++++----------------
 1 file changed, 21 insertions(+), 19 deletions(-)

diff --git a/molexpress/datasets/encoders.py b/molexpress/datasets/encoders.py
index 442cc44..d40d5b0 100644
--- a/molexpress/datasets/encoders.py
+++ b/molexpress/datasets/encoders.py
@@ -17,20 +17,20 @@ def __init__(
         self.node_encoder = MolecularNodeEncoder(atom_featurizers)
         self.edge_encoder = MolecularEdgeEncoder(bond_featurizers, self_loops=self_loops)
 
-    def __call__(self, molecules: list[types.Molecule | types.SMILES | types.InChI]) -> np.ndarray:
-        molecular_graphs = []
+    def __call__(self, residues: list[types.Molecule | types.SMILES | types.InChI]) -> np.ndarray:
+        residue_graphs = []
         residue_sizes = []
-        for molecule in molecules:
-            molecule = chem_ops.get_molecule(molecule)
-            molecular_graph = {
-                **self.node_encoder(molecule), 
-                **self.edge_encoder(molecule)
+        for residue in residues:
+            residue = chem_ops.get_molecule(residue)
+            residue_graph = {
+                **self.node_encoder(residue), 
+                **self.edge_encoder(residue)
             }
-            molecular_graphs.append(molecular_graph)
-            residue_sizes.append(molecule.GetNumAtoms())
-        graph = self._merge_molecular_graphs(molecular_graphs)
-        graph["residue_size"] = np.array(residue_sizes)
-        return graph 
+            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 
     
     @staticmethod
     def _collate_fn(
@@ -43,16 +43,18 @@ def _collate_fn(
             Merges list of graphs into a single disjoint graph.
         """
 
-        x, y = list(zip(*data))
+        disjoint_peptide_graphs, y = list(zip(*data))
 
-        disjoint_graph = PeptideGraphEncoder._merge_molecular_graphs(x)
-        disjoint_graph["peptide_size"] = np.concatenate([
-            graph["residue_size"].shape[:1] for graph in x
+        disjoint_peptide_batch_graph = PeptideGraphEncoder._merge_molecular_graphs(
+            disjoint_peptide_graphs
+        )
+        disjoint_peptide_batch_graph["peptide_size"] = np.concatenate([
+            g["residue_size"].shape[:1] for g in disjoint_peptide_graphs
         ]).astype("int32")
-        disjoint_graph["residue_size"] = np.concatenate([
-            graph["residue_size"] for graph in x
+        disjoint_peptide_batch_graph["residue_size"] = np.concatenate([
+            g["residue_size"] for g in disjoint_peptide_graphs
         ]).astype("int32")
-        return disjoint_graph, np.stack(y)
+        return disjoint_peptide_batch_graph, np.stack(y)
 
     @staticmethod
     def _merge_molecular_graphs(