make build_atomic_graph and build_residue_graph look similar

this is a preparation for the next commit, where the functions are unified.
here only variables are renamed and spacing is changed so that it is easy to see what
the similarities and differences between the functions are.

deeprank2/molstruct/residue.py

@@ -97,7 +97,7 @@ def __repr__(self) -> str:
 
     @property
     def position(self) -> np.array:
-        return np.mean([atom.position for atom in self._atoms], axis=0)
+        return self.get_center()
 
     def get_center(self) -> NDArray:
         """Find the center position of a `Residue`.

deeprank2/utils/graph.py

@@ -59,7 +59,6 @@ def __init__(self, id_: Atom | Residue):
             raise TypeError(type(id_))
 
         self.id = id_
-
         self.features = {}
 
     @property
@@ -319,8 +318,10 @@ def get_all_chains(self) -> list[str]:
         return list(chains)
 
 
-def build_atomic_graph( # pylint: disable=too-many-locals
-    atoms: list[Atom], graph_id: str, max_edge_length: float
+def build_atomic_graph(
+    atoms: list[Atom],
+    graph_id: str,
+    max_edge_length: float,
 ) -> Graph:
     """Builds a graph, using the atoms as nodes.
 
@@ -333,19 +334,18 @@ def build_atomic_graph( # pylint: disable=too-many-locals
 
     distances = distance_matrix(positions, positions, p=2)
     neighbours = distances < max_edge_length
+    atom_index_pairs = np.transpose(np.nonzero(neighbours))
 
     graph = Graph(graph_id)
-    for atom1_index, atom2_index in np.transpose(np.nonzero(neighbours)):
-        if atom1_index != atom2_index:
+    for index1, index2 in atom_index_pairs:
+        if index1 != index2:
 
-            atom1 = atoms[atom1_index]
-            atom2 = atoms[atom2_index]
-            contact = AtomicContact(atom1, atom2)
+            node1 = Node(atoms[index1])
+            node2 = Node(atoms[index2])
+            contact = AtomicContact(node1.id, node2.id)
 
-            node1 = Node(atom1)
-            node2 = Node(atom2)
-            node1.features[Nfeat.POSITION] = atom1.position
-            node2.features[Nfeat.POSITION] = atom2.position
+            node1.features[Nfeat.POSITION] = node1.id.position
+            node2.features[Nfeat.POSITION] = node2.id.position
 
             graph.add_node(node1)
             graph.add_node(node2)
@@ -355,11 +355,13 @@ def build_atomic_graph( # pylint: disable=too-many-locals
 
 
 def build_residue_graph( # pylint: disable=too-many-locals
-    residues: list[Residue], graph_id: str, max_edge_length: float
+    residues: list[Residue],
+    graph_id: str,
+    max_edge_length: float,
 ) -> Graph:
     """Builds a graph, using the residues as nodes.
 
-    The max edge distance is in Ångströms.
+    The max edge length is in Ångströms.
     It's the shortest interatomic distance between two residues.
     """
 
@@ -379,8 +381,6 @@ def build_residue_graph( # pylint: disable=too-many-locals
         positions[atom_index] = atom.position
 
     distances = distance_matrix(positions, positions, p=2)
-
-    # determine which atoms are close enough
     neighbours = distances < max_edge_length
 
     atom_index_pairs = np.transpose(np.nonzero(neighbours))
@@ -390,26 +390,20 @@ def build_residue_graph( # pylint: disable=too-many-locals
 
     # build the graph
     graph = Graph(graph_id)
-    for residue1_index, residue2_index in residue_index_pairs:
+    for index1, index2 in residue_index_pairs:
+        if index1 != index2:
 
-        residue1: Residue = residues[residue1_index]
-        residue2: Residue = residues[residue2_index]
+            node1 = Node(residues[index1])
+            node2 = Node(residues[index2])
+            contact = ResidueContact(node1.id, node2.id)
 
-        if residue1 != residue2:
+            node1.features[Nfeat.POSITION] = node1.id.position
+            node2.features[Nfeat.POSITION] = node2.id.position
 
-            contact = ResidueContact(residue1, residue2)
-
-            node1 = Node(residue1)
-            node2 = Node(residue2)
-            edge = Edge(contact)
-
-            node1.features[Nfeat.POSITION] = residue1.get_center()
-            node2.features[Nfeat.POSITION] = residue2.get_center()
-
-            # The same residue will be added  multiple times as a node,
+            # The same residue will be added multiple times as a node,
             # but the Graph class fixes this.
             graph.add_node(node1)
             graph.add_node(node2)
-            graph.add_edge(edge)
+            graph.add_edge(Edge(contact))
 
     return graph