function to create bipartite networks from scaffold graphs

Author: Oliver Scott

scaffoldgraph/utils/bipartite.py

@@ -0,0 +1,40 @@
+"""
+scaffoldgraph.utils.bipartite
+
+Defines functions for creating bipartite graphs from scaffold graphs.
+"""
+
+from scaffoldgraph.core import ScaffoldGraph
+
+
+def make_bipartite_graph(graph):
+    """Collapse a scaffold hierarchy into a bipartite representation.
+
+    Scaffold --> Molecule
+
+    The returned output will inherit the class of the input graph.
+
+    Parameters
+    ----------
+    graph : sg.core.ScaffoldGraph
+        A scaffold graph template for producing a bipaertite
+        graph.
+
+    Returns
+    -------
+    sg.core.ScaffoldGraph
+        Bipartite scaffoldgraph where the scaffold hierarchy
+        has been collapsed.
+
+    """
+    if not issubclass(type(graph), ScaffoldGraph):
+        raise ValueError(f'{graph} must be a ScaffoldGraph')
+    graph_type = type(graph)
+    B = graph_type(None)
+    for scf, sdata in graph.get_scaffold_nodes(True):
+        B.add_node(scf, **sdata)
+        for mol, mdata in graph.get_molecules_for_scaffold(scf, True):
+            if not B.molecule_in_graph(mol):
+                B.add_node(mol, **mdata)
+            B.add_edge(scf, mol)
+    return B