Merge pull request #52 from Julicancode/3D_to_2D

Update visualisation of molecules to 2D

src/konnektor/visualization/widget.py

@@ -25,11 +25,15 @@ def get_node_connectivities(cg: LigandNetwork) -> list[int]:
 
 # some code borrowed from pen:
 # https://iwatobipen.wordpress.com/2020/03/30/draw-scaffold-tree-as-network-with-molecular-image-rdkit-cytoscape/
-def mol2svg(mol: Chem.Mol) -> str:
+def mol2svg(mol: Chem.Mol, represent_molecules_twoD:bool=False) -> str:
     try:
         Chem.rdmolops.Kekulize(mol)
     except:
         pass
+
+    if represent_molecules_twoD:
+        Chem.rdDepictor.Compute2DCoords(mol)
+
     drawer = rdMolDraw2D.MolDraw2DSVG(350, 300)
     rdMolDraw2D.PrepareAndDrawMolecule(drawer, mol)  # , legend=mol.GetProp("_Name"))
     drawer.SetColour((184 / 256, 87 / 256, 65 / 256))  # Transparent white background
@@ -64,6 +68,7 @@ def _build_cytoscape(
     network: gufe.LigandNetwork,
     layout: str = "concentric",
     show_molecules: bool = True,
+    represent_molecules_twoD: bool = False,
     show_mappings: bool = False,
 ) -> ipycytoscape.CytoscapeWidget:
     ligands = list(network.nodes)
@@ -95,7 +100,7 @@ def _build_cytoscape(
             {
                 "name": n.name,
                 "classes": "ligand",
-                "img": mol2svg(n.to_rdkit()),
+                "img": mol2svg(n.to_rdkit(),  represent_molecules_twoD=represent_molecules_twoD),
                 "col": c,
             },
         )
@@ -218,6 +223,7 @@ def draw_network_widget(
     network: gufe.LigandNetwork,
     layout: str = "cose",
     show_molecules: bool = True,
+    represent_molecules_twoD: bool = False
     show_mappings: bool = False,
 ) -> ipycytoscape.CytoscapeWidget:
     """For use in a jupyter noterbook, visualise a LigandNetwork
@@ -231,6 +237,8 @@ def draw_network_widget(
       defaults to 'cose'
     show_molecule: bool, optional
       if to show molecule images on the representation, default True
+    represent_molecules_twoD: bool, optional
+      show the molecules in the nodes as 2D representations.
     show_mappings: bool, optional
       if to show mapping images on the representation, default False
     """
@@ -243,12 +251,14 @@ def interactive_widget(
         network=network,
         layout=layout,
         show_molecules=show_molecules,
+        represent_molecules_twoD=represent_molecules_twoD,
         show_mappings=show_mappings,
     ):
         v = _build_cytoscape(
             network=network,
             layout=layout,
             show_molecules=show_molecules,
+            represent_molecules_twoD=represent_molecules_twoD,
             show_mappings=show_mappings,
         )
         return v