Merge pull request #223 from datamol-io/fix/parse-args-in-lasso

Allow additional args for colors in lasso

Author: maclandrol

datamol/viz/_lasso_highlight.py

@@ -6,7 +6,7 @@
 # - possibility to do this for multiple target molecules at once
 # - have the option to write to a file like to_image
 
-from typing import List, Iterator, Tuple, Union, Optional, Any, cast
+from typing import List, Dict, Iterator, Tuple, Union, Optional, Any, cast
 
 from collections import defaultdict
 from collections import namedtuple
@@ -400,6 +400,10 @@ def lasso_highlight_image(
     line_width: int = 2,
     scale_padding: float = 1.0,
     verbose: bool = False,
+    highlight_atoms: Optional[List[List[int]]] = None,
+    highlight_bonds: Optional[List[List[int]]] = None,
+    highlight_atom_colors: Optional[List[Dict[int, DatamolColor]]] = None,
+    highlight_bond_colors: Optional[List[Dict[int, DatamolColor]]] = None,
     **kwargs: Any,
 ):
     """Create an image of a list of molecules with substructure matches using lasso-based highlighting.
@@ -408,7 +412,7 @@ def lasso_highlight_image(
     Args:
         target_molecules:  One or a list of molecules to be highlighted.
         search_molecules: The substructure to be highlighted.
-        atom_indices: Atom indices to be highlighted substructure.
+        atom_indices: Atom indices to be highlighted as substructure using the lasso visualization.
         legends: A string or a list of string as legend for every molecules.
         n_cols: Number of molecules per column.
         mol_size: The size of the image to be returned
@@ -421,6 +425,10 @@ def lasso_highlight_image(
         line_width: width of drawn lines.
         scale_padding: Padding around the molecule when drawing to scale.
         verbose: Whether to print the verbose information.
+        highlight_atoms: The atoms to highlight, a list for each molecule. It's the `highlightAtoms` argument of the RDKit drawer object.
+        highlight_bonds: The bonds to highlight, a list for each molecule. It's the `highlightBonds` argument of the RDKit drawer object.
+        highlight_atom_colors: The colors to use for highlighting atoms, a list of dict mapping atom index to color for each molecule.
+        highlight_bond_colors: The colors to use for highlighting bonds, a list of dict mapping bond index to color for each molecule.
         **kwargs: Additional arguments to pass to the drawing function. See RDKit
             documentation related to `MolDrawOptions` for more details at
             https://www.rdkit.org/docs/source/rdkit.Chem.Draw.rdMolDraw2D.html.
@@ -551,9 +559,38 @@ def lasso_highlight_image(
     # EN: the following is edge-case free after trying 6 different logics, but may break if RDKit changes the way it draws molecules
     scaling_val = Point2D(scale_padding, scale_padding)
 
+    if isinstance(highlight_atoms, list) and isinstance(highlight_atoms[0], int):
+        highlight_atoms = [highlight_atoms] * len(target_molecules)
+    if isinstance(highlight_bonds, list) and isinstance(highlight_bonds[0], int):
+        highlight_bonds = [highlight_bonds] * len(target_molecules)
+    if isinstance(highlight_atom_colors, dict):
+        highlight_atom_colors = [highlight_atom_colors] * len(target_molecules)
+    if isinstance(highlight_bond_colors, dict):
+        highlight_bond_colors = [highlight_bond_colors] * len(target_molecules)
+
+    # make sure we are using rdkit colors
+    if highlight_atom_colors is not None:
+        highlight_atom_colors = [
+            {k: to_rdkit_color(v) for k, v in _.items()} for _ in highlight_atom_colors
+        ]
+    if highlight_bond_colors is not None:
+        highlight_bond_colors = [
+            {k: to_rdkit_color(v) for k, v in _.items()} for _ in highlight_bond_colors
+        ]
+
+    kwargs["highlightAtoms"] = highlight_atoms
+    kwargs["highlightBonds"] = highlight_bonds
+    kwargs["highlightAtomColors"] = highlight_atom_colors
+    kwargs["highlightBondColors"] = highlight_bond_colors
+
     try:
-        drawer.DrawMolecules(mols_to_draw, legends=legends, **kwargs)
-    except Exception:
+        drawer.DrawMolecules(
+            mols_to_draw,
+            legends=legends,
+            **kwargs,
+        )
+    except Exception as e:
+        logger.error(e)
         raise ValueError(
             "Failed to draw molecules. Some arguments neither match expected MolDrawOptions, nor DrawMolecule inputs. Please check the input arguments."
         )
@@ -567,8 +604,18 @@ def lasso_highlight_image(
         h_pos, w_pos = np.unravel_index(ind, (n_rows, n_cols))
         offset_x = int(w_pos * mol_size[0])
         offset_y = int(h_pos * mol_size[1])
+
+        ind_kwargs = kwargs.copy()
+        if isinstance(ind_kwargs["highlightAtoms"], list):
+            ind_kwargs["highlightAtoms"] = ind_kwargs["highlightAtoms"][ind]
+        if isinstance(ind_kwargs["highlightAtomColors"], list):
+            ind_kwargs["highlightAtomColors"] = ind_kwargs["highlightAtomColors"][ind]
+        if isinstance(ind_kwargs["highlightBonds"], list):
+            ind_kwargs["highlightBonds"] = ind_kwargs["highlightBonds"][ind]
+        if isinstance(ind_kwargs["highlightBondColors"], list):
+            ind_kwargs["highlightBondColors"] = ind_kwargs["highlightBondColors"][ind]
         drawer.SetOffset(offset_x, offset_y)
-        drawer.DrawMolecule(mol, legend=legends[ind], **kwargs)
+        drawer.DrawMolecule(mol, legend=legends[ind], **ind_kwargs)
         offset = None
         if draw_mols_same_scale:
             offset = drawer.Offset()

datamol/viz/utils.py

@@ -141,6 +141,12 @@ def to_rdkit_color(color: Optional[DatamolColor]) -> Optional[RDKitColor]:
     Args:
         color: A datamol color: hex, rgb, rgba or None.
     """
+    if color is None:
+        return None
+
     if isinstance(color, str):
         return mcolors.to_rgba(color)  # type: ignore
+    if isinstance(color, (tuple, list)) and len(color) in [3, 4] and any(x > 1 for x in color):
+        return tuple(x / 255 if i < 3 else x for i, x in enumerate(color))
+
     return color

tests/test_viz_lasso_highlight.py

@@ -17,6 +17,30 @@ def test_from_mol():
     assert dm.lasso_highlight_image(mol, smarts_list)
 
 
+def test_with_highlight():
+    smi = "CO[C@@H](O)C1=C(O[C@H](F)Cl)C(C#N)=C1ONNC[NH3+]"
+    mol = dm.to_mol(smi)
+    smarts_list = "CONN"
+    highlight_atoms = [4, 5, 6]
+    highlight_bonds = [1, 2, 3, 4]
+    highlight_atom_colors = {4: (230, 230, 250), 5: (230, 230, 250), 6: (230, 230, 250)}
+    highlight_bond_colors = {
+        1: (230, 230, 250),
+        2: (230, 230, 250),
+        3: (230, 230, 250),
+        4: (230, 230, 250),
+    }
+    assert dm.lasso_highlight_image(
+        mol,
+        smarts_list,
+        highlight_atoms=highlight_atoms,
+        highlight_bonds=highlight_bonds,
+        highlight_atom_colors=highlight_atom_colors,
+        highlight_bond_colors=highlight_bond_colors,
+        continuousHighlight=False,
+    )
+
+
 def test_original_working_solution_list_single_str():
     smi = "CO[C@@H](O)C1=C(O[C@H](F)Cl)C(C#N)=C1ONNC[NH3+]"
     smarts_list = ["CONN"]