Release 10.0.3 (#292)

## What's new

* feat: allow passing size param to RDKit endpoints
(#290)

package.json

@@ -1,7 +1,7 @@
 {
   "name": "visyn_core",
   "description": "Core repository for datavisyn applications.",
-  "version": "10.0.2",
+  "version": "10.0.3",
   "author": {
     "name": "datavisyn GmbH",
     "email": "[email protected]",

visyn_core/rdkit/img_api.py

@@ -17,20 +17,22 @@
 
 
 @app.get("/", response_class=SvgResponse)
-def draw_smiles(structure: SmilesMolecule, substructure: SmilesMolecule | None = None, align: SmilesMolecule | None = None):
-    return draw(structure.mol, aligned(structure.mol, align and align.mol) or substructure and substructure.mol)
+def draw_smiles(
+    structure: SmilesMolecule, substructure: SmilesMolecule | None = None, align: SmilesMolecule | None = None, size: int = 300
+):
+    return draw(structure.mol, size=size, substructure=aligned(structure.mol, align and align.mol) or substructure and substructure.mol)
 
 
 @app.post("/")
-def multiple_images(structures: set[SmilesMolecule]):
-    return {m: draw(m.mol) for m in structures}
+def multiple_images(structures: set[SmilesMolecule], size: int = 300):
+    return {m: draw(m.mol, size=size) for m in structures}
 
 
 @app.get("/murcko/", response_class=SvgResponse)
-def draw_murcko(structure: SmilesMolecule):
+def draw_murcko(structure: SmilesMolecule, size: int = 300):
     """https://www.rdkit.org/docs/GettingStartedInPython.html#murcko-decomposition"""
     murcko = MurckoScaffold.GetScaffoldForMol(structure.mol)
-    return draw(murcko)
+    return draw(murcko, size=size)
 
 
 @app.get("/similarity/", response_class=SvgResponse)
@@ -44,12 +46,12 @@ def draw_molecule_similarity(structure: SmilesMolecule, reference: SmilesMolecul
 
 
 @app.post("/mcs/", response_class=SvgResponse)
-def draw_maximum_common_substructure_molecule(structures: list[SmilesMolecule]):
+def draw_maximum_common_substructure_molecule(structures: list[SmilesMolecule], size: int = 300):
     unique = [m.mol for m in set(structures)]
     mcs = maximum_common_substructure_query_mol(unique)
     if not mcs or not isinstance(mcs, Mol):
         return Response("null", status_code=HTTP_204_NO_CONTENT)
-    return draw(mcs)
+    return draw(mcs, size=size)
 
 
 @app.post("/substructures/")

visyn_core/rdkit/util/draw.py

@@ -1,44 +1,34 @@
-from collections.abc import Callable
-
 from rdkit.Chem import Mol  # type: ignore
 from rdkit.Chem.Draw import SimilarityMaps, rdMolDraw2D  # type: ignore
 from rdkit.Chem.Draw.rdMolDraw2D import MolDraw2DSVG  # type: ignore
 from rdkit.Chem.Draw.SimilarityMaps import GetSimilarityMapForFingerprint  # type: ignore
 
 
-def _draw_wrapper(draw_inner: Callable[[MolDraw2DSVG, ...], None]) -> Callable[..., str]:  # type: ignore
-    """Function wrapper for drawing
-
-    Can annotate any function that takes a drawer as first arg, ignores its return type
-    Passes a drawer into annotated function
-    Passes on args and kwargs
-    Returns a svg as string
-    """
-
-    def inner(*args, **kwargs):
-        drawer = rdMolDraw2D.MolDraw2DSVG(300, 300)
-        _options = drawer.drawOptions()
-        _options.clearBackground = False
-
-        draw_inner(drawer, *args, **kwargs)
+def get_drawer(size: int):
+    drawer = rdMolDraw2D.MolDraw2DSVG(size, size)
+    _options = drawer.drawOptions()
+    _options.clearBackground = False
+    return drawer
 
-        drawer.FinishDrawing()
-        return drawer.GetDrawingText().replace("<?xml version='1.0' encoding='iso-8859-1'?>\n", "")
 
-    return inner
+def finish_drawing(drawer: MolDraw2DSVG) -> str:
+    drawer.FinishDrawing()
+    return drawer.GetDrawingText().replace("<?xml version='1.0' encoding='iso-8859-1'?>\n", "")
 
 
-@_draw_wrapper
-def draw(drawer: MolDraw2DSVG, structure, substructure=None):
+def draw(structure, *, size: int, substructure: str | None = None):
+    drawer = get_drawer(size)
     highlight_atoms = structure.GetSubstructMatch(substructure) if substructure else None
     drawer.DrawMolecule(structure, highlightAtoms=highlight_atoms, highlightBonds=None, highlightAtomColors=None, highlightBondColors=None)
+    return finish_drawing(drawer)
 
 
 def _similarity(m, i):
     """https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/Draw/SimilarityMaps.py"""
     return SimilarityMaps.GetMorganFingerprint(m, i, radius=2, fpType="bv")
 
 
-@_draw_wrapper
-def draw_similarity(drawer: MolDraw2DSVG, ref: Mol, probe=Mol, *_):  # ignore args after probe
+def draw_similarity(ref: Mol, probe=Mol, *_):  # ignore args after probe
+    drawer = get_drawer(300)
     GetSimilarityMapForFingerprint(ref, probe, fpFunction=_similarity, draw2d=drawer)
+    return finish_drawing(drawer)