Implementation of Interaction Occurence Percentage in LigNetwork (#234)

* Update network.py Addition of Occurence Percentage * Update CHANGELOG.md added change * chore: expose interaction data as both label and hover title * chore: fix ruff --------- Co-authored-by: Cédric Bouysset <[email protected]>
chemosim-lab · Dec 18, 2024 · f1fcb31 · f1fcb31
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diff --git a/.github/workflows/formatting_linting.yml b/.github/workflows/formatting_linting.yml
@@ -19,12 +19,17 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Code formatting
-        uses: chartboost/ruff-action@v1
+        uses: astral-sh/ruff-action@v2
         with:
-          args: "check --preview"
+          args: "format --diff"
 
       - name: Notebook formatting
         uses: psf/black@stable
         with:
           src: "docs/notebooks/"
-          jupyter: true
+          jupyter: true
+
+      - name: Code linting
+        uses: astral-sh/ruff-action@v2
+        with:
+          args: "check --preview --diff"
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,8 +8,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
-- `VdWContact` now accepts a `preset` parameter to easily use different van der Waals radii values:
-  one of `mdanalysis` (default), `rdkit`, or `csd`.
+- `LigNetwork` now optionally displays the percentage of interaction occurence when
+  `show_interaction_data` is enabled. The type of data shown on both the label and
+  hover title can be modified.
+- `VdWContact` now accepts a `preset` parameter to easily use different van der Waals
+  radii values: one of `mdanalysis` (default), `rdkit`, or `csd`.
 - `IFP.interactions()` iterator that yields all interaction data for a given frame in
   a single flat structure. This makes iterating over the `fp.ifp` results a bit
   easier / less nested.
@@ -323,4 +326,4 @@ tests.
 
 ## [0.2.1] - 2019-10-02
 
-Base version for this changelog
+Base version for this changelog
diff --git a/prolif/fingerprint.py b/prolif/fingerprint.py
@@ -475,7 +475,7 @@ def run(
 
         converter_kwargs = converter_kwargs or ({}, {})
         if n_jobs is None:
-            n_jobs = int(os.environ.get("PROLIF_N_JOBS", 0)) or None
+            n_jobs = int(os.environ.get("PROLIF_N_JOBS", "0")) or None
         if residues == "all":
             residues = list(Molecule.from_mda(prot, **converter_kwargs[1]).residues)
         if n_jobs != 1:
@@ -869,6 +869,8 @@ def plot_lignetwork(
         carbon: float = 0.16,
         width: str = "100%",
         height: str = "500px",
+        fontsize: int = 20,
+        show_interaction_data: bool = False,
     ):
         """Generate and display a :class:`~prolif.plotting.network.LigNetwork` plot from
         a fingerprint object that has been used to run an analysis.
@@ -910,6 +912,10 @@ def plot_lignetwork(
             Width of the IFrame window.
         height : str
             Height of the IFrame window.
+        fontsize: int
+            Font size used for the atoms, residues, and edge labels.
+        show_interaction_data: bool
+            Show the occurence of each interaction on the corresponding edge.
 
         Notes
         -----
@@ -924,6 +930,9 @@ def plot_lignetwork(
         :class:`prolif.plotting.network.LigNetwork`
 
         .. versionadded:: 2.0.0
+
+        .. versionchanged:: 2.1.0
+            Added the ``show_interaction_data`` argument and exposed the ``fontsize``.
         """
         from prolif.plotting.network import LigNetwork
 
@@ -941,7 +950,12 @@ def plot_lignetwork(
             rotation=rotation,
             carbon=carbon,
         )
-        return ligplot.display(width=width, height=height)
+        return ligplot.display(
+            width=width,
+            height=height,
+            fontsize=fontsize,
+            show_interaction_data=show_interaction_data,
+        )
 
     def plot_barcode(
         self,

diff --git a/prolif/parallel.py b/prolif/parallel.py
@@ -103,7 +103,7 @@ class TrajectoryPool:
     """
 
     def __init__(
-        self, n_processes, fingerprint, residues, tqdm_kwargs, rdkitconverter_kwargs,
+        self, n_processes, fingerprint, residues, tqdm_kwargs, rdkitconverter_kwargs
     ):
         self.tqdm_kwargs = tqdm_kwargs
         self.tracker = Value(c_uint32, lock=True)
@@ -142,7 +142,7 @@ def executor(cls, args):
             lig_mol = Molecule.from_mda(lig, **cls.converter_kwargs[0])
             prot_mol = Molecule.from_mda(prot, **cls.converter_kwargs[1])
             data = cls.fp.generate(
-                lig_mol, prot_mol, residues=cls.residues, metadata=True,
+                lig_mol, prot_mol, residues=cls.residues, metadata=True
             )
             ifp[int(ts.frame)] = data
             with cls.tracker.get_lock():

diff --git a/prolif/plotting/network.py b/prolif/plotting/network.py
@@ -99,6 +99,10 @@ class LigNetwork:
         more control and allow them to provide their own 2D coordinates. Added support
         for displaying peptides as the "ligand". Changed the default color for
         VanDerWaals.
+
+    .. versionchanged:: 2.1.0
+        Added the ``show_interaction_data`` argument and exposed the ``fontsize`` in
+        ``display``.
     """
 
     COLORS: ClassVar = {
@@ -265,6 +269,8 @@ def __init__(
         self._default_interaction_color = "#dbdbdb"
         self._non_single_bond_spacing = 0.06
         self._dash = [10]
+        self._edge_title_formatter = "{interaction}: {distance:.2f}Å"
+        self._edge_label_formatter = "{weight_pct:.0f}%"
         # regroup interactions of the same color
         temp = defaultdict(list)
         interactions = set(df.index.get_level_values("interaction").unique())
@@ -491,10 +497,10 @@ def _make_non_single_bond(self, ids, btype):
         for perp in (p, -p):
             for point in xyz:
                 xy = point[:2] + perp * dist
-                _id = hash(xy.tobytes())
-                nodes.append(_id)
-                self.nodes[_id] = {
-                    "id": _id,
+                id_ = hash(xy.tobytes())
+                nodes.append(id_)
+                self.nodes[id_] = {
+                    "id": id_,
                     "x": xy[0],
                     "y": xy[1],
                     "shape": "text",
@@ -577,10 +583,16 @@ def _make_interactions(self, mass=2):
             else:
                 i = self._DISPLAYED_ATOM.get(interaction, 0)
                 origin = lig_indices[i]
+            int_data = {
+                "interaction": interaction,
+                "distance": distance,
+                "weight": weight,
+                "weight_pct": weight * 100,
+            }
             edge = {
                 "from": origin,
                 "to": prot_res,
-                "title": f"{interaction}: {distance:.2f}Å",
+                "title": self._edge_title_formatter.format_map(int_data),
                 "interaction_type": self._interaction_types.get(
                     interaction,
                     interaction,
@@ -594,6 +606,9 @@ def _make_interactions(self, mass=2):
                 "width": weight * self._max_interaction_width,
                 "group": "interaction",
             }
+            if self.show_interaction_data:
+                edge["label"] = self._edge_label_formatter.format_map(int_data)
+                edge["font"] = self._edge_label_font
             self.edges.append(edge)
 
     def _get_ring_centroid(self, indices):
@@ -635,10 +650,19 @@ def _make_graph_data(self):
         self._patch_hydrogens()
         self.nodes = list(self.nodes.values())
 
-    def _get_js(self, width="100%", height="500px", div_id="mynetwork", fontsize=20):
+    def _get_js(
+        self,
+        width="100%",
+        height="500px",
+        div_id="mynetwork",
+        fontsize=20,
+        show_interaction_data=False,
+    ):
         """Returns the JavaScript code to draw the network"""
         self.width = width
         self.height = height
+        self.show_interaction_data = show_interaction_data
+        self._edge_label_font = {"size": fontsize}
         self._make_graph_data()
         options = {
             "width": width,
@@ -816,7 +840,15 @@ def _get_legend(self, height="90px"):
 
     @requires("IPython.display")
     def display(self, **kwargs):
-        """Prepare and display the network"""
+        """Prepare and display the network.
+
+        Parameters
+        ----------
+        width: str = "100%"
+        height: str = "500px"
+        fontsize: int = 20
+        show_occurence: bool = False
+        """
         html = self._get_html(**kwargs)
         doc = escape(html)
         self._iframe = (

diff --git a/tests/test_fingerprint.py b/tests/test_fingerprint.py
@@ -18,8 +18,9 @@ def detect(self, res1, res2):
 
 def test_interaction_base(sdf_suppl):
     interaction = Dummy()
-    _repr = repr(interaction)
-    assert _repr.startswith("<") and ".Dummy at " in _repr
+    repr_ = repr(interaction)
+    assert repr_.startswith("<")
+    assert ".Dummy at " in repr_
     assert callable(interaction)
     mol = sdf_suppl[0]
     metadata = next(interaction.detect(mol, mol))