docs(notebook): expose --shape / --reach / --probe in maws.ipynb

The CLI driver notebook had no surface for the three new sampling
flags. Added:

- A markdown cell explaining what shape, reach, and probe mean for
  the new surface-aware sampler (with the rule of thumb for each
  default).
- shape / reach / probe parameter assignments in both the commented
  template parameter cell and the active parameter cell.
- --shape / --reach / --probe flags appended to the corresponding
  CLI invocation cells.

Defaults match the CLI: shape=shell, reach=10.0, probe=1.4.

Author: siddharth7113

notebooks/maws/maws.ipynb

@@ -49,6 +49,22 @@
     "You can edit the following cell and change the parameters to run the MAWS program"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "7fb27b941602401d91542211134fc71a",
+   "metadata": {},
+   "source": [
+    "### Surface-aware sampling parameters (new in 2026)\n",
+    "\n",
+    "MAWS now restricts the initial pose search to the region just outside the ligand surface, computed from the ligand atoms automatically. Three knobs:\n",
+    "\n",
+    "- **`shape`** — geometry of the search envelope around the ligand. `shell` (default) hugs the surface most tightly; `sphere` is a simple bounding sphere; `cube` is the bounding box.\n",
+    "- **`reach`** — how far past the ligand surface the envelope extends, in ångströms. Roughly the distance an aptamer atom can sit beyond the protein. Default `10.0` Å — about one nucleotide's worth of slack.\n",
+    "- **`probe`** — radius of the rolling probe used to define the SAS surface, in ångströms. A candidate pose is rejected if any aptamer atom would land within `vdW(atom) + probe` of any protein atom. Default `1.4` Å (water-equivalent, the convention used by Chimera/PyMOL/FreeSASA).\n",
+    "\n",
+    "Keep the defaults unless your target is unusual (very small ligand, very deep pocket, etc.).\n"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -81,7 +97,16 @@
     "# chunk_1 = 5000\n",
     "\n",
     "# # Second chunk size (default: 5000)\n",
-    "# chunk_2 = 5000"
+    "# chunk_2 = 5000\n",
+    "\n",
+    "# # Sampling envelope shape: cube | sphere | shell  (default: shell)\n",
+    "# shape = \"shell\"\n",
+    "\n",
+    "# # How far the envelope extends beyond the ligand surface, in Å (default: 10)\n",
+    "# reach = 10.0\n",
+    "\n",
+    "# # vdW probe radius for SAS rejection, in Å (default: 1.4, water-like)\n",
+    "# probe = 1.4\n"
    ]
   },
   {
@@ -99,7 +124,10 @@
     "#   --moleculetype \"{mol_type}\" \\\n",
     "#   --beta {beta} \\\n",
     "#   --firstchunksize {chunk_1} \\\n",
-    "#   --secondchunksize {chunk_2}"
+    "#   --secondchunksize {chunk_2} \\\n",
+    "#   --shape {shape} \\\n",
+    "#   --reach {reach} \\\n",
+    "#   --probe {probe}\n"
    ]
   },
   {
@@ -134,7 +162,16 @@
     "chunk_1 = 5000\n",
     "\n",
     "# Second chunk size (default: 5000)\n",
-    "chunk_2 = 5000"
+    "chunk_2 = 5000\n",
+    "\n",
+    "# Sampling envelope shape: cube | sphere | shell (default: shell)\n",
+    "shape = \"shell\"\n",
+    "\n",
+    "# How far the envelope extends beyond the ligand surface, in Å (default: 10)\n",
+    "reach = 10.0\n",
+    "\n",
+    "# vdW probe radius for SAS rejection, in Å (default: 1.4, water-like)\n",
+    "probe = 1.4"
    ]
   },
   {
@@ -155,7 +192,10 @@
     "  --secondchunksize {chunk_2} \\\n",
     "  --clean-pdb \\\n",
     "  --remove-h \\\n",
-    "  --drop-hetatm"
+    "  --drop-hetatm \\\n",
+    "  --shape {shape} \\\n",
+    "  --reach {reach} \\\n",
+    "  --probe {probe}"
    ]
   },
   {
@@ -188,4 +228,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}