Clean up notebooks

charnley · Jan 4, 2025 · 95e816b · 95e816b
1 parent 3da31a3
commit 95e816b
Show file tree

Hide file tree

Showing 3 changed files with 29 additions and 719 deletions.
diff --git a/notebooks/coord_funcs.py b/notebooks/coord_funcs.py
@@ -25,5 +25,5 @@ def rotate_coord(angle, coord, axis=[0, 1]):
     U = get_rotation_matrix(angle)
     _xy = np.dot(coord[:, axis], U)
     _coord = np.array(coord, copy=True)
-    _coord[:, :2] = _xy
+    _coord[:, axis] = _xy
     return _coord
diff --git a/notebooks/figures.ipynb b/notebooks/figures.ipynb
@@ -46,14 +46,6 @@
     "import rmsd as rmsdlib"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "8d24b792-ea7d-4611-ab3c-b64a1177815b",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -138,7 +130,7 @@
    "id": "3cf67d24-ad0a-4130-a3cd-d3f8d79e59cd",
    "metadata": {},
    "source": [
-    "# What"
+    "# Explain problem"
    ]
   },
   {
@@ -209,81 +201,73 @@
   },
   {
    "cell_type": "markdown",
-   "id": "4630b581-9f43-4f0d-9fd7-bb8912f659b1",
+   "id": "faa92f45-9f5f-4f4e-9021-dd3e1c9d271a",
    "metadata": {},
    "source": [
-    "# QML"
+    "# Reorder problem"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "fb946f75-651f-4f68-a99c-a4c88979b991",
+   "id": "9d6ce450-e2f3-42ca-9904-bcfe6873d92d",
    "metadata": {},
    "outputs": [],
    "source": [
-    "def qml_illustration():\n",
+    "def reorder():\n",
     "\n",
-    "    coord = [\n",
+    "    coord1 = [\n",
     "        [0,0,0],\n",
     "        [1,1,0],\n",
     "        [2,0,0],\n",
     "    ]\n",
-    "    coord = np.array(coord, dtype=float)\n",
-    "    atoms = [6, 6, 6]\n",
+    "    coord1 = np.array(coord1, dtype=float) / 1.2\n",
+    "    coord1 -= rmsdlib.centroid(coord1)\n",
+    "    coord2 = np.array(coord1, copy=True)\n",
+    "    atoms1 = [6, 6, 6]\n",
     "\n",
-    "    coord -= rmsdlib.get_cm(atoms, coord)\n",
+    "    coord2 /= 1.5\n",
+    "    coord2 -= rmsdlib.centroid(coord1)\n",
+    "    coord2[:,1] -= 0.5\n",
+    "    coord1[:,1] += 0.2\n",
     "    \n",
     "    fig, ax = plot_funcs.get_plot()\n",
     "    plot_funcs.set_axis_default(ax)\n",
-    "    plot_funcs.plot_molecule(ax, [\"\"]*3, coord)\n",
-    "    plot_funcs.plot_representation(ax, atoms, coord)\n",
+    "    plot_funcs.plot_molecule(ax, [\"1\", \"2\", \"3\"], coord1)\n",
+    "    plot_funcs.plot_molecule(ax, [\"2\", \"3\", \"1\"], coord2, hatch=\"\\\\\\\\\\\\\")\n",
     "\n",
-    "    save_figure(fig, \"fig_reorder_qml\")\n",
+    "    save_figure(fig, \"fig_reorder_problem\")\n",
     "\n",
-    "qml_illustration()"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "faa92f45-9f5f-4f4e-9021-dd3e1c9d271a",
-   "metadata": {},
-   "source": [
-    "# Reorder problem"
+    "reorder()"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9d6ce450-e2f3-42ca-9904-bcfe6873d92d",
+   "id": "fb946f75-651f-4f68-a99c-a4c88979b991",
    "metadata": {},
    "outputs": [],
    "source": [
-    "def reorder():\n",
+    "def qml_illustration():\n",
     "\n",
-    "    coord1 = [\n",
+    "    coord = [\n",
     "        [0,0,0],\n",
     "        [1,1,0],\n",
     "        [2,0,0],\n",
     "    ]\n",
-    "    coord1 = np.array(coord1, dtype=float) / 1.2\n",
-    "    coord1 -= rmsdlib.centroid(coord1)\n",
-    "    coord2 = np.array(coord1, copy=True)\n",
-    "    atoms1 = [6, 6, 6]\n",
+    "    coord = np.array(coord, dtype=float)\n",
+    "    atoms = [6, 6, 6]\n",
     "\n",
-    "    coord2 /= 1.5\n",
-    "    coord2 -= rmsdlib.centroid(coord1)\n",
-    "    coord2[:,1] -= 0.5\n",
-    "    coord1[:,1] += 0.2\n",
+    "    coord -= rmsdlib.get_cm(atoms, coord)\n",
     "    \n",
     "    fig, ax = plot_funcs.get_plot()\n",
     "    plot_funcs.set_axis_default(ax)\n",
-    "    plot_funcs.plot_molecule(ax, [\"1\", \"2\", \"3\"], coord1)\n",
-    "    plot_funcs.plot_molecule(ax, [\"2\", \"3\", \"1\"], coord2, hatch=\"\\\\\\\\\\\\\")\n",
+    "    plot_funcs.plot_molecule(ax, [\"\"]*3, coord)\n",
+    "    plot_funcs.plot_representation(ax, atoms, coord)\n",
     "\n",
-    "    save_figure(fig, \"fig_reorder_problem\")\n",
+    "    save_figure(fig, \"fig_reorder_qml\")\n",
     "\n",
-    "reorder()"
+    "qml_illustration()"
    ]
   },
   {