Fix Binder and jupyter notebooks

README.md

@@ -7,7 +7,7 @@ Procrustes
 [![GPLv3 License](https://img.shields.io/badge/License-GPL%20v3-yellow.svg)](https://opensource.org/licenses/)
 [![Build Status](https://travis-ci.com/theochem/procrustes.svg?branch=master)](https://travis-ci.com/theochem/procrustes)
 [![Documentation Status](https://readthedocs.org/projects/procrustes/badge/?version=latest)](https://procrustes.readthedocs.io/en/latest/?badge=latest)
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/[email protected]:theochem/procrustes.git/master)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/theochem/procrustes/master?filepath=docs%2Fnotebooks%2F)
 
 The Procrustes library provides a set of functions for transforming a matrix to make it
 as similar as possible to a target matrix. For more information, visit

docs/notebooks/Atom_Atom_Mapping.ipynb

@@ -143,7 +143,7 @@
    ],
    "source": [
     "# the permutation matrix\n",
-    "res[\"array_u\"]"
+    "res[\"t\"]"
    ]
   },
   {
@@ -160,7 +160,7 @@
    "outputs": [],
    "source": [
     "# Compute the transformed molecule A\n",
-    "new_A = np.dot(res[\"array_u\"].T, np.dot(res[\"new_a\"], res[\"array_u\"])).astype(int)"
+    "new_A = np.dot(res[\"t\"].T, np.dot(res[\"new_a\"], res[\"t\"])).astype(int)"
    ]
   },
   {

docs/notebooks/Chirality_Check.ipynb

@@ -38,7 +38,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -128,7 +128,7 @@
     "                     remove_zero_col=False,\n",
     "                     remove_zero_row=False)\n",
     "\n",
-    "if res[\"e_opt\"]/res_ref[\"e_opt\"] > 10:\n",
+    "if res[\"error\"]/res_ref[\"error\"] > 10:\n",
     "    print(\"These two compounds are enantiomers \" \n",
     "          \"and there is at least one chiral center in each of them.\")\n",
     "else:\n",
@@ -145,7 +145,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -182,7 +182,7 @@
     "                        remove_zero_col=False,\n",
     "                        remove_zero_row=False)\n",
     "\n",
-    "    if res[\"e_opt\"] / res_ref[\"e_opt\"] > 10:\n",
+    "    if res[\"error\"] / res_ref[\"error\"] > 10:\n",
     "        print(\"These two compounds are enantiomers \"\n",
     "              \"and there is at least one chiral center in each of them.\")\n",
     "    else:\n",
@@ -246,7 +246,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [

docs/notebooks/Protein_Structure_Alignment.ipynb

@@ -585,7 +585,7 @@
    ],
    "source": [
     "# now new_A is the array after rotation\n",
-    "new_A_transformed = np.dot(res[\"new_a\"], res[\"array_u\"])\n",
+    "new_A_transformed = np.dot(res[\"new_a\"], res[\"t\"])\n",
     "\n",
     "rmsd_after = compute_rmsd(new_A_transformed, res[\"new_b\"])\n",
     "print(rmsd_after)"

docs/notebooks/Ranking_by_Reordering.ipynb

@@ -163,7 +163,7 @@
     "                            remove_zero_row=False,\n",
     "                            mode=perm_mode)\n",
     "    # Compute the rank\n",
-    "    _, rank = np.where(res[\"array_u\"] == 1)\n",
+    "    _, rank = np.where(res[\"t\"] == 1)\n",
     "    rank += 1\n",
     "\n",
     "    return rank"
@@ -187,7 +187,15 @@
    "cell_type": "code",
    "execution_count": 4,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Maximum iteration reached! Change=4.783354588670838e-07\n"
+     ]
+    }
+   ],
    "source": [
     "# compute the rank\n",
     "rank = ranking(D)"