Merge pull request #101 from dprada/main

Conversion from multiple items fixed
uibcdf · Mar 21, 2023 · cb0efcc · cb0efcc
2 parents b0c74ff + 7a330a7
commit cb0efcc
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diff --git a/docs/contents/user/tools/basic/add.ipynb b/docs/contents/user/tools/basic/add.ipynb
@@ -35,16 +35,29 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "172a505ca0c145ebbb7bb02a221ccfea",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": []
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
     "import molsysmt as msm"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -62,7 +75,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -79,9 +92,52 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<style type=\"text/css\">\n",
+       "</style>\n",
+       "<table id=\"T_ace0f\">\n",
+       "  <thead>\n",
+       "    <tr>\n",
+       "      <th id=\"T_ace0f_level0_col0\" class=\"col_heading level0 col0\" >form</th>\n",
+       "      <th id=\"T_ace0f_level0_col1\" class=\"col_heading level0 col1\" >n_atoms</th>\n",
+       "      <th id=\"T_ace0f_level0_col2\" class=\"col_heading level0 col2\" >n_groups</th>\n",
+       "      <th id=\"T_ace0f_level0_col3\" class=\"col_heading level0 col3\" >n_components</th>\n",
+       "      <th id=\"T_ace0f_level0_col4\" class=\"col_heading level0 col4\" >n_chains</th>\n",
+       "      <th id=\"T_ace0f_level0_col5\" class=\"col_heading level0 col5\" >n_molecules</th>\n",
+       "      <th id=\"T_ace0f_level0_col6\" class=\"col_heading level0 col6\" >n_entities</th>\n",
+       "      <th id=\"T_ace0f_level0_col7\" class=\"col_heading level0 col7\" >n_peptides</th>\n",
+       "      <th id=\"T_ace0f_level0_col8\" class=\"col_heading level0 col8\" >n_structures</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <td id=\"T_ace0f_row0_col0\" class=\"data row0 col0\" >molsysmt.MolSys</td>\n",
+       "      <td id=\"T_ace0f_row0_col1\" class=\"data row0 col1\" >26</td>\n",
+       "      <td id=\"T_ace0f_row0_col2\" class=\"data row0 col2\" >3</td>\n",
+       "      <td id=\"T_ace0f_row0_col3\" class=\"data row0 col3\" >1</td>\n",
+       "      <td id=\"T_ace0f_row0_col4\" class=\"data row0 col4\" >1</td>\n",
+       "      <td id=\"T_ace0f_row0_col5\" class=\"data row0 col5\" >1</td>\n",
+       "      <td id=\"T_ace0f_row0_col6\" class=\"data row0 col6\" >1</td>\n",
+       "      <td id=\"T_ace0f_row0_col7\" class=\"data row0 col7\" >1</td>\n",
+       "      <td id=\"T_ace0f_row0_col8\" class=\"data row0 col8\" >1</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n"
+      ],
+      "text/plain": [
+       "<pandas.io.formats.style.Styler at 0x7fa178f1acd0>"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "msm.info(molecular_system_A)"
    ]
@@ -97,11 +153,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
-    "msm.add(molecular_system_A, [molecular_system_B, molecular_system_C])"
+    "msm.add(molecular_system_A, molecular_system_B)\n",
+    "msm.add(molecular_system_A, molecular_system_C)"
    ]
   },
   {
@@ -123,16 +180,59 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<style type=\"text/css\">\n",
+       "</style>\n",
+       "<table id=\"T_6986d\">\n",
+       "  <thead>\n",
+       "    <tr>\n",
+       "      <th id=\"T_6986d_level0_col0\" class=\"col_heading level0 col0\" >form</th>\n",
+       "      <th id=\"T_6986d_level0_col1\" class=\"col_heading level0 col1\" >n_atoms</th>\n",
+       "      <th id=\"T_6986d_level0_col2\" class=\"col_heading level0 col2\" >n_groups</th>\n",
+       "      <th id=\"T_6986d_level0_col3\" class=\"col_heading level0 col3\" >n_components</th>\n",
+       "      <th id=\"T_6986d_level0_col4\" class=\"col_heading level0 col4\" >n_chains</th>\n",
+       "      <th id=\"T_6986d_level0_col5\" class=\"col_heading level0 col5\" >n_molecules</th>\n",
+       "      <th id=\"T_6986d_level0_col6\" class=\"col_heading level0 col6\" >n_entities</th>\n",
+       "      <th id=\"T_6986d_level0_col7\" class=\"col_heading level0 col7\" >n_peptides</th>\n",
+       "      <th id=\"T_6986d_level0_col8\" class=\"col_heading level0 col8\" >n_structures</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <td id=\"T_6986d_row0_col0\" class=\"data row0 col0\" >molsysmt.MolSys</td>\n",
+       "      <td id=\"T_6986d_row0_col1\" class=\"data row0 col1\" >88</td>\n",
+       "      <td id=\"T_6986d_row0_col2\" class=\"data row0 col2\" >9</td>\n",
+       "      <td id=\"T_6986d_row0_col3\" class=\"data row0 col3\" >3</td>\n",
+       "      <td id=\"T_6986d_row0_col4\" class=\"data row0 col4\" >3</td>\n",
+       "      <td id=\"T_6986d_row0_col5\" class=\"data row0 col5\" >3</td>\n",
+       "      <td id=\"T_6986d_row0_col6\" class=\"data row0 col6\" >3</td>\n",
+       "      <td id=\"T_6986d_row0_col7\" class=\"data row0 col7\" >3</td>\n",
+       "      <td id=\"T_6986d_row0_col8\" class=\"data row0 col8\" >1</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n"
+      ],
+      "text/plain": [
+       "<pandas.io.formats.style.Styler at 0x7fa178ff7520>"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "msm.info(molecular_system_A, element='system')"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 8,
    "metadata": {
     "tags": [
      "remove-input"
@@ -148,11 +248,26 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 10,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "136224f4932f4237afebcf203d6f7902",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "NGLWidget()"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
-    "msm.view(molecular_system_A, standardize=True)"
+    "msm.view(molecular_system_A, standard=True)"
    ]
   },
   {
@@ -182,7 +297,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.9.15"
   }
  },
  "nbformat": 4,