Merge pull request #10 from Jhsmit/local_data

Local data
Jhsmit · Apr 25, 2024 · 236f134 · 236f134
2 parents bda9a6e + 5ce362d
commit 236f134
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Showing 5 changed files with 91 additions and 62 deletions.
diff --git a/README.md b/README.md
@@ -28,6 +28,29 @@ view = PDBeMolstar(molecule_id='1qyn', theme='light', hide_water=True)
 view
 ```
 
+Loading local data, hiding the buttons:
+
+```python
+from pathlib import Path 
+fpth = Path().resolve() / 'assets' / '6vsb.bcif'
+custom_data = {
+    'data': fpth.read_bytes(),
+    'format': 'cif',
+    'binary': True,
+    }
+view = PDBeMolstar(
+    custom_data=custom_data, 
+    hide_controls_icon=True, 
+    hide_expand_icon=True, 
+    hide_settings_icon=True, 
+    hide_selection_icon=True, 
+    hide_animation_icon=True,
+    hide_water=True,
+    hide_carbs=True,
+)
+view
+```
+
 See the example notebook for more advanced usage. 
 Solara example code can be found [here](https://github.com/Jhsmit/ploomber-solara-ipymolstar)
 

diff --git a/assets/6vsb.bcif b/assets/6vsb.bcif
diff --git a/example.ipynb b/example.ipynb
@@ -12,7 +12,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "scrolled": true
+   },
    "outputs": [],
    "source": [
     "view = PDBeMolstar(\n",
@@ -25,6 +27,28 @@
     "view"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# load local files via custom_data\n",
+    "from pathlib import Path \n",
+    "fpth = Path().resolve() / 'assets' / '6vsb.bcif'\n",
+    "custom_data = {\n",
+    "    'data': fpth.read_bytes(),\n",
+    "    'format': 'cif',\n",
+    "    'binary': True,\n",
+    "    }\n",
+    "view = PDBeMolstar(\n",
+    "    custom_data=custom_data, \n",
+    "    hide_water=True,\n",
+    "    hide_carbs=True,\n",
+    ")\n",
+    "view"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

diff --git a/src/ipymolstar/widget.js b/src/ipymolstar/widget.js
@@ -76,10 +76,22 @@ function getHideCanvasControls(model) {
   return hideCanvasControls;
 }
 
+function getCustomData(model) {
+  var customData = model.get("custom_data");
+
+  if (customData && 'data' in customData) {
+    var url = URL.createObjectURL(new Blob([customData.data]));
+    customData.url = url;
+    delete customData.data;
+  }
+
+  return customData;
+}
+
 function getOptions(model) {
   var options = {
     moleculeId: model.get("molecule_id"),
-    customData: model.get("custom_data"),
+    customData: getCustomData(model),
     assemblyId: model.get("assembly_id"),
     defaultPreset: model.get("default_preset"),
     ligandView: model.get("ligand_view"),
@@ -184,7 +196,6 @@ function render({ model, el }) {
 
   viewerInstance.events.loadComplete.subscribe(() => {
     // trigger callabacks which need to be called after loading
-    console.log("load complete");
     Object.values(callbacksLoadComplete).forEach((callback) => callback());
   });
 

diff --git a/tests/test_notebook.ipynb b/tests/test_notebook.ipynb
@@ -11,7 +11,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -29,25 +29,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "c716fd207a7642c3a8148d6429c0f456",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "VBox(children=(PDBeMolstar(bg_color='#F7F7F7', height='200px', molecule_id='1qyn'), PDBeMolstar(bg_color='#F7F…"
-      ]
-     },
-     "execution_count": 16,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "\n",
     "v1 = PDBeMolstar(molecule_id='1qyn', height=\"200px\")\n",
@@ -65,33 +49,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "f20a9b627be1495a8680c6deb41aecfc",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "PDBeMolstar(bg_color='#F7F7F7', height='150px', molecule_id='1qyn')"
-      ]
-     },
-     "execution_count": 27,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "v = PDBeMolstar(molecule_id='1qyn', height='150px')\n",
     "v"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 28,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -108,25 +76,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 34,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "81d95973cf31465eac4767d2043a203f",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "PDBeMolstar(bg_color='#F7F7F7', custom_data={'url': 'https://www.ebi.ac.uk/pdbe/model-server/v1/1cbs/atoms?lab…"
-      ]
-     },
-     "execution_count": 34,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "custom_data = dict(url='https://www.ebi.ac.uk/pdbe/model-server/v1/1cbs/atoms?label_entity_id=1&auth_asym_id=A&encoding=bcif', format='cif', binary=True)\n",
     "v = PDBeMolstar(custom_data=custom_data, height='150px')\n",
@@ -135,20 +87,39 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 35,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "new_custom_data = dict(url='https://www.ebi.ac.uk/pdbe/model-server/v1/1qyn/atoms?label_entity_id=1&auth_asym_id=A&encoding=bcif', format='cif', binary=True)\n",
-    "v.cumstom_data = new_custom_data"
+    "v.custom_data = new_custom_data"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "from pathlib import Path \n",
+    "fpth = Path().resolve().parent / 'assets' / '6vsb.bcif'\n",
+    "custom_data = {\n",
+    "    'data': fpth.read_bytes(),\n",
+    "    'format': 'cif',\n",
+    "    'binary': True,\n",
+    "    }\n",
+    "view = PDBeMolstar(\n",
+    "    custom_data=custom_data, \n",
+    "    hide_controls_icon=True, \n",
+    "    hide_expand_icon=True, \n",
+    "    hide_settings_icon=True, \n",
+    "    hide_selection_icon=True, \n",
+    "    hide_animation_icon=True,\n",
+    "    hide_water=True,\n",
+    "    hide_carbs=True,\n",
+    ")\n",
+    "view"
+   ]
   }
  ],
  "metadata": {