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Make two molecules clickable independently #10

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177 changes: 72 additions & 105 deletions notebooks/Jupyter_widget.ipynb
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@
"name": "stdout",
"output_type": "stream",
"text": [
"2018.09.3\n",
"Fri Nov 8 12:18:50 2019\n"
"2022.03.4\n",
"Fri Sep 16 18:35:34 2022\n"
]
}
],
Expand Down Expand Up @@ -50,78 +50,7 @@
"outputs": [
{
"data": {
"application/javascript": [
"// make sure our module is only defined\n",
"// only once.\n",
"require.undef('molsvg_widget');\n",
"\n",
"// Define the `molsvg_widget` module using the Jupyter widgets framework.\n",
"define('molsvg_widget', [\"@jupyter-widgets/base\"],\n",
" function(widgets) {\n",
"\n",
" // The frontend class:\n",
" var MolSVGView = widgets.DOMWidgetView.extend({\n",
"\n",
" // This method creates the HTML widget.\n",
" render: function() {\n",
" this.svg_div = document.createElement('div');\n",
" this.el.appendChild(this.svg_div);\n",
" this.model.on('change:svg', this.svg_changed, this);\n",
" this.svg_changed();\n",
" },\n",
" \n",
" // called when the SVG is updated on the Python side\n",
" svg_changed: function() {\n",
" var txt = this.model.get('svg'); \n",
" this.svg_div.innerHTML = txt;\n",
" var sels = this.svg_div.getElementsByClassName(\"atom-selector\");\n",
" for(var i=0;i<sels.length;i++){\n",
" sels[i].onclick = (evt) => { return this.atom_clicked(evt) };\n",
" }\n",
" \n",
" },\n",
"\n",
" // callback for when an atom is clicked\n",
" atom_clicked: function(evt) {\n",
" //alert(\" \"+evt+\"|\"+this);\n",
" if(!evt.currentTarget.getAttribute('class')){\n",
" return;\n",
" }\n",
" var satmid = evt.currentTarget.getAttribute('class').match(/atom-([0-9]+)/);\n",
" if(satmid.length >1){\n",
" var atmid = Number(satmid[1]);\n",
" var curSel = this.model.get('selected_atoms');\n",
" var splitSel = curSel.split(',');\n",
" var selItms = [];\n",
" var idx = -1;\n",
" //alert(\"|\"+atmid+\"|\"+curSel+\"|len: \"+splitSel.length);\n",
" if(curSel != \"\" && splitSel.length>0){\n",
" selItms = Array.from(splitSel).map(item => Number(item));\n",
" idx = selItms.indexOf(atmid);\n",
" }\n",
" if(idx == -1){\n",
" selItms = selItms.concat(atmid);\n",
" evt.currentTarget.style[\"stroke-width\"]=3;\n",
" evt.currentTarget.style[\"stroke-opacity\"]=1;\n",
" evt.currentTarget.style[\"stroke\"]='#AA22FF';\n",
" } else {\n",
" selItms.splice(idx,1);\n",
" evt.currentTarget.style[\"stroke-width\"]=1;\n",
" evt.currentTarget.style[\"stroke-opacity\"]=0;\n",
" evt.currentTarget.style[\"stroke\"]='#FFFFFF';\n",
" }\n",
" this.model.set('selected_atoms',String(selItms));\n",
" this.touch();\n",
" }\n",
" }\n",
"\n",
" });\n",
"\n",
" return {\n",
" MolSVGView : MolSVGView\n",
" };\n",
"});\n"
],
"application/javascript": "// make sure our module is only defined\n// only once.\nrequire.undef('molsvg_widget');\n\n// Define the `molsvg_widget` module using the Jupyter widgets framework.\ndefine('molsvg_widget', [\"@jupyter-widgets/base\"],\n function(widgets) {\n\n // The frontend class:\n var MolSVGView = widgets.DOMWidgetView.extend({\n\n // This method creates the HTML widget.\n render: function() {\n this.svg_div = document.createElement('div');\n this.el.appendChild(this.svg_div);\n this.model.on('change:svg', this.svg_changed, this);\n this.svg_changed();\n },\n \n // called when the SVG is updated on the Python side\n svg_changed: function() {\n var txt = this.model.get('svg'); \n this.svg_div.innerHTML = txt;\n var sels = this.svg_div.getElementsByClassName(\"atom-selector\");\n for(var i=0;i<sels.length;i++){\n sels[i].onclick = (evt) => { return this.atom_clicked(evt) };\n }\n \n },\n\n // callback for when an atom is clicked\n atom_clicked: function(evt) {\n //alert(\" \"+evt+\"|\"+this);\n if(!evt.currentTarget.getAttribute('class')){\n return;\n }\n var satmid = evt.currentTarget.getAttribute('class').match(/atom-([0-9]+)/);\n if(satmid.length >1){\n var atmid = Number(satmid[1]);\n var curSel = this.model.get('selected_atoms');\n var splitSel = curSel.split(',');\n var selItms = [];\n var idx = -1;\n //alert(\"|\"+atmid+\"|\"+curSel+\"|len: \"+splitSel.length);\n if(curSel != \"\" && splitSel.length>0){\n selItms = Array.from(splitSel).map(item => Number(item));\n idx = selItms.indexOf(atmid);\n }\n if(idx == -1){\n selItms = selItms.concat(atmid);\n evt.currentTarget.style[\"stroke-width\"]=3;\n evt.currentTarget.style[\"stroke-opacity\"]=1;\n evt.currentTarget.style[\"stroke\"]='#AA22FF';\n } else {\n selItms.splice(idx,1);\n evt.currentTarget.style[\"stroke-width\"]=1;\n evt.currentTarget.style[\"stroke-opacity\"]=0;\n evt.currentTarget.style[\"stroke\"]='#FFFFFF';\n }\n this.model.set('selected_atoms',String(selItms));\n this.touch();\n }\n }\n\n });\n\n return {\n MolSVGView : MolSVGView\n };\n});\n",
"text/plain": [
"<IPython.core.display.Javascript object>"
]
Expand Down Expand Up @@ -206,16 +135,16 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'2018.09.3'"
"'2022.03.4'"
]
},
"execution_count": 6,
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -227,27 +156,30 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 5,
"metadata": {},
"outputs": [
{
"ename": "AttributeError",
"evalue": "'MolDraw2DSVG' object has no attribute 'TagAtoms'",
"output_type": "error",
"traceback": [
"\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[1;31mAttributeError\u001b[0m Traceback (most recent call last)",
"\u001b[1;32m<ipython-input-4-f6b660c3c788>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m\u001b[0m\n\u001b[0;32m 3\u001b[0m \u001b[0mdm\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mDraw\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mPrepareMolForDrawing\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mm\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 4\u001b[0m \u001b[0md\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mDrawMolecule\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mdm\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 5\u001b[1;33m \u001b[0md\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mTagAtoms\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mdm\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 6\u001b[0m \u001b[0md\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mFinishDrawing\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 7\u001b[0m \u001b[0msvg\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0md\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mGetDrawingText\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;31mAttributeError\u001b[0m: 'MolDraw2DSVG' object has no attribute 'TagAtoms'"
]
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "894e66564dbd475f9c5dfd976e001bcb",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"MolSVGWidget(svg=\"<?xml version='1.0' encoding='iso-8859-1'?>\\n<svg version='1.1' baseProfile='full'\\n …"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"m = Chem.MolFromSmiles('C1OCC1N')\n",
"d = rdMolDraw2D.MolDraw2DSVG(200,150)\n",
"dm = Draw.PrepareMolForDrawing(m)\n",
"d.DrawMolecule(dm)\n",
"d.\n",
"d.TagAtoms(dm)\n",
"d.FinishDrawing()\n",
"svg = d.GetDrawingText()\n",
"w = MolSVGWidget(svg=svg)\n",
Expand All @@ -256,16 +188,16 @@
},
{
"cell_type": "code",
"execution_count": 60,
"execution_count": 9,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'8,17,12'"
"'3,1'"
]
},
"execution_count": 60,
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -276,26 +208,56 @@
},
{
"cell_type": "code",
"execution_count": 59,
"execution_count": 7,
"metadata": {},
"outputs": [],
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "6c3dccbb18d640f3b4aad51f9e7a4633",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"MolSVGWidget(svg=\"<?xml version='1.0' encoding='iso-8859-1'?>\\n<svg version='1.1' baseProfile='full'\\n …"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"esomprazole = Chem.MolFromSmiles('COc1ccc2[nH]c([S@@+]([O-])Cc3ncc(C)c(OC)c3C)nc2c1')\n",
"d = rdMolDraw2D.MolDraw2DSVG(200,150)\n",
"dm = Draw.PrepareMolForDrawing(esomprazole)\n",
"d.DrawMolecule(dm)\n",
"d.TagAtoms(dm)\n",
"d.FinishDrawing()\n",
"svg = d.GetDrawingText()\n",
"w.svg = svg"
"d2 = rdMolDraw2D.MolDraw2DSVG(200,150)\n",
"dm2 = Draw.PrepareMolForDrawing(esomprazole)\n",
"d2.DrawMolecule(dm2)\n",
"d2.TagAtoms(dm2)\n",
"d2.FinishDrawing()\n",
"svg2 = d2.GetDrawingText()\n",
"w2 = MolSVGWidget(svg=svg2)\n",
"w2.svg = svg2\n",
"w2"
]
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 10,
"metadata": {},
"outputs": [],
"source": []
"outputs": [
{
"data": {
"text/plain": [
"'7,10'"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"w2.selected_atoms"
]
}
],
"metadata": {
Expand All @@ -310,7 +272,7 @@
"id": "b640cd77331a55f2179cd1dc2d7bbd8d"
},
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3.9.7",
"language": "python",
"name": "python3"
},
Expand All @@ -324,7 +286,12 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.4"
"version": "3.9.7"
},
"vscode": {
"interpreter": {
"hash": "a805e4787fe41e208b9e9ee3ee0be5f857b11e5edac61fba9adbad0693aa92c1"
}
}
},
"nbformat": 4,
Expand Down