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greglandrum/Bond highlighting.ipynb

Created August 4, 2022 04:44
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Bond highlighting.ipynb
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Bond highlighting.ipynb
{
"cells": [
{
"metadata": {
"ExecuteTime": {
"start_time": "2022-08-04T04:25:35.708896Z",
"end_time": "2022-08-04T04:25:38.247049Z"
},
"trusted": true
},
"cell_type": "code",
"source": "from rdkit import Chem\nfrom rdkit.Chem import Draw\nfrom rdkit.Chem.Draw import IPythonConsole\nimport rdkit\nprint(rdkit.__version__)",
"execution_count": 1,
"outputs": [
{
"output_type": "stream",
"text": "2022.03.4\n",
"name": "stdout"
}
]
},
{
"metadata": {
"ExecuteTime": {
"start_time": "2022-08-04T04:25:45.937764Z",
"end_time": "2022-08-04T04:25:45.952655Z"
},
"trusted": true
},
"cell_type": "code",
"source": "m = Chem.MolFromSmiles('c1ccccc1C(=O)O')\nm",
"execution_count": 2,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 2,
"data": {
"text/plain": "<rdkit.Chem.rdchem.Mol at 0x7f32be6bf280>",
"image/png": 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\n"
},
"metadata": {}
}
]
},
{
"metadata": {
"ExecuteTime": {
"start_time": "2022-08-04T04:29:38.018036Z",
"end_time": "2022-08-04T04:29:38.023688Z"
},
"trusted": true
},
"cell_type": "code",
"source": "IPythonConsole.drawOptions.addBondIndices = True\nm",
"execution_count": 3,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 3,
"data": {
"text/plain": "<rdkit.Chem.rdchem.Mol at 0x7f32be6bf280>",
"image/png": 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\n"
},
"metadata": {}
}
]
},
{
"metadata": {},
"cell_type": "markdown",
"source": "Drawing bonds with arbitrary colors:"
},
{
"metadata": {
"ExecuteTime": {
"start_time": "2022-08-04T04:41:12.056576Z",
"end_time": "2022-08-04T04:41:12.064756Z"
},
"trusted": true
},
"cell_type": "code",
"source": "from IPython.display import SVG\nd2d = Draw.MolDraw2DSVG(300,300)\ndos = d2d.drawOptions()\ndos.useBWAtomPalette()\ndos.continuousHighlight = False\nd2d.DrawMolecule(m,highlightAtoms=[],highlightBonds=[0,2,4,7], \n highlightBondColors={0:(1,0,0),2:(0,1,0),4:(0,0,1),7:(1,0,1) })\nd2d.FinishDrawing()\nSVG(d2d.GetDrawingText())",
"execution_count": 17,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 17,
"data": {
"text/plain": "<IPython.core.display.SVG object>",
"image/svg+xml": "<svg xmlns=\"http://www.w3.org/2000/svg\" xmlns:rdkit=\"http://www.rdkit.org/xml\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" version=\"1.1\" baseProfile=\"full\" xml:space=\"preserve\" width=\"300px\" height=\"300px\" viewBox=\"0 0 300 300\">\n<!-- END OF HEADER -->\n<rect style=\"opacity:1.0;fill:#FFFFFF;stroke:none\" width=\"300.0\" height=\"300.0\" x=\"0.0\" y=\"0.0\"> </rect>\n<path class=\"bond-0 atom-0 atom-1\" d=\"M 119.3,210.9 L 48.9,210.9\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:3.8px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-0 atom-0 atom-1\" d=\"M 108.7,196.8 L 59.4,196.8\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:3.8px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-1 atom-1 atom-2\" d=\"M 48.9,210.9 L 13.6,149.8\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-2 atom-2 atom-3\" d=\"M 13.6,149.8 L 48.9,88.8\" style=\"fill:none;fill-rule:evenodd;stroke:#00FF00;stroke-width:3.8px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-2 atom-2 atom-3\" d=\"M 31.1,147.7 L 55.8,105.0\" style=\"fill:none;fill-rule:evenodd;stroke:#00FF00;stroke-width:3.8px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-3 atom-3 atom-4\" d=\"M 48.9,88.8 L 119.3,88.8\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-4 atom-4 atom-5\" d=\"M 119.3,88.8 L 154.5,149.8\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:3.8px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-4 atom-4 atom-5\" d=\"M 112.4,105.0 L 137.0,147.7\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:3.8px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-5 atom-5 atom-6\" d=\"M 154.5,149.8 L 225.0,149.8\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-6 atom-6 atom-7\" d=\"M 218.9,146.3 L 246.7,98.0\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-6 atom-6 atom-7\" d=\"M 231.1,153.4 L 258.9,105.1\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-7 atom-6 atom-8\" d=\"M 225.0,149.8 L 253.0,198.4\" style=\"fill:none;fill-rule:evenodd;stroke:#FF00FF;stroke-width:3.8px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-8 atom-5 atom-0\" d=\"M 154.5,149.8 L 119.3,210.9\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"atom-7\" d=\"M 251.0 88.9 Q 251.0 84.1, 253.4 81.4 Q 255.8 78.8, 260.2 78.8 Q 264.6 78.8, 267.0 81.4 Q 269.3 84.1, 269.3 88.9 Q 269.3 93.7, 266.9 96.5 Q 264.6 99.2, 260.2 99.2 Q 255.8 99.2, 253.4 96.5 Q 251.0 93.8, 251.0 88.9 M 260.2 97.0 Q 263.2 97.0, 264.9 95.0 Q 266.5 92.9, 266.5 88.9 Q 266.5 85.0, 264.9 83.0 Q 263.2 81.0, 260.2 81.0 Q 257.1 81.0, 255.5 83.0 Q 253.8 85.0, 253.8 88.9 Q 253.8 92.9, 255.5 95.0 Q 257.1 97.0, 260.2 97.0 \" fill=\"#000000\"/>\n<path class=\"atom-8\" d=\"M 251.0 210.9 Q 251.0 206.1, 253.4 203.4 Q 255.8 200.8, 260.2 200.8 Q 264.6 200.8, 267.0 203.4 Q 269.3 206.1, 269.3 210.9 Q 269.3 215.8, 266.9 218.5 Q 264.6 221.2, 260.2 221.2 Q 255.8 221.2, 253.4 218.5 Q 251.0 215.8, 251.0 210.9 M 260.2 219.0 Q 263.2 219.0, 264.9 217.0 Q 266.5 214.9, 266.5 210.9 Q 266.5 207.0, 264.9 205.0 Q 263.2 203.0, 260.2 203.0 Q 257.1 203.0, 255.5 205.0 Q 253.8 207.0, 253.8 210.9 Q 253.8 214.9, 255.5 217.0 Q 257.1 219.0, 260.2 219.0 \" fill=\"#000000\"/>\n<path class=\"atom-8\" d=\"M 270.8 201.0 L 273.5 201.0 L 273.5 209.5 L 283.7 209.5 L 283.7 201.0 L 286.4 201.0 L 286.4 220.9 L 283.7 220.9 L 283.7 211.7 L 273.5 211.7 L 273.5 220.9 L 270.8 220.9 L 270.8 201.0 \" fill=\"#000000\"/>\n</svg>"
},
"metadata": {}
}
]
},
{
"metadata": {},
"cell_type": "markdown",
"source": "Adding text labels to bonds:"
},
{
"metadata": {
"ExecuteTime": {
"start_time": "2022-08-04T04:43:23.533060Z",
"end_time": "2022-08-04T04:43:23.563902Z"
},
"trusted": true
},
"cell_type": "code",
"source": "molcp = Chem.Mol(m)\nmolcp.GetBondWithIdx(0).SetProp('bondNote','4.5')\nmolcp.GetBondWithIdx(2).SetProp('bondNote','129')\n\nfrom IPython.display import SVG\nd2d = Draw.MolDraw2DSVG(300,300)\ndos = d2d.drawOptions()\ndos.useBWAtomPalette()\ndos.continuousHighlight = False\nd2d.DrawMolecule(molcp)\nd2d.FinishDrawing()\nSVG(d2d.GetDrawingText())",
"execution_count": 20,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 20,
"data": {
"text/plain": "<IPython.core.display.SVG object>",
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198.6 Q 264.1 196.7, 261.2 196.7 Q 258.3 196.7, 256.7 198.6 Q 255.1 200.5, 255.1 204.3 Q 255.1 208.1, 256.7 210.1 Q 258.3 212.0, 261.2 212.0 \" fill=\"#000000\"/>\n<path class=\"atom-8\" d=\"M 271.4 194.7 L 274.0 194.7 L 274.0 202.9 L 283.8 202.9 L 283.8 194.7 L 286.4 194.7 L 286.4 213.9 L 283.8 213.9 L 283.8 205.1 L 274.0 205.1 L 274.0 213.9 L 271.4 213.9 L 271.4 194.7 \" fill=\"#000000\"/>\n<path class=\"note\" d=\"M 89.9 219.3 L 91.1 219.3 L 91.1 220.3 L 89.9 220.3 L 89.9 222.5 L 88.7 222.5 L 88.7 220.3 L 83.7 220.3 L 83.7 219.5 L 87.9 213.0 L 89.9 213.0 L 89.9 219.3 M 85.3 219.3 L 88.7 219.3 L 88.7 213.8 L 85.3 219.3 \" fill=\"#000000\"/>\n<path class=\"note\" d=\"M 91.7 221.2 L 93.1 221.2 L 93.1 222.5 L 91.7 222.5 L 91.7 221.2 \" fill=\"#000000\"/>\n<path class=\"note\" d=\"M 97.5 216.5 Q 98.3 216.5, 99.0 216.9 Q 99.7 217.3, 100.1 217.9 Q 100.5 218.6, 100.5 219.5 Q 100.5 220.5, 100.0 221.2 Q 99.5 221.9, 98.7 222.3 Q 97.9 222.7, 97.0 222.7 Q 96.2 222.7, 95.3 222.3 Q 94.5 222.0, 94.0 221.4 L 94.8 220.5 Q 95.2 221.0, 95.8 221.3 Q 96.5 221.6, 97.1 221.6 Q 97.9 221.6, 98.5 221.0 Q 99.1 220.5, 99.1 219.5 Q 99.1 218.5, 98.5 218.0 Q 97.9 217.6, 97.0 217.6 Q 96.2 217.6, 95.2 217.9 L 94.5 217.6 L 94.9 213.0 L 99.9 213.0 L 99.7 214.0 L 96.0 214.0 L 95.8 216.9 Q 96.6 216.5, 97.5 216.5 \" fill=\"#000000\"/>\n<path class=\"note\" d=\"M 14.2 109.9 L 16.3 109.9 L 16.3 102.8 L 13.9 103.5 L 13.6 102.7 L 16.6 101.4 L 17.5 101.6 L 17.5 109.9 L 19.4 109.9 L 19.4 111.0 L 14.2 111.0 L 14.2 109.9 \" fill=\"#000000\"/>\n<path class=\"note\" d=\"M 20.0 103.3 Q 20.4 102.4, 21.2 101.9 Q 22.0 101.3, 23.2 101.3 Q 24.7 101.3, 25.5 102.1 Q 26.3 102.9, 26.3 104.3 Q 26.3 105.7, 25.2 107.1 Q 24.2 108.4, 22.0 109.9 L 26.4 109.9 L 26.4 111.0 L 20.0 111.0 L 20.0 110.1 Q 21.8 108.9, 22.8 107.9 Q 23.9 107.0, 24.4 106.1 Q 24.9 105.3, 24.9 104.4 Q 24.9 103.5, 24.5 102.9 Q 24.0 102.4, 23.2 102.4 Q 22.4 102.4, 21.9 102.7 Q 21.4 103.0, 21.0 103.7 L 20.0 103.3 \" fill=\"#000000\"/>\n<path class=\"note\" 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},
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]
},
{
"metadata": {},
"cell_type": "markdown",
"source": "Both:"
},
{
"metadata": {
"ExecuteTime": {
"start_time": "2022-08-04T04:43:45.369581Z",
"end_time": "2022-08-04T04:43:45.375139Z"
},
"trusted": true
},
"cell_type": "code",
"source": "molcp = Chem.Mol(m)\nmolcp.GetBondWithIdx(0).SetProp('bondNote','4.5')\nmolcp.GetBondWithIdx(2).SetProp('bondNote','129')\n\nfrom IPython.display import SVG\nd2d = Draw.MolDraw2DSVG(300,300)\ndos = d2d.drawOptions()\ndos.useBWAtomPalette()\ndos.continuousHighlight = False\nd2d.DrawMolecule(molcp,highlightAtoms=[],highlightBonds=[0,2,4,7], \n highlightBondColors={0:(1,0,0),2:(0,1,0),4:(0,0,1),7:(1,0,1) })\nd2d.FinishDrawing()\nSVG(d2d.GetDrawingText())",
"execution_count": 21,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 21,
"data": {
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197.6 Q 264.6 195.7, 261.8 195.7 Q 258.9 195.7, 257.3 197.6 Q 255.8 199.4, 255.8 203.1 Q 255.8 206.9, 257.3 208.8 Q 258.9 210.7, 261.8 210.7 \" fill=\"#000000\"/>\n<path class=\"atom-8\" d=\"M 271.7 193.8 L 274.2 193.8 L 274.2 201.8 L 283.8 201.8 L 283.8 193.8 L 286.4 193.8 L 286.4 212.6 L 283.8 212.6 L 283.8 203.9 L 274.2 203.9 L 274.2 212.6 L 271.7 212.6 L 271.7 193.8 \" fill=\"#000000\"/>\n<path class=\"note\" d=\"M 94.1 217.8 L 95.2 217.8 L 95.2 218.9 L 94.1 218.9 L 94.1 221.0 L 92.8 221.0 L 92.8 218.9 L 88.0 218.9 L 88.0 218.0 L 92.1 211.6 L 94.1 211.6 L 94.1 217.8 M 89.5 217.8 L 92.8 217.8 L 92.8 212.5 L 89.5 217.8 \" fill=\"#000000\"/>\n<path class=\"note\" d=\"M 95.8 219.7 L 97.2 219.7 L 97.2 221.0 L 95.8 221.0 L 95.8 219.7 \" fill=\"#000000\"/>\n<path class=\"note\" d=\"M 101.4 215.1 Q 102.2 215.1, 102.9 215.5 Q 103.6 215.9, 104.0 216.5 Q 104.4 217.2, 104.4 218.0 Q 104.4 219.0, 103.9 219.7 Q 103.4 220.4, 102.7 220.8 Q 101.9 221.1, 101.0 221.1 Q 100.2 221.1, 99.4 220.8 Q 98.6 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},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "",
"execution_count": null,
"outputs": []
}
],
"metadata": {
"kernelspec": {
"name": "python3",
"display_name": "Python 3",
"language": "python"
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"toc": {
"nav_menu": {},
"number_sections": true,
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"skip_h1_title": false,
"base_numbering": 1,
"title_cell": "Table of Contents",
"title_sidebar": "Contents",
"toc_cell": false,
"toc_position": {},
"toc_section_display": true,
"toc_window_display": false
},
"language_info": {
"name": "python",
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"nbconvert_exporter": "python",
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"data": {
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"nbformat": 4,
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