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greglandrum/debugdraw.ipynb

Created May 4, 2023 13:56
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debugDraw.ipynb
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debugdraw.ipynb
{
"cells": [
{
"metadata": {
"ExecuteTime": {
"start_time": "2023-05-04T13:26:51.137213Z",
"end_time": "2023-05-04T13:26:53.090363Z"
},
"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": "2023.09.1pre\n",
"name": "stdout"
}
]
},
{
"metadata": {
"ExecuteTime": {
"start_time": "2023-05-04T13:55:37.172455Z",
"end_time": "2023-05-04T13:55:37.186864Z"
},
"trusted": true
},
"cell_type": "code",
"source": "from IPython.display import SVG\nfrom PIL import Image\ndef debugDraw(mol,size=(350,350),drawer=None,asSVG=True,useBW=True,includeHLabels=True,addAtomIndices=True,\n addBondIndices=False):\n if drawer is None:\n if asSVG:\n drawer = Draw.MolDraw2DSVG(size[0],size[1])\n else:\n drawer = Draw.MolDraw2DCairo(size[0],size[1])\n if useBW:\n drawer.drawOptions().useBWAtomPalette()\n \n drawer.drawOptions().addAtomIndices = addAtomIndices\n drawer.drawOptions().addBondIndices = addBondIndices\n \n if includeHLabels:\n for atom in mol.GetAtoms():\n if atom.GetTotalNumHs():\n atom.SetProp('atomNote',f'H{atom.GetTotalNumHs()}')\n\n aromAtoms = [x.GetIdx() for x in mol.GetAtoms() if x.GetIsAromatic()]\n clrs = {x:(.9,.9,.2) for x in aromAtoms}\n aromBonds = [x.GetIdx() for x in mol.GetBonds() if x.GetIsAromatic()]\n \n Draw.PrepareMolForDrawing(mol,kekulize=False,addChiralHs=False)\n drawer.drawOptions().prepareMolsBeforeDrawing = False\n \n drawer.DrawMolecule(mol,highlightAtoms=aromAtoms,highlightAtomColors=clrs,highlightBonds=aromBonds)\n \n drawer.FinishDrawing()\n return drawer.GetDrawingText()\n\nSVG(debugDraw(Chem.MolFromSmiles('c1c(C(=O)[O-])cccc1c1nccc2c([13CH3])[nH]nc21')))",
"execution_count": 31,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 31,
"data": {
"text/plain": "<IPython.core.display.SVG object>",
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