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@apahl
Created March 4, 2016 07:36
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### Disturbed molecule depiction after generation of 2D coordinates"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/pahl/anaconda3/envs/chem/lib/python3.5/site-packages/rdkit/Chem/PeriodicTable.py:131: FutureWarning: split() requires a non-empty pattern match.\n",
" splitLine = blankExpr.split(line)\n",
"/home/pahl/anaconda3/envs/chem/lib/python3.5/site-packages/IPython/html.py:14: ShimWarning: The `IPython.html` package has been deprecated. You should import from `notebook` instead. `IPython.html.widgets` has moved to `ipywidgets`.\n",
" \"`IPython.html.widgets` has moved to `ipywidgets`.\", ShimWarning)\n"
]
},
{
"data": {
"text/plain": [
"'2015.09.2'"
]
},
"execution_count": 1,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"import rdkit\n",
"from rdkit.Chem import AllChem as Chem\n",
"from rdkit.Chem import Draw\n",
"from rdkit.Chem.Draw import IPythonConsole\n",
"rdkit.__version__"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"This molecule renders fine:"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"image/png": 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Xw8/Pr9XZZxYuXIjr169j5syZyM7OxoABqs9xra2tsWTJEnh4eGD06NEaef5h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\nkjUWIRERydr/AQVWczbnnvHRAAAAAElFTkSuQmCC\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7ff6f96ce030>"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sm = \"[#6]1:[#6]:[#6]2:[#6]3-[#6]-[#16]-[#6]-[#6]-[#6]:3:[#7](:[#6]:2:[#6]:[#6]:1)-[#6](-[#6])=[#8]\"\n",
"mol = Chem.MolFromSmarts(sm)\n",
"mol"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"... but after generating 2D coordinates, it looks weird:"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"image/png": 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Xn59PX3/9NQ0ePJjU1dXp/ocfEh0/3viUNTOT6PvvX7Nqxl4dByFrNy5evEj6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\nY4wpNQ5CxhhjSu3/AeA2QZXvsPuMAAAAAElFTkSuQmCC\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7ff6f96ce030>"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol.Compute2DCoords()\n",
"mol"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.5.1"
}
},
"nbformat": 4,
"nbformat_minor": 0
}
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