"
]
},
"execution_count": 365,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# view:\n",
"p = py3Dmol.view(width=400,height=400)\n",
"p.removeAllModels()\n",
"for mol in allmol_m7_rdkit: \n",
" mb = Chem.MolToMolBlock(mol)\n",
" p.addModel(mb,'sdf') \n",
"p.setStyle({'stick':{'radius':'0.15'}})\n",
"p.setBackgroundColor('0xeeeeee')\n",
"p.zoomTo()\n",
"p.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Summary"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Let's align all generated conformers: //todo fixme: align all conformers!//"
]
},
{
"cell_type": "code",
"execution_count": 366,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"\n",
""
],
"text/plain": [
""
]
},
"execution_count": 366,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"p = py3Dmol.view(width=400,height=400)\n",
"p.removeAllModels()\n",
"allmol = allmol_m7_balloon[1:]+allmol_m7_rdkit[1:]\n",
"\n",
"m7b = Chem.MolToMolBlock(m7_crystal)\n",
"\n",
"for i, mol in enumerate(allmol):\n",
" AllChem.AlignMolConformers(mol,atomIds=core_m7)\n",
" mq = Chem.MolToMolBlock(mol)\n",
" p.addModel(mq,'sdf')\n",
"p.setStyle({'stick':{'radius':'0.15'}})\n",
"p.setBackgroundColor('0xeeeeee')\n",
"p.zoomTo()\n",
"p.show()"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
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"language_info": {
"codemirror_mode": {
"name": "ipython",
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"file_extension": ".py",
"mimetype": "text/x-python",
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