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greglandrum/Github3984.ipynb

Created April 20, 2021 14:05
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Github3984.ipynb
{
"cells": [
{
"metadata": {
"trusted": true
},
"id": "8cb9d69e",
"cell_type": "code",
"source": "from rdkit import Chem\nfrom rdkit.Chem import AllChem\nfrom rdkit.Chem.Draw import IPythonConsole\nIPythonConsole.ipython_3d = True\nimport rdkit\nprint(rdkit.__version__)",
"execution_count": 1,
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": "2021.03.1\n"
}
]
},
{
"metadata": {
"trusted": true
},
"id": "a5f6ff73",
"cell_type": "code",
"source": "input_file = \"data/moleculeA.sdf\"\n#input_file = \"data/moleculeB.sdf\"\n\nsuppl = Chem.SDMolSupplier(input_file, removeHs=False) #open input file and take the first molecule\nmol = suppl[0] #take the first and only molecule\nChem.AssignStereochemistryFrom3D(mol)\nmol",
"execution_count": 11,
"outputs": [
{
"data": {
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},
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"output_type": "display_data"
},
{
"data": {
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\n",
"text/html": "",
"text/plain": "<rdkit.Chem.rdchem.Mol at 0x7f904cce5280>"
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
]
},
{
"metadata": {
"trusted": true
},
"id": "ad721314",
"cell_type": "code",
"source": "Chem.MolToSmiles(mol)",
"execution_count": 12,
"outputs": [
{
"data": {
"text/plain": "'[H]Oc1c([H])c([H])c2c([H])c1-c1c([H])c(c([H])c([H])c1O[H])C([H])([H])[C@@]([H])(O[H])[C@]([H])(O[H])C([H])([H])[C@@]([H])(O[H])[C@]([H])(O[H])C2([H])[H]'"
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
]
},
{
"metadata": {
"trusted": true
},
"id": "cffdba8f",
"cell_type": "code",
"source": "params=AllChem.ETKDGv2() #prepare the parameters for conformer generation\nparams.numThreads=1\nparams.randomSeed=1\nparams.useRandomCoords=True\nparams.useBasicKnowledge = False\nids=AllChem.EmbedMultipleConfs(mol, 10, params)\nprint(\"%d conformers generated\" % len(ids))\n",
"execution_count": 25,
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": "10 conformers generated\n"
}
]
},
{
"metadata": {
"trusted": true
},
"id": "59c66fd3",
"cell_type": "code",
"source": "params=AllChem.ETKDGv3()\nparams.numThreads=1\nparams.randomSeed=1\nparams.useRandomCoords=True\nprint(AllChem.EmbedMolecule(mol, params))",
"execution_count": 18,
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": "-1\n"
}
]
},
{
"metadata": {
"trusted": true
},
"id": "ec06c22e",
"cell_type": "code",
"source": "params=AllChem.ETDG() #prepare the parameters for conformer generation\nparams.numThreads=1\nparams.randomSeed=1\nparams.useMacrocycleTorsions = True\nparams.ETversion=2\nparams.useRandomCoords=True\nids=AllChem.EmbedMultipleConfs(mol, 1, params)\nprint(\"%d conformers generated\" % len(ids))\n",
"execution_count": 20,
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": "1 conformers generated\n"
}
]
},
{
"metadata": {
"trusted": true
},
"id": "f5670dfd",
"cell_type": "code",
"source": "mol",
"execution_count": 21,
"outputs": [
{
"data": {
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7fNdG7stEWr9+ff8TysvLYZDWKACYmJgAADkdCqFxBdPo1GZnB3Z2g335yy+/MBgMe3v77OzsFy9e2NjYvPPOOwIKhMlkNjQ0iIuLKysrD3gCOZFLoGlUR0dn+vTpdXV1ZAybN28WXF1oMsG+UTQo8onez8+PUxBcXeXl5QRBaGlpDbYHMieN8rLCHn8UFRVDQkL09PSYTCYA7Nu3T0AVoUkG0ygaWH5+fkZGhoyMjKmp6Z07d6ZNm+bh4SG46oZ+ogcAOTk5NTW19vZ2sgtVEOLi4np7e5csWcLjCwUIkTCNooGRLdD169efO3eOIAgvLy/pvw/ij66hx5dIZPeo4Abrp+fmmhsaurm59f/K0dGRU/70008zMzMFFAOaiDCNogF0dXWdO3cOAN5///2oqCgQ8BM98JZGBds9ymB4RUY+KC31W7my/5cFBQWccmVlJWcZf4QA0yga0KVLlxoaGuh0elVVVV1dnbGxsbW1tUBr5L01Kqg0+ttv0NkJtrYwY4ZA7o8mLxypn+S6urrExMQ4ZVFRUV7e5uSMKd2/f59CobyFMes39o1CX2tUUA/1ioqwbBk4Ow/4ZUdHx8KFC8lyUVFRQECAQGJAExOm0cmMwWBYWlpyFh5dunRpWFiYoaHha6d1dXVVVlaWlZWVl5eXlZUVFRXdvHlTXFzc29tbRkbGz8+PfINToHhpjdJoNGFh4ZKSEhaLxZnJP1JsNhw4AElJICQECgow0BM9AEhJSZHr9QHA2rVrR6dqNFlgGp1aWltb09LSyHRZXl5OFmpqal6bRaSqqlpbW7tz584ff/xRX19f0FExGIympiZJScmZM2cOcZqEhISent6jR49KSkpGbQZreDiUlkJyMggLw9Wr4OUFaWkDLr06Qo6OjklJSWR527ZtmzdvJneKRpMAptFJjsVicYaVGQzGzz//zP02EUlERERLS0tHR0dHR0dXV1dHR6empmbPnj0RERGFhYWXLl0aOruNHOeJ/o0dDqampo8ePcrPzx+1NBobC0eOgLAwAICzM+zeDdXVoKHBfUp8fHxzc7OpqamcnJy8vHxFRYUwef5wcHfplpWVdXR0jDh0NF5gGp3k2traoqOjyfLz588NDAzmzp3LSZfkf2toaPR/U97BwWHlypVpaWk2Njbx8fHkeqACwssTPcnExOTixYs8do+S2zoFBgaSh2fOnHFxcXl9Jebnz/82pqSkBPX1r6XRwMBAFovFnQcTEhLIpfgRAkyjk96MGTMOHz5MlrOyshwdHbds2cLLhebm5hkZGatWrbp//761tfX58+ddXFxGJaSioqKUlBQtLa1ly5aRn/AyvkQa1pwnFosVGhrKSaOnTp2ytrZ+PY1qakJ5OaipAQAQBJSVgZbWa/dRVVV9+vQp9yfce/PxqLm52d7enizjygCTDE54QoNSVVVNSUlZt24dg8FYtWrVt99+y/etysrKwsPDfXx8NDU1aTTaBx98EBYWxvmWbI1q9ctf/Y3+DPyAAPjqK2huBjYbjh4Fc/P+E540NTVf+4SPVabk5eVv95k3bx7/AaPxB1ujk5moqOiaNWs4h8uXLx9uM0pCQiIqKsrU1PSzzz779NNPS0tLf/rpJ17Wyuvt7c3NzU1OTk5OTk5NTW1sbOR8paKiYmdn58w1tWiIlUZfo6+vLykpWVVV1draystvqa2t5SyYX1hY+Nq37e3twg4OEiwWrF/fw2S2m5vLnD3b/yav5XdpaWly8VOEXhnTLUzQhBETEyMlJQUA8+fPf/78+YDn9PT0kBsrubu7y8vLc/+ZKSsru7u7h4SEZGZm9t/NydzcHADu37/PSyQWFhYA8Oeff77xzLa2Nj09ved95s2bV1xczH3C7t27I/39CR0dIjIyPT191apVA96HezFsAFi5ciUvcb5m3rx5bDabLAcGBubl5fFxEzQ+YWsU8cTd3V1fX9/Nze3OnTvkoBP3bh+kffv2ca+KpK2tvbCPrq5u/3u2tLTcuXPn9u3b5KuW/Z+dB2RqapqdnZ2Xl2djY/PGk4WFhWf0PaQP3IhOT4fycmCxhrjJa61R/taNNjY2VlZWPnnypIuLyw8//MDHHdC4hWkU8WrOnDkZGRlubm6ZmZlWVlb9B53mz58/a9YsOzs7MnUOmBbb2tru3bv3xx9//PHHHw8ePCDnq1IoFCEhofDw8C+++OKNYfD3Smh3d3dPTw/x2nbi7e3FBQU3RURAWbkoK2uwa0eeRgmC+O233xoaGniZjYAmHEyjaBhUVVVTU1P9/PzOnz+/atWq//znP7t27eJ86+jo+OjRo/5X1dfXJycnp6SkJCcnFxQUcHKZuLj43Llz7e3t5eTkPv7446+//trR0dGqb2PnwZCD9Xfv3u3t7R1scVISlUq1t7eXl5dvb2/v7e2lUqmysrJ/O6Ow8HFv77RZsyAvr7q6erD7cKdRZWVlPuZ+FT14UFdXp6WlRf5/AJpsxrhTAU1Avb29e/bsIafK+/v7d3V19T/n2bNnMTExQUFBdDqde1K9pKSkra3trl27kpKSOjo6OOd/9NFHAKCnp9fW1jZ01e7u7iIiIiIiIoqKiu7u7mfOnHnx4sVg5zc0NDQ3N3d2dg747W4VlUgA4sIFgiCG6BslCGL69Olk/N7e3kOEN6g9e+oVFdO/+oqfa9G4h2kU8enChQvk8sYLFiwgB51qa2tjYmL8/f1pNBp36pSSkuKkTiaTOeDdOjs7yY2gAwICBquxqalp7ty55D05eQ0AxMTEHBwcQkJCSktLeY+/rKRks6ZmhIIC0dFBEER6erqLs3N1ejpBEER3N9HSwn0ypxUZGRnJexV/odMJAOLaNX6uReMeplHEv/T0dHLbIiUlpdc6EKdPn75ixYpvv/02PT29u7ubl7sVFBSQeTkuLq7/t9nZ2WrkJPm+sfInT56EhIQ4ODhwjx3p6uoGBQUlJSWxWCzywtTU1LCwsO+++y4jI4P7huQOoCtdXcnDioqKgzt3Et3dxJYthLU14epKWFoSffMBONOzyM1OhqexkRAWJqSkCK7WN5pMKMRrne4IDUdNTY2VlZWIiEhlZaW0tLSVlZWDg4Otra2VlRUfWzEfPXp027ZtioqKeXl53HvbnT17NiAgoLOzEwBWr14dGxvL3Sva0tJCjlnFxcXV19eTH1Kp1EWLFrm6ujY0NFRVVU2bNs3FxWXRokWcqwwMDB4/fnzjxo3Fixf/FcHx43D/Ppw4ARQKPHoEzs7snJyKurp///vfV69eVVJSiouL09TU5OwO/WY3b0JODlCpoKoKrq7D/QdBEwKmUTRSNBqtqKjoxIkTvr6+Q4/5vBFBEC4uLteuXXNyctqzZ09jY+PSpUs/+eQTcuamqKioq6trTEzMYCuDsNnsnJyc+Pj4hISErL6Rd2FhYXNzcxcXF1dXVwsLC7K34c8//7S1tVVVVa2qquK+W6+ra6WnZ6a4eFlZWUFBQWBc3Mfd3XeYTACQlJQkt7oDAAkJCU1NTS0tLS0trW2mprNlZUFbGzQ1QV0dRLiGbQMDgcGANWugqAguXIDbt2H4b5Gi8Q/TKBqR6upqDQ0NaWnppqYmPpqf/X344Yfnz59vbW1dv349QRBPnjzJyMiQlJRUUFBITEzU09PjrEI9tIqKisTExPj4ePIBn/xQW1t76dKlLi4uV69eDQsLCwwM/Oc//1lSUlKUm1v8558lNTVnGhq2AHBeNY0FCAMo0dCYMWNGdna2vLy8rq5uZWVlQ0MDp6JKGxvN9PRXB8LCoKoKWlqgrQ3vvw87d0JW1qtl9/buBXFx+Oyzkf8TofEG0ygakRMnTmzevNnNze3y5cujcsPt27cLCwsfPnxYVFTU0dFRRkZGTk7Ow8Njy5Yt/L1Kz2AwPDw8Hj582Nvby3nkp1AG/ss/JSSUr6paYWVlaGhobGS0Zs+e3qtXqcbGDAZDTk5OWFi4tbVVQkKio6OjoqKisrKyqqrKvalJvrAQKiqgshJqa4GzcusPP0B+Phw79uowMRFOnoRffuHjJ6BxDueNohH5/fffAcDJyWkU76mmprZmzZqLFy8mJibKy8sbGxvv3r2b77tJS0sfP36cQqFoamoWFBQkJCTExMTU19fX1NTIAugB6ALQKJTZBga6Tk6m69eLbdwIH38MmpoQFgZWVmBsTN6ERqPl5eVlZ2fPmzdPSkqKRqMNMIG0uxuqq6GyEqqqgEqF7Oy/vmKxQEKC71+BxjNMo4h/bDb75s2bMNpp9OrVq1paWmRfpKKi4u3btxsbG7lHh4aLnEVQUFAQGxubkJCQnZ0NAGE2Nv4PHsD8+eDiAu7uoKr66uyff4aICGhqAhsbiIri3MTGxiYvLy8jI2Oo9ZlERUFHB8g1VqqrYfdu6OoCshfi+nXAhZ0mKUyjiH93795tbm42MDAY8JV5vm3atMnLy0tdXf3AgQNFRUW3bt0i31ziQ0NDw40bN5KSkpKTk588eUJ+qKCg4OzsrLdmDSxZAlTq69eYmcFA77xbW1uHh4dnZGTwWre6Onz4ISxZAi4uUFgIjY0QEsLfr0DjHKZRxD9BPNFzaGtrz549Oy8vz8fH59atW7xf2NPT8/DhQ3K8nvPavri4uIyMjKenp4uLy7Jly4KDg0uqq5f0z6GDI1dCSUtLG8Zv+Pe/YfVqyM8HJycwMxPEFk9oPMA0ivh3/fp1GO00amZmpqGhAQDe3t6zZ8/29PSsqKj47LPP7ty5M/SFeXl5SUlJSUlJKSkpnJ2OJCUlFyxYYGxsHBoaKiIism/fPiUlJQCQlZVVV1cfVmCGhoby8vK1tbXV1dVDX9vQ0NDY2PhqBSwNjZTycjtz82HVhSaYMZz6jya05uZmYWFhMTExBoMhuFqePHkiLS0NAOfOnev/7fPnz8nXTzX+vnuSrq6uv7//lStXOO+eurm5AcC2bdtGEgy560lMTMzQp12+fJnzSiubzVZVVR1JpWj8w9Yo4tPLly99fHxYLNa0adMEV4uurm5wcPCmTZs+/PBDW1tbLS0tJpOZlpZGvraUnZ1N9M1bUlJSsrOzc3BwcHZ25rw2ynHgwIH4+Phjx47t2LHjtZzLO2tr6+vXr2dkZHBW1EcI8KEe8UFbW7uiokJDQ+PkyZNeXl4ZGRnW1taCq87Pzy8xMTEmJmbJkiXa2tppaWnkW6EAQKVS7ezsli5d6ujoOPS27yYmJp6entHR0fv379fU1CRnufr6+nI2vOMF2T3KyyhTbm7ukSNHAIDAedlTAKZRNGwsrrXiu7u7ezkTzgUmODg4Li6uqanpyZMnQkJCdDrdwcHBwcFhwYIF4uLiPN7k66+/jo2NPXnyZFJS0vLlywGA+7V9XlhZWQkJCWVlZbFYrAHrJQgiKSmJzWbLyMjo6+sDptEpYmz7FNBENHPmzEd9nJyc0tLSBF3j5s2byT9XY2PjhoYGvu/j5+cHAOvWreP7DmSb97XFogiCYLPZV65csbS0BIBt27Zh3+iUgq1RNGxMJvPQoUNkuaSkRNDVnT9/PiIiQkJCQkhIqLi4uKWlRVFRkb9bffXVVz///HN0dHRAQAC5hCiVSuXxJX2StbV1QUFBRkYGZ5X+9vb2kydPHj58uLKyEgDU1NQoOLFpqhnrPI4mHmVlZU559erVAm2N5uXlkTuSRkZGkm3JXbt2jeSG9vb2ACAqKionJycrK3v8+PFhXR4REQEAnp6eBEE0NDQcPHiQ0zOgp6cXEhLCZDKrqqq4Ny5948g+mugwjaJhe2tplMFgkLMv/fz8CIJIT08HACUlpQG3LeFRQEAAuTh0RkbGjRs3hrspCLmVnpqaWlBQELVv9r6FhcWZM2fILfPQFDSi1SHR1LRixQpO2draWkFBQUAVbdy4saioyNTUlFxv1Nra2szMrL6+PiEhge97SkpKLl26FAD27Nkz3GsJgqivrxcTE6upqQkNDe3o6HB2dk5JScnKyvLx8RlsFVQ06WEaRcMWGRnJKe/cudPQ0FAQtQQHB8FqJd4AAAaVSURBVMfGxkpLS8fExJDP9QDg6+sLACNclE9JSYlKpf7++++nTp3i8ZLW1tbw8HAzM7MlS5Z0dXUJCwsbGxvfv38/ISFhwYIFIwkGTQKYRtE4VVlZSaFQTp8+bWRkxPmQTqfv3LmTk/4++eQTPu7MZrPJjUPI5amGdvfuXV9fXxUVlYCAgLy8PDU1NT8/PzabXVNTo0Ou5ISmPEyjaLzYu3dvSkoKWb59+7acnFxWVtbq1au5z2lpaXnx4gVnq5IoroXseOfg4HD+/PmZM2fW1tY+e/ZswHMYDEZ4eLiFhYW1tfXp06dZLJaDg0NMTEx5efmJEyeWLl3a1tZ29OhRPmpHkw+mUTRe1NTUMBgMstzW1lZbWztnzhwB1TVt2jSyJfvw4UPi7zPki4qKPv30Uy0trYCAgAcPHsjKygYFBT169CgpKcnd3Z3cKGXv3r0AcPTo0ZaWFgFFiCYQTKNofCGHPoc4ISEhYWEfPu7v7OxsZmYGAIGBgSoqKs3Nzb/++isAsFis2NhYR0dHGo327bfftrS00On0sLCw2trao0eP6unpcd/ExsbGwcGhtbWVHPtCUxzuxYTGi82bN9+9e5cc929qarKxsQkLC3vtnPj4+Pj4+PDwcPJQRUVlsKdyXhw7duzDDz+cNWvWP/7xj5MnTzY2NgLA9OnTvby8AgMD33nnnSGuJfcWlZGRqaiokJWV5TsGNAlgaxSNI//9739v3bp169atAwcOvIXqNm3apKurW1VVdejQocbGRk7zMywsbOgcCgDz5s1bvHgxNkgRYBpFU1N7ezsAiIqKfvzxxz09Perq6pmZmZmZmf7+/lSel8Tft28fABw5cuTFixcCjBWNe5hG0XihoaExffp0siwjIzPgqqArVqz4/vvvOYelpaW835/NZnPKCxcuJJfT9/LyEhERefbs2XAXwwcAW1vbRYsWtba2/jDQ3k1o6sC+UTRVzJ07NzIyktwd77fffps5cyadTgeAVatWxcXFhYaGbt26dbj3TEtLmz9/vqysbHl5OfaQTlnYGkWTSkNDw7Fjx8gyQRC6urqcNag8PDy++eYbsrx8+XIyhwLA2rVrASA6OpqP6mxtbRcuXCgqKlpUVDTS0NGEhWkUTSrNzc0XLlwgyxQKpbW1lbOm37/+9a+0tDRyOJ6bm5ubjIxMenr648eP+ajxm2+++eCDD8iF8QEgMDCwp6eH3/DRhIRpFE1msrKyv/76a1VVFQBQqdRHjx71X6tUQkLCzc1tnpoa4/ff+ahCWlqae1uRa9eucXfCoqkA0yiabHJzc5361NXV+fj4HD58mPxKQkJiwEt+2rAhrbbWoq83AKFhwdXv0WRjamp65coVsmxiYrJ169bbt28PfQnV3h5mzoTCQsjJgeHvKZ+Zmcl5paqurm64l6OJDtMommwoFApnvzkKhTJz5kxy2fyhiIiAuzv88ANER/ORRi0tLRMTE8kyLvs0BeFDPUIAAODtDQAQHQ2C3+gUTTKYRtGkoq+vf+nSJc5hWlratGnTeLrSxgb09eHpU7hzZ1g1CgkJkcs+kcTExHBLu6kGp98j1OeLL+DXX+G772D58rEOBU0kmEYR6tPZCeHhcP06CAnBypWweTNguxLxAIeYEOpz4AA0NUFsLLDZEBAAra2wc+dYx4QmAGyNItRHRQWePAFy+7znz8HGBp48GeuY0ASAQ0wIAQDAy5cgJgZ9W5DCzJnQ0gLYyEA8wDSKEAAAUKnAZALnPc72dqBSsW8U8QLTKEIAAEChwPLlwHkf9MgRcHcf04DQhIF9owj1aWmBLVuguhp6e8HICIKDgcc5p2hqwzSKEJfycvj6a9DXhy++GOtQ0ISBD/UIcXn2DM6cgWvXxjoONJFgGkWIS0cHAADPu9ohBJhGEeL2ors7x9CwXklprANBEwmmUYT+8tuLF3NKSrbh8vVoODCNIvSXjo4OAJDiTMJHiAeYRhH6C6ZRxAec8IQQAEB9fX1qaqqVlVVJSYmamtrNmzcDAwPHOig0MWAaRQgAIDs7+8svv7x69Sp5qKam9vTpUyEhfFxDb4Z/JQghNCK43ihCr+Tk5Kxfv54st7S0jG0waALBNIrQK0ZGRgcPHiTLN27cGNtg0ASCaRShVyQkJNTV1cky9ooi3uHfCkIIjQiO1CMEAMBkMuvq6nR0dMjDwsJCGo02tiGhiQLTKEIIjQg+1COE0IhgGkUIoRHBNIoQQiOCaRQhhEYE0yhCCI3I/wNt8kts3zpy2wAAA2l6VFh0cmRraXRQS0wgcmRraXQgMjAyMS4wMy4xAAB4nL3Sa2yTVRgH8Oc979uue9/e27WbwNZJNyrSwRxQxKzP0cZNIMIumW5KYjc21i/c6YKgpSOOEUDFC8wLIWGAi8t0apyUyd5zIBI7dMhlNcZN3Acj44PjlsCAEH0znB/4rD7JP788yck5zzk5V9RPLoJWRi0C3K/ZWgq1xAU99WmK0n+lASYkk+rBoyn9g1eD/K3wgGRymWECIkzsIQgPtP+X/84UCggRArqwWWtIWMgCIkYIeUh7qrBo9Ei6iHZrj24K6NMiRK+EDWnhNJMn3RAhhqkgp4fTp4EiR4hsASUbjDlg8oDVDOZcMD8MNgtYpoPFCw4rWDPAmicRmx1smRr5YHeC3Q32GZLgdIDDJRGHD5yPgHMmZDwKbj/kzwJfAThFvUBESacdb0iXFb3JDDpJr8gWm93psLqFyT80O/n0M+rJH39WlWqJXj+cZImhELt9y0oTch4f/u1g8cpzwzjWYeJ3jNtw9RrEkXfLWGDwEO47mIvjKxLHL69ai8rIL9i0r0fdNDyGJa0+1l3Uwz7Oy6Kk4BjLCXSxraszaeOG+fzNGsJW1neiNVTBO6I2nJP3Em6JZ/NPT1SiZ/5ZbOzuYjTwFH/y+xfxzLLz6uE/XPzi4GK6cWcxc37mRnHkFDt95jjmdFagCG526Fg+v3R0DDd3v8+uzSzD1HIzXZaKs+lLF3J7SwV1DTzHlrbfZEPyNLqqLIMLPP71s1trafPl6+yHc/WsPbmAfpdVxwp++hXj67/FNcWF3PSanp2s3EN3db7Crib83C5baHfoLvN+/gI/Gx1lTYZB1vLNPFpFGvnQ7fq+JQGRNrWKeGP8AjYvmELXjSu86G0//bC/hr9h8bHyrxpw99Ed3CaO4ukOmd46v5eBK857H9+GC/2vq5GQxGPVzXT0o1618lS0uL/Wwq/GyvGxD6pRRCOvqs2k0WgoOF63kx3oqeZrv+wPvhNrYXWxFDtyZxSvBfao+9tKg9k2L7306st9HTNivEZ4nk5tCwYTX/SzRTuK6EZfFZ/V3oDl92I0eWEuz012sbe27KIDgROsatF2tX13DvX3/amW7vfSyO9zaeWcUkz1hvnyFe9RdcCgbk+VcPpEId070MobQjp0/QUQqSxumfMMkAAAA4t6VFh0TU9MIHJka2l0IDIwMjEuMDMuMQAAeJyVV8uuJDUM3fdX5Aduye84ay4SEhqQkGCPBAsWzGr+XzgVJ7dGAg1u9aJcTk7bJ8d2+tfPn3//+88/Xm1+fnn/8a8v7Xz4/fVq0puM1uBfv2OM9hsBwNz/BhcOtfUk1GVi0AXWR/uu/RfE83uj4KXWdaF0U1woNJ8KKHRpd5974YI+YD7h1amKQsiy9gIaLLwu3SsocDmKLxTqQdmNYoxSQwEiXXsHD8qMmIsorHGk9143w/XO1Ll2RoL3ScfJRCgj34n1GgqLpkrYsS/GXaHIrsJmgxnn0xtf5FrJKDhVc1pP3ncs0s1qKE49YzGyvrMcJdXxBSyWeOq7ojB4+bmiXZ6nOuv4QrsZmhUlIAWUycu4VTfrUnSs3KSX6ujmZakk8Hz4is+ghjIVq7BiiabTExmZHij0LZSoaRJZKACmK5aBCBWUqbAhWd08cOENsqd28duxiHKywcyQdQ48Kih8KXFm5KN7RjW4UkcRi3tPlbjz7i/iFdXFDtW7jiKjbpshJdX2w/9HkUsRMpbhHRIPpaTdOGneehm22OWoo46FWCanaHm+prdeJlcCJRQOtY+caqCrjmI2amRZ4CWYRM5JErFAaoii1xVioQsXp21ySpsXiAotoMBhY2qtz07zJjHfSCoZTXYpJwmaZafBDhW9xO8CUE41wJ6qo669xguY2dIfCOVsZIteXDojMEjFkgDvLuWVM5o7ZKkueBnIiyF2qJxRmzcyyOkMjrhOmt0q2g0UHgKJInva27zX1U6aIDmlNe3v+KSEEvc6411HtnLja4SMK50hONCR2kXf1a1dvRaLg+Z9I5r3ntgjaqsUy3DJjumk2cfjzlDiRea098zjdBoyKqkuesnYUygCyF6nPXpEjReyZKN3T9UpYqkzSMyPXYPIbAsFwYpn1PPuE71JOP8RKEGhpvG+D8gxbBuot43LE2v4LKM2u1p61mvZxuxU6Yl3ejzSZp2nRx+/M42PPdbIjxGv/SzrDT8CHU+PtyA/98RFZzrPslnQ6cHbKXvZlEJ6aDq3J5bZw8OHg4h/XhzSkMYnn6j3ZGvxxvI0Pjz+hLbGXxmHg9Aj9gc00cPgxY4ttPGAJn14+MMTHODTkIchiwN8zTUEjwiIN1oYcgBimdDTOBxElHKg40fkJBexyOEgoGQn96m17396f/0DOT9xfLDBtrkAAAK8elRYdFNNSUxFUyByZGtpdCAyMDIxLjAzLjEAAHiclVQ7aiRRDLzKhjb0NPp/6MTgxJkPYCbyNXz4LWlmweli6Ha/epJKpdJ8fdw/v/n75evj/vp8yvPNtwE+fyHP5zfP+32/9vH1/vZ2f3x+Pr9/f/7HTXnc+rj/+Xm52Ukk0QefxKl93OiU9NS4bnqSWshBZ/n8DWZMGX7d5BRWzQ0LmjtpmW2DeFYWTiibrAt3UpxtEga1y+Qh9ybRQ/AfCRLy6ZGug6EAJQOS2DA+i4MPvMNxAqCMWC5c5XbPJW2SJpMuUH0gEnGqAI/W5hyqqWoXnc6aADYdDQUT101XjCYEiGQ3IzQUdxdStwgDVDFcAHnpg52xA5FTW1qGpllMEE68xA89OVpsWzPSh0gUkwfqm9Aqq2HuK4Sa29DS4kQU2oUePUFcSVMpeYP0NJLWoeeEHmeKqsw9kJSj2yUaVjlT7EQ7B0YuKcajRJTQ9FnJ2xa0gPoNqCSnOkSSCD+WVvM1sxBvcECA9Zxzkm+ANNV04tVlSzww3LpmTDSWwGUq5mWuBS8AUkzHNz+UaN0pR7ZcGL+YrZ5EM3bka2ZaBFy2doeuDOAQOPfAmNZeSM7Mg3UyJ7CCm8YNmQUSgzhjfiNUw8gzfW24Z9NKlAJSb5sYrmBZbo7dyMsQC39NUFc0zHWboRhENdhXeH2MBfHOqcTjSuRzUV3eGEXu1FEbxABBMtke4RjTp94VyAcT1aP2v+WREEE+DMt13A+rqNLWJBoXoi9c9+JaYvFs0JHaR78if5gEYRjmWoNWwXw4FRYxxcZPDHnM2OMpudCINLuiDL8CgYW2F8Ga5kDcNhRQp7D522ap0KxcworLHCxj97Zx+ZgfDaFdzsYy7rKD6xja0sFsRzq/VNOQYItsKZSajvcsePqHK5vVd3eo7fXnL1XUIb9eWl3dAAAAAElFTkSuQmCC\n",
"text/html": "",
"text/plain": "<rdkit.Chem.rdchem.Mol at 0x7f904cce5280>"
},
"execution_count": 21,
"metadata": {},
"output_type": "execute_result"
}
]
},
{
"metadata": {
"trusted": true
},
"id": "892711d0",
"cell_type": "code",
"source": "params=AllChem.KDG() #prepare the parameters for conformer generation\nparams.numThreads=1\nparams.randomSeed=1\nparams.useRandomCoords=True\nids=AllChem.EmbedMultipleConfs(mol, 1, params)\nprint(\"%d conformers generated\" % len(ids))\n",
"execution_count": 22,
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": "0 conformers generated\n"
}
]
},
{
"metadata": {
"trusted": true
},
"id": "02aae58b",
"cell_type": "code",
"source": "# results from changing planarityTolerance to 1.0 (original value 0.7)\nnm = Chem.MolFromMolBlock('''Unnamed\n RDKit 3D\n\n 47 49 0 0 0 0 0 0 0 0999 V2000\n 2.8829 0.3205 0.8831 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.8091 1.1214 0.1976 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.3891 2.0680 -0.7783 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.0454 2.2122 -1.0847 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.2155 1.3896 -0.3717 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.5553 0.4609 0.6201 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.1366 1.1887 -1.1929 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8982 2.3191 -1.1199 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.2403 2.1364 -1.3765 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.7221 0.8256 -1.6812 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.8817 -0.2763 -1.7403 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.5602 -0.1013 -1.5133 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.6489 3.1157 -2.0274 O 0 0 0 0 0 0 0 0 0 0 0 0\n -0.4186 3.5666 -0.8187 O 0 0 0 0 0 0 0 0 0 0 0 0\n 3.4854 -0.8851 1.5934 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.5858 -1.6280 -1.7279 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.6786 -2.1818 1.4213 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.8285 -2.7174 -0.9672 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.0530 -2.2601 0.2485 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.6339 -2.2344 0.3408 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.2761 -2.6722 0.6047 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.5762 -3.2488 1.4131 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1.8403 -1.4452 -0.3976 H 0 0 0 0 0 0 0 0 0 0 0 0\n -1.5333 -1.0241 0.7032 O 0 0 0 0 0 0 0 0 0 0 0 0\n -2.4243 -3.6142 -0.8468 H 0 0 0 0 0 0 0 0 0 0 0 0\n 4.8744 1.0525 0.3827 H 0 0 0 0 0 0 0 0 0 0 0 0\n 4.1611 2.6539 -1.2546 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.7689 0.0150 1.3460 H 0 0 0 0 0 0 0 0 0 0 0 0\n -2.9664 2.9357 -1.3622 H 0 0 0 0 0 0 0 0 0 0 0 0\n -3.8021 0.7045 -1.8733 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.1955 -0.9459 -1.8082 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1.9842 4.0570 -2.1368 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.7421 4.4167 -1.2295 H 0 0 0 0 0 0 0 0 0 0 0 0\n 4.5209 -1.0604 1.1382 H 0 0 0 0 0 0 0 0 0 0 0 0\n 3.6854 -0.6983 2.6217 H 0 0 0 0 0 0 0 0 0 0 0 0\n -3.5396 -1.5286 -1.1458 H 0 0 0 0 0 0 0 0 0 0 0 0\n -2.7723 -1.9521 -2.7375 H 0 0 0 0 0 0 0 0 0 0 0 0\n 2.1660 -2.3022 2.4298 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8061 -3.0836 -1.8908 O 0 0 0 0 0 0 0 0 0 0 0 0\n -1.6927 -2.9139 1.0453 H 0 0 0 0 0 0 0 0 0 0 0 0\n 2.1786 -3.3237 -0.4911 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.2507 -2.6721 1.7920 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.2733 -3.8203 0.4890 H 0 0 0 0 0 0 0 0 0 0 0 0\n 3.8266 -3.5731 2.2942 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.4265 -3.8836 -1.4270 H 0 0 0 0 0 0 0 0 0 0 0 0\n -1.4097 -0.9348 1.6655 H 0 0 0 0 0 0 0 0 0 0 0 0\n 3.1455 -3.1573 -0.5900 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 2 0\n 1 6 1 0\n 15 1 1 0\n 2 3 1 0\n 2 26 1 0\n 3 4 2 0\n 3 27 1 0\n 4 5 1 0\n 4 13 1 0\n 5 6 2 0\n 5 7 1 0\n 6 28 1 0\n 7 8 2 0\n 7 12 1 0\n 9 8 1 0\n 8 14 1 0\n 10 9 2 0\n 9 29 1 0\n 11 10 1 0\n 10 30 1 0\n 12 11 2 0\n 11 16 1 0\n 12 31 1 0\n 13 32 1 0\n 14 33 1 0\n 17 15 1 0\n 15 34 1 0\n 15 35 1 0\n 18 16 1 0\n 16 36 1 0\n 16 37 1 0\n 20 17 1 0\n 17 22 1 0\n 17 38 1 0\n 18 19 1 0\n 18 25 1 0\n 18 39 1 0\n 19 21 1 0\n 19 24 1 0\n 19 40 1 0\n 21 20 1 0\n 20 23 1 0\n 20 41 1 0\n 21 42 1 0\n 21 43 1 0\n 22 44 1 0\n 24 46 1 0\n 39 45 1 0\n 41 47 1 0\nM END\n''',removeHs=False)\nnm",
"execution_count": 27,
"outputs": [
{
"data": {
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\n",
"text/html": "",
"text/plain": "<rdkit.Chem.rdchem.Mol at 0x7f90f2398280>"
},
"execution_count": 27,
"metadata": {},
"output_type": "execute_result"
}
]
},
{
"metadata": {
"trusted": true
},
"id": "93516ce7",
"cell_type": "code",
"source": "",
"execution_count": null,
"outputs": []
}
],
"metadata": {
"kernelspec": {
"name": "python3",
"display_name": "Python 3",
"language": "python"
},
"language_info": {
"name": "python",
"version": "3.9.1",
"mimetype": "text/x-python",
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"pygments_lexer": "ipython3",
"nbconvert_exporter": "python",
"file_extension": ".py"
},
"toc": {
"base_numbering": 1,
"nav_menu": {},
"number_sections": true,
"sideBar": true,
"skip_h1_title": false,
"title_cell": "Table of Contents",
"title_sidebar": "Contents",
"toc_cell": false,
"toc_position": {},
"toc_section_display": true,
"toc_window_display": false
},
"gist": {
"id": "",
"data": {
"description": "Github3984.ipynb",
"public": true
}
}
},
"nbformat": 4,
"nbformat_minor": 5
}
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