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RDKit BRICS and RECAP Tutorial
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{
"metadata": {
"name": "RECAP and BRICS"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"RECAP and BRICS\n",
"====\n",
"\n",
"Some references.\n",
"\n",
"- Lewell, X. Q., Judd, D. B., Watson, S. P. & Hann, M. M. RECAP - Retrosynthetic Combinatorial Analysis Procedure: A Powerful New Technique for Identifying Privileged Molecular Fragments with Useful Applications in Combinatorial Chemistry. JCICS 38, 511\u2013512 (1998).\n",
"- Degen, J., Wegscheid-Gerlach, C., Zaliani, A. & Rarey, M. On the Art of Compiling and Using \u2018Drug-Like\u2019 Chemical Fragment Spaces. ChemMedChem 3, 1503\u20131507 (2008)."
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"from rdkit import Chem\n",
"from rdkit.Chem import AllChem\n",
"from rdkit.Chem.Draw import IPythonConsole\n",
"from rdkit.Chem import Draw\n",
"from rdkit.Chem import Recap,BRICS"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 16
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"cdk2mols = [x for x in Chem.SDMolSupplier('data/cdk2.sdf') if x is not None]\n",
"for m in cdk2mols: AllChem.Compute2DCoords(m)"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 2
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"BRICS\n",
"===="
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"m1 = cdk2mols[0]\n",
"m1"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"png": 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T5dKlSw553n379onZbJawsLB6j/5tjDNnzsjIkSPFw8NDnnvuOcnOzlbttUmfGITkMNev\nX5fHHntMevbsKVevXpV//vOfEhsbKyaTSV555RVtRm/W4MCBAxIUFCQhISFy6NChWrc/evSo/Pzn\nPxej0ShTpkyRy5cvq1DlHTabTdatWycPPvigDBgwQDIzMxv1fKdPn5YRI0aIh4eHPP/8804JDIvF\nIjNnzhRPT0+ZOHFipS9JjpaVlSXPPPOMeHh4yC9/+Us5e/as016LmhYGITlUQUGBxMbGSkhIiHh5\necnUqVNVD4z6sFqtMnv2bPHy8pIXXnhBrl69et82qampMnz4cPH09JQJEybI+fPn1S/0LhcvXpRR\no0aJj4+PvP7663Lz5s167X93YIwePVrS0tKcVOkdJ06cuD3VYvv27Q7taHNycuTFF18UT09PGTRo\nUJ1HLBNVYBCSw6WmpgqARp2DU9upU6ekZ8+e0rZtW9m6davY7XbJzMyUsWPHioeHhzz99NOSnp6u\ndZmV7Ny5Uzp06CDdunWTlJSUWrfPycmRiRMniqenpzz11FNy8uRJFaq8o7y8XJYtWyYmk0mGDRvW\n6KkWP/74o0yfPl28vb2lb9++8u9//9tBlZK7YRCSw3311VcCoN6ditbKy8tlxYoVYjKZ5PHHHxdP\nT08ZMmSInDp1SuvSqlVQUCDx8fHi6ekp06ZNq3IaS25urkybNk0eeOAB6devn3z++ecaVHrHt99+\nKwMHDhQ/Pz9JSkqq9wjea9euyfz588XX11eio6Nl3759uprMT66HQUgOd/jwYTEajVqX0WCnTp0S\no9Eof/nLX7Qupc4+//xzCQ8Pl8DAQNmzZ4+IKIExb948ad68ucTExMj+/ftdJjDsdrts2rRJWrdu\nLbGxsXLmzJla9ykqKpIlS5ZIq1atJDIyUnbs2OEyvw/pG4OQHO7AgQPSqlUrrctosJycHAHg1KkK\nzlBaWiqJiYliNBolLi5OWrZsKVFRUbJr1y6XDYy8vDwZN26cGI1GSUhIqHKqRUlJiaxatUratm0r\nnTt3ls2bN7vchH3SN4OIi1/ynnTn008/xdSpU/H9999rXUqNtm3bho4dOyL2nhvlfvPNNwgPD0dR\nUZEubzablpaGgwcPonXr1vjVr34FDw8PrUuq1b59+xAfHw9vb2+sX78ejz/+OMrLy7Fx40YsXrwY\nIoKFCxdiwoQJ8PLy0rpcamI8tS6Amh693KR1/fr1+MUvfnFfEFosFgCAyWTSoqxGi4iIQIQO7m94\ntyeffBJff/01EhMTMWDAAAwdOhSnT59GYWEh5s6di0mTJsHHx0frMqmJ4v0IyeH0EoTV1VmxvFkz\n/vdQU/PmzbFixQocOXIEqampGDhwILKzszF9+nSGIDkV/6eTw1ksFl0cUqwtCEkb0dHRuHTpEsaN\nGwc/Pz+tyyE3wCAkh9NLkFgsFgahCyovL0dZWRnfA1INg5Acrri4WBcfYuwIXZPVagUAvgekGgYh\nOZxegoRB6JoYhKQ2BiE5nB6CxG63o7i4uMpzmXqovymrCEI9nGempoFBSA6nhyApLi4GUHXXUV1A\nkjrYEZLaOI+QHM7bOwL+/h20LqNGNX3Y6iHImzKr1Qpvb29dXAiAmgYGITnchQsJiIzUuoqaVUya\nZxC6nupG8xI5C4OQHM5qBVz9yGJJiQ96934XJtP9hdpsfnjwwQc0qIoAfhEh9TEIyeGsVsDVP8eK\nijrg2LGX8EAVeXflylIEBKhfEymsVivP0ZKqOFiGHE4PQVjRtRoMVa/T6WVGmwR2hKQ2BiE5nF6C\nsLoa9VB/U8YgJLUxCMnhLBbXD5LagpBH5rTDICS1MQjJoWw2oLTU9YOwprBmR6gtBiGpjUFIDmWz\nAe++CwQFaV1JzWoKOz10tE0Zg5DUxiAkh2jVCtiwATAagZdeAlq2BMxmrauqHs8Rui6OGiW1MQjJ\nIYxGYPFi4OrVqtfb7cDvfw+kpqpbV3WKi6s+DygCvPwyEBamfk2kYEdIamMQkkOYTMCkScD8+VWv\nLysDCguBmBhg3jygpETd+u51b9dX0dEaDEBCAvDww67d0TZlVqsVJs5fIRUxCMlhpk8HDh8Gjh69\nf52PD/Dhh8CePcD27UC3bsChQ+rXWOHeIKytoyX1sCMktTEIyWGMRiApCZgyRRk0U5WBA4HTp4GR\nI4EnnwReeAG4dk3dOgGgc2cgKurO49o6WlIPrzVKamMQkkP17w9ERADr1lW/jckELF0KpKQo5wwj\nIoBt25Tzc2qZOxeYPLnyspo6WlIPO0JSG4OQHG7ZMmDFitrPA3bvroTOrFlKZzhsGJCTo06NValL\nR0vOx1GjpDYGITlcu3ZKuJWVKY/Lyqrv9jw9gRkzgDNngPJy4Ne/3oi33noLNo2SqC4dLTkXO0JS\nG4OQHOL8+cqPf/tb4Pp15WeLBRg1Crh0qfr9zWbg738Hfv3r5njttdfQp08fnDlzxnkF16CuHS05\nB4OQ1MYgJKdr2RIoKlI6rbVrlTmFVTEYgLFjRyMtLQ2hoaGIjo7GggULUFpa6pS6bLaqR67e29GS\nem7evImbN28yCElVDEJyOg8P4B//ANasARYuBPr2BdLSqt8+ICAAmzZtwu7du/HJJ5+gW7duSE5O\ndlg9IsCOHcoUjvffV5bV1NGSeqxWKwAwCElVDEJShcEAjB8PpKcDgYHKQJlFi2ruuuLi4nD69GkM\nHz4ccXFxmDhxIq43Ip1EgH37gEcfVWoZORJYv77BT0dOUFJSAk9PTwYhqcogouagdSLF3r3K9AWT\nCXj//XPo3bvmq3SfPHkSL774Ii5fvow1a9Zg9OjRMFR1V91qfP65Mkfw+HHldV95BWjTprG/BTlD\nxUdSfd5fosZgR0iaeOop4Ouvgf/5nwt44olwxMfH48aNG9Vu37NnT6SkpODll1/GggULbh9Cq82p\nUxcwaBDws58p5yizsoCVKxmCrsxgMDAESVXsCElzx48fx8SJE5Gfn4+kpCSMGjWqxu3Ly8vh5eVV\n4zZnz55FQkIC/vd//4aXXsrHtGktEBzsyKqJqKlgR0iai4mJwfHjxzF16lSMGzcOo0aNwqUa5lrU\nFILZ2dl47rnn0K1bNwDAl1+exNtvMwSJqHoMQnIJXl5emDNnDlJTU3Hjxg1ERkZi3bp1sFc31+Ie\nFy9eRHx8PMLDw5GXl4cjR45gx44diLr7gqJERFVgEJJLCQkJwcGDB7Fq1SosWLAA/fr1Q3p6erXb\n5+fnY8aMGQgJCcHZs2dx8OBB7Nu3DzExMSpWTUR6xiAkl2MwGDBhwgSkpaXhJz/5Cbp3745XX30V\nZXfNtSgoKEBCQgKCgoLw2WefYefOnfjss8/Qt29fDSsnIj3iYBlyeXv27MHkyZPh6+uLNWvW4Pjx\n41i+fDnat2+PP/zhDxg1ahRHGRJRgzEISReKioqwcOFCbN++HV5eXli8eDGeeeYZeHh4aF0aEekc\ng5B0xd/fH1u2bMGgQYO0LoWImgieIyRdsVqtePDBB7Uug4iaEAYh6QbvTEBEzsAgJN3gnQmIyBkY\nhKQbDEIicgYGIekGg5CInIFBSLrBICQiZ2AQkm5YrVb4+Phw7iARORSDkHTDarWyGyQih2MQkm5Y\nLBYGIRE5HIOQdIMdIRE5A4OQdINBSETOwCAk3bBarfD19dW6DCJqYjy1LoCorjw9n0R4+GNal0FE\nTQyDkHTjhx/+G1eval0FETU1PDRKumGxADxFSESOxiAk3bBaGYRE5HgMQtINqxXgWBkicjQGIemG\n1QqYTFpXQURNDYOQdIOHRonIGThqlHTjmWeAnj21roKImhp2hOQyzOaal730EhAdfedxq1bAhg21\nPwcRUU0YhKRbRiOweDE4t5CIGoVBSLplMgGTJgHz52tdCRHpGc8RkssoLATCw+9fBgC7dgF79wJ2\nOzB0KDBihLJ8+nTlvOHRo0CvXqqWS0RNBIOQXEaLFkB6euVlFef8jh0D1q5Vfh48+E4QGo1AUhIw\nZQqQkqJaqUTUhPDQKOnCH/8I5OUBM2YooXe3/v2BiAhg3TpNSiMinWNHSLqwfz9w4gSQmAi0bn3/\n+mXLlEOjpaXq10ZE+saOkHRhzRrgm2+AadOAuXPvX9+uHTBrFlBWpnppRKRzBhERrYsgIiLSCjtC\nIiJyawxCIiJyawxCIiJyawxCIiJyawxCIiJyawxCIiJyawxCIiJyawxCIiJyawxCIiJyawxCIiJy\nawxCIiJyawxCIiJyawxCIiJyawxCIiJyawxCIiJya/8P664c0jstB4gAAAAASUVORK5CYII=\n",
"prompt_number": 3,
"text": [
"<rdkit.Chem.rdchem.Mol at 0x10767afa0>"
]
}
],
"prompt_number": 3
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pieces = BRICS.BRICSDecompose(m1)"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 4
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pieces"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"prompt_number": 5,
"text": [
"set(['[4*]CC(=O)C(C)C', '[14*]c1nc(N)nc2[nH]cnc21', '[3*]O[3*]'])"
]
}
],
"prompt_number": 5
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"cdk2mols[20]"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"png": 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jxwkLC8PBwQFXV1e1yxFmIpNlhFlFRUXh7OxsltmiiqIQEhJC06ZNWb58OQ4O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\nQiGEEDbt/wMMyDAsAUmU6gAAAABJRU5ErkJggg==\n",
"prompt_number": 6,
"text": [
"<rdkit.Chem.rdchem.Mol at 0x107fff590>"
]
}
],
"prompt_number": 6
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pieces = BRICS.BRICSDecompose(cdk2mols[20])\n",
"pieces"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"prompt_number": 7,
"text": [
"set(['[3*]OC',\n",
" '[1*]C(=O)NN(C)C',\n",
" '[14*]c1[nH]nc2c1C(=O)c1c-2cccc1[16*]',\n",
" '[5*]N[5*]',\n",
" '[16*]c1ccc([16*])cc1'])"
]
}
],
"prompt_number": 7
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"allfrags=set()\n",
"for m in cdk2mols:\n",
" pieces = BRICS.BRICSDecompose(m)\n",
" allfrags.update(pieces)\n",
"allfrags"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"prompt_number": 8,
"text": [
"set(['[4*]CC[NH3+]',\n",
" '[14*]c1cnc[nH]1',\n",
" '[16*]c1cc([16*])c2c3c(ccc2F)NC(=O)c31',\n",
" '[16*]c1ccc([16*])c(Cl)c1',\n",
" '[15*]C1CCCC1',\n",
" '[14*]c1ccc[nH]1',\n",
" '[16*]c1ccc([N+](=O)[O-])cc1',\n",
" '[14*]c1cc([14*])[nH]n1',\n",
" '[5*]N[5*]',\n",
" '[16*]c1ccccc1',\n",
" '[16*]c1ccc(S(N)(=O)=O)cc1',\n",
" '[15*]C1CC1',\n",
" '[16*]c1cnc2[nH]ncc2c1[16*]',\n",
" '[14*]c1nc(N)nc(N)c1N=O',\n",
" '[1*]C(N)=O',\n",
" '[14*]c1[nH]nc2c1C(=O)c1c-2cccc1[16*]',\n",
" '[16*]c1c(F)cc(Br)cc1F',\n",
" '[5*]N[CH+](=N)N',\n",
" '[7*]C1c2cc(S([12*])(=O)=O)ccc2NC1=O',\n",
" '[5*]N/C=C1\\\\C(=O)Nc2ccccc21',\n",
" '[4*]CC(O)C[4*]',\n",
" '[16*]c1cccc(Cl)c1',\n",
" '[1*]C(=O)NN(C)C',\n",
" '[5*]N1CCCC([15*])C1',\n",
" '[14*]c1nccs1',\n",
" '[14*]c1nc2c(ncn2C)c([14*])n1',\n",
" '[14*]c1cnco1',\n",
" '[4*]C(CO)C(C)C',\n",
" '[7*]C1c2cc([16*])ccc2NC1=O',\n",
" '[7*]C[8*]',\n",
" '[14*]c1ccccn1',\n",
" '[16*]c1cc(C)ccc1F',\n",
" '[14*]c1c(C)nc2ccccn12',\n",
" '[1*]C(=O)NN1CC[NH+](C)CC1',\n",
" '[14*]c1[nH]cc2c1CCNC2=O',\n",
" '[15*]C1CC[NH+](C)CC1',\n",
" '[9*]n1cnc2c1nc([14*])nc2[14*]',\n",
" '[3*]OC',\n",
" 'NS(=O)(=O)c1ccc(N/N=C2/c3cc(Br)ccc3NC2=O)cc1',\n",
" '[14*]c1[nH]ccc1[16*]',\n",
" '[16*]c1ccc2c(c1)CS(=O)(=O)C2',\n",
" '[5*][NH+](C)C',\n",
" '[14*]c1nc(N)nc2[nH]cnc21',\n",
" '[1*]C([1*])=O',\n",
" '[4*]C[8*]',\n",
" '[8*]C(C)C',\n",
" '[16*]c1ccccc1Cl',\n",
" '[4*]CC(=O)C(C)C',\n",
" '[1*]C(C)=O',\n",
" '[14*]c1ccnc([14*])n1',\n",
" '[15*]C1CC[NH+](C)CC1O',\n",
" '[14*]c1cnc([14*])o1',\n",
" '[1*]C(=O)C(C)C',\n",
" '[4*]C(CC)CO',\n",
" '[8*]CS([12*])(=O)=O',\n",
" '[16*]c1ccc([16*])cc1',\n",
" '[14*]c1cc(=O)c2c(O)cc(O)c([16*])c2o1',\n",
" '[7*]C1c2cc([N+](=O)[O-])ccc2NC1=O',\n",
" '[4*]CCO',\n",
" '[8*]CC',\n",
" '[6*]C(N)=O',\n",
" '[15*]C1CCCCC1',\n",
" '[14*]c1[nH]cc2c1CCOC2=O',\n",
" '[13*]C1CCCO1',\n",
" '[11*]S[11*]',\n",
" '[5*]N([5*])[5*]',\n",
" '[5*]NC',\n",
" '[7*]C1c2cc(S(=O)(=O)O)ccc2NC1=O',\n",
" '[7*]C1Oc2c(c(O)cc(O)c2[16*])C1=O',\n",
" '[7*]C1Nc2ccccc2C1=O',\n",
" '[14*]c1cccs1',\n",
" '[13*]C1CCC(=O)N1',\n",
" '[12*]S(=O)(=O)c1ccc([16*])cc1',\n",
" '[6*]C([6*])=O',\n",
" '[7*]C1c2c(ccc([N+](=O)[O-])c2[16*])NC1=O',\n",
" '[14*]c1cnc([14*])s1',\n",
" '[4*]CCCC',\n",
" '[14*]c1nc([14*])c(N=O)c(N)n1',\n",
" '[16*]c1ccncc1',\n",
" '[16*]c1cccc2c1C1CCCN1C2=O',\n",
" '[16*]c1cnc2n[nH]cc2c1[16*]',\n",
" '[15*]C1CCC([NH3+])CC1',\n",
" '[3*]O[3*]',\n",
" '[15*]C1CC=CCC1',\n",
" '[5*]N/C=C1\\\\C(=O)Nc2ccc3ncsc3c21',\n",
" '[14*]c1sc(C)nc1C',\n",
" '[6*]C(=O)[O-]',\n",
" '[5*]N/C=C1/c2cc([16*])ccc2NC1=O',\n",
" '[14*]c1nc2[nH]cnc2c([14*])n1',\n",
" '[16*]c1ccc(N/N=C2\\\\C(=O)Nc3ccc4ncsc4c32)cc1'])"
]
}
],
"prompt_number": 8
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"len(allfrags)"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"prompt_number": 9,
"text": [
"90"
]
}
],
"prompt_number": 9
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"len(cdk2mols)"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"prompt_number": 10,
"text": [
"47"
]
}
],
"prompt_number": 10
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"If you are interested in the final pieces from a BRICS decomposition, it is more efficient to use `BRICS.BreakBRICSBonds()`. This doesn't do as much book-keeping work as `BRICS.BRICSDecompose()`, so it's considerably faster."
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"m = Chem.Mol(cdk2mols[0].ToBinary())\n",
"m"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"png": 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"prompt_number": 11,
"text": [
"<rdkit.Chem.rdchem.Mol at 0x10800eb50>"
]
}
],
"prompt_number": 11
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"fragmented=BRICS.BreakBRICSBonds(m)\n",
"pieces=Chem.GetMolFrags(fragmented,asMols=True)\n",
"Draw.MolsToGridImage(pieces)"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"png": 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bWzw06uHhUVZWxuFwqqur39xX6O7du3v27ImMjOzSpUtgYODw4cNV9bnA4XB4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\n",
"prompt_number": 22,
"text": [
"<Image.Image image mode=RGB size=600x200 at 0x1080AD680>"
]
}
],
"prompt_number": 22
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"from rdkit.Chem.Draw import MolDrawing\n",
"reload(MolDrawing)"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"prompt_number": 21,
"text": [
"<module 'rdkit.Chem.Draw.MolDrawing' from '/Users/landrgr1/RDKit_trunk/rdkit/Chem/Draw/MolDrawing.py'>"
]
}
],
"prompt_number": 21
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Using BRICS to build molecules\n",
"-----"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"import random\n",
"random.seed(127)\n",
"\n",
"fragms = [Chem.MolFromSmiles(x) for x in allfrags]\n",
"ms = BRICS.BRICSBuild(fragms)"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 35
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"ms"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"prompt_number": 36,
"text": [
"<generator object BRICSBuild at 0x34b5460>"
]
}
],
"prompt_number": 36
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"ms.next()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"png": 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"prompt_number": 37,
"text": [
"<rdkit.Chem.rdchem.Mol at 0x2f8daa0>"
]
}
],
"prompt_number": 37
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"ms.next()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"png": 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"prompt_number": 38,
"text": [
"<rdkit.Chem.rdchem.Mol at 0x2f8d320>"
]
}
],
"prompt_number": 38
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"ms.next()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"png": 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"prompt_number": 39,
"text": [
"<rdkit.Chem.rdchem.Mol at 0x2f8dcf8>"
]
}
],
"prompt_number": 39
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"ms.next()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"png": 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Qq9Xi/PnzWsckJiYKS0tLkZmZqWAyosfHa4RUJ+zZswcxMTFYs2YN7OzsZMeplpubG0aN\nGoXRo0drPauvTZs2CAoKwtixY7Xuy5OtrKwM48aNw5gxY9CqVatqx/xx5uLYsWPh6uqqcEKix8Mi\nJKOXnZ2NQYMGISwsDC+99JLsODWaNm0a8vLysHz5cq1joqKicPnyZaxYsULBZI9u6dKlKCgoQGRk\npNYxsbGxKCoqwpQpUxRMRlQ7LEIyakIIBAYGwt3dvcYfzIaiUaNGmDZtGqZMmaL1rD47O7v7Ywzh\nzjh/lZeXh6lTp2L69OmwsbGpdkxubi6ioqLw4Ycf1tkzF6luYRGSUdNoNEhOTsb69eu1rlw0NCNG\njEDLli0xc+ZMrWOCgoLg6OhY4xgZoqKi4Obmhv/+V/vtxiIjI+Hu7o6hQ4cqmIzoCci+SEmGxZgW\nyxw/flyo1WqxefNm2VEe28GDB4WFhYX4+eeftY5JSkoS9evXF+fOnVMwmXYnT54UKpVKHDp0SOuY\n1NRUoVKpxJEjRxRMRvRkuH2CqjCW7RM3btxA586d0bNnTyxbtkx2nFoZMGAACgoKsGfPHq1jHmWL\nglJeeeUVODg41Li14+WXX4aTkxO+/PJLBZMRPRm+NUpGKTg4GBYWFtBoNLKj1Nr8+fNx+PBhJCQk\naB0THR2NvXv3IjExUcFkD9q+fTuOHTtW451v4uPjkZKSUuMddIgMEYuQjM7atWuxYcMGbNq0CVZW\nxnuauLOzM8aPH4+xY8eipKSk2jGurq4YN24cQkJCUFoq52DYkpIShISEYMKECWjRokW1Y+7evYuJ\nEydi0qRJJnfmIhk/FiEZlYyMDAQFBWHOnDlo37697DhPbPLkySgtLcWiRYu0jgkPD0dxcTFiY2MV\nTPanBQsWoKysDJMmTdI6JiYmBgC0nrlIZNBkX6Qkw2LIi2VKSkrEv/71L/Haa6+JiooK2XF0Zs2a\nNcLGxkZcu3ZN65iVK1cKOzs78dtvvymYTIirV68KGxsbsX79eq1jsrKyhLW1tYiLi1MwGZHucLEM\nVZGamoo333wTjo6OCAgIwMCBA+Ho6Cg7FoDKmdHatWuRmppqsHePqQ0hBLp37442bdpoXfgjhMAL\nL7yAf/7zn4rODIcNG4bz589j//79WscMHToUly5dMtqDhYk4I6QHHDx4UAQHBwtnZ2dRv3594ePj\nIz7//HORm5srLdOePXuM4h6ctXX8+HGhUqlESkqK1jFHjhwRKpVKpKamKpLp2LFjQqVSiR9//FHr\nmKNHjyqaiUgfOCOkGp0+fRpxcXFISEjATz/9hE6dOqF///4YNGgQ3NzcFMmQk5OD559/HsOHDze4\nDea6FBgYiPT0dBw8eBBmZmbVjhk8eDCysrKwb98+vWYRQsDLywtt27bVeju4iooKeHp6okuXLliy\nZIle8xDpleQiJiOSmZkpNBqN8PLyEmZmZqJt27bigw8+0OuG74qKCvHqq6+Kbt26idLSUr29jiHI\nzs4WjRo1Ehs2bNA65sqVK8La2lrvNxFYu3atsLW1FTk5OVrHrFq1SjRu3Fhcv35dr1mI9I1FSLXy\n66+/VluKp0+f1unraDQaYW9vLy5duqTTz2uoZs2aJVq0aCFu3rypdcyMGTNEy5YtxZ07d/SS4ebN\nm8LJyUnMnTtX65iioiLRrFkzERMTo5cMREpiEdITu3TpktBoNMLb21uoVCrh6uoq3n//fXHgwIEn\n+rw//vijUKvVJrUasaSkRLi7u4tp06ZpHXPr1i3h4uIitm3bppcMmzZtEq6urjUWbXh4uGjXrl2d\nn6WTaeA1QtKp3Nxc7Nq1C3Fxcdi9ezecnJzg5+eHgIAAeHl5ab329Xd/3EKtR48eNR5ZVBdt27YN\n77zzDs6ePYtnnnmm2jGFhYVo3Lix3jLU9PkzMjLQvn177Ny5E97e3nrLQKQUFiHpTX5+PhISEhAX\nF4dvvvkGjo6OeP311xEQEIBu3brB3Fz7/RyGDx+Ow4cPIyUlBQ0bNlQwtWHo27cv7O3tsW7dOtlR\nHuDv74+SkpIabw1HZExYhKSIgoIC7NixAwkJCdi1axesrKzQt29fBAQEoG/fvrCwsLg/dt26dRg+\nfDiSk5PrxN1jauPMmTPo2LEjkpKSDOqw4T179sDX1xenTp1SbNUwkb6xCElxt2/fRlJSEuLi4rB1\n61ao1Wr4+PggICAAHh4e8PT0RFRUFIKDg2VHlWrMmDE4dOgQfvjhhxpnz0opKytDx44d0bdvX0RH\nR8uOQ6QzLEKSqrCwEDt27EB8fDx2796N5s2bw93dHYmJiQbxw1+mgoICtG7dGnPmzKnxIFylfPrp\np5g+fTrS09O1nk5PZIxYhGQwbt68iQsXLsDDwwNqtVp2HIOwaNEizJgxA+np6bC1tZWWIy8vD61b\nt8bs2bMxYsQIaTmI9IFFSGTASktL0aFDB2RnZ1e5jqq0srIyeHp6IiEhASqVSloOIn3gVzSRAdu3\nbx9++eUXLF68GM2bN5eapU+fPqhXr57UDET6wBkhkYEqLS3F888/D19fX8yZM0d2HKI6y7RXIxAZ\nsCVLlqCwsBARERGyoxDVaZwREhmg3NxctG7dGtHR0QaxYpSoLmMREhmg0aNHIyUlBUeOHDH5bSRE\n+sbFMkQG5uTJk1i6dCm+//57liCRAjgjJDIwr7zyChwdHbF27VrZUYhMAmeERAZk27ZtOHbsGNLS\n0mRHITIZfN+FyEDcvXsX48ePR2hoKJycnGTHITIZLEIiA6HRaFBRUYGJEyfKjkJkUniNkMgAXL16\nFR4eHli+fDkGDhwoOw6RSWEREhmAwMBA/PLLL/juu+9kRyEyOVwsQyRZcnIy1qxZg5SUFNlRiEwS\nZ4REEgkAAcOHw6a8HCtWrJAdh8gksQiJJNpTUIC5Fy9irYsLHOztZcchMklcNUokyZ2KCnx8+TKG\nNG/OEiSSiEVIJMnq7GxY1quHtxwcZEchMmksQiIJrt27h9U5ORjbogUszMxkxyEyaSxCIgk+ycpC\nZ2trdLe1lR2FyOSxCIkU9uPNm9hXUIAQZ2fZUYgILEIiRVUAmH/5Mt5o2hQtLS1lxyEisAiJFJWQ\nl4fse/cQ9PTTsqMQ0e9YhEQKuVlejkVZWfhf8+ZoVK+e7DhE9DveYo1IB8ZnZmJ/YWGVjzlYWGBX\nhw73H6/IzoadSoU3mzZVOB0R1YRFSKQj3W1tq7zlqTL/8w2XSyUlWJeTgwXu7qjH7RJEBoVFSKQj\njVQqtLayqva5T65cwQuNGsHTxkbhVET0MCxCIj3LvHMHh4qKsKldO9lRiKgaLEIiHUnIy0NCXt79\nx6OdnPB/jo5IzM9HgIMDWqjVEtMRkTYsQiId+fs1wib16wMAOlpbo0PDhrJiEdFDsAiJdETbNcIX\neRs1IoPGfYRERGTSWIRERGTSWIRERGTSzIQQQnYIIiIiWTgjJCIik8YiJCIik8YiJCIik8YiJCIi\nk8YiJCIik8YiJCIik8YiJCIik8YiJCIik8YiJCIik8YiJCIik8YiJCIik8YiJCIik/b/YDFZJYuM\nGOIAAAAASUVORK5CYII=\n",
"prompt_number": 40,
"text": [
"<rdkit.Chem.rdchem.Mol at 0x2f8df50>"
]
}
],
"prompt_number": 40
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"prods = [ms.next() for x in range(100)]"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 41
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"prods = [(x.GetNumAtoms(),x) for x in prods]"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 42
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"prods.sort(reverse=True)"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 43
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"prods[0][1]"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"png": 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AgQNp0KCBqVsRZZxcNSpK7N69ezRs2JCpU6cy6v69BmiWW8vPz2fLli1G6SM5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\n",
"prompt_number": 44,
"text": [
"<rdkit.Chem.rdchem.Mol at 0x34cd938>"
]
}
],
"prompt_number": 44
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"prods[1][1]"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"png": 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yysqA4cOByEigY0fu9cCBQNu2wIABtX60srIS+fn5yMvLw5MnT5Cfn4/8/Hwk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\nvPb/UdrrFW+94MMAAAAASUVORK5CYII=\n",
"prompt_number": 45,
"text": [
"<rdkit.Chem.rdchem.Mol at 0x34cd668>"
]
}
],
"prompt_number": 45
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"prods[10][1]"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAYAAABNcIgQAAAdR0lEQVR4nO3deVhU9f4H8Deyiiio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\nR9GiRQs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Ej2MQEpFadOzYEXFxcTh8+DDOnj0LR0dHrFixAjU1NaiursakSZOwbNky7N69\nGxMmTJC6XaJavHyCiNSuqqoKy5cvx7x58+Dm5gZTU1OcO3cOu3btQp8+faRuj0gFg5CINCY3Nxeh\noaEwMjLC7Nmz0aVLF6lbInoMg5CIiHQazxESEZFOYxASEZFOYxASEZFOYxASEZFOYxASEZFOYxAS\nEZFOYxASEZFOYxASEZFOYxASEZFOYxASEZFOYxASEZFOYxASEZFOYxASEZFOYxASEZFOYxASEZFO\nYxASEZFO+38xYwGPv4WbQQAAAABJRU5ErkJggg==\n",
"prompt_number": 46,
"text": [
"<rdkit.Chem.rdchem.Mol at 0x34c8c08>"
]
}
],
"prompt_number": 46
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"RECAP\n",
"====\n",
"\n",
"Here the implementation behaves somewhat differently: it returns a hierarchy of fragments."
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"m=cdk2mols[35]\n",
"m"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"png": 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eeAP9+vXTy9hEhsAgpHazsrJCYGCgqctoxtQdoUajAQCTBqFardYJZ33/TOq6wyNHjuDz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\nRU5ErkJggg==\n",
"prompt_number": 23,
"text": [
"<rdkit.Chem.rdchem.Mol at 0x287e280>"
]
}
],
"prompt_number": 23
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pieces = Recap.RecapDecompose(m)\n",
"pieces"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"prompt_number": 24,
"text": [
"<rdkit.Chem.Recap.RecapHierarchyNode at 0x2f6d8d0>"
]
}
],
"prompt_number": 24
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pieces.children"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"prompt_number": 25,
"text": [
"{'[*]C(C)C': <rdkit.Chem.Recap.RecapHierarchyNode at 0x2f784d0>,\n",
" '[*]C(CO)C(C)C': <rdkit.Chem.Recap.RecapHierarchyNode at 0x2f78450>,\n",
" '[*]c1ccc(C(=O)[O-])c(Cl)c1': <rdkit.Chem.Recap.RecapHierarchyNode at 0x2f78410>,\n",
" '[*]c1nc(NC(CO)C(C)C)nc2c1ncn2C(C)C': <rdkit.Chem.Recap.RecapHierarchyNode at 0x2f78490>,\n",
" '[*]c1nc2c(ncn2C(C)C)c(Nc2ccc(C(=O)[O-])c(Cl)c2)n1': <rdkit.Chem.Recap.RecapHierarchyNode at 0x2f78390>,\n",
" '[*]n1cnc2c1nc(NC(CO)C(C)C)nc2Nc1ccc(C(=O)[O-])c(Cl)c1': <rdkit.Chem.Recap.RecapHierarchyNode at 0x2f78510>}"
]
}
],
"prompt_number": 25
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"Chem.MolFromSmiles('[*]c1nc2c(ncn2C(C)C)c(Nc2ccc(C(=O)[O-])c(Cl)c2)n1')"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"png": 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jKT4+ni5evKjT/Dt27CBzc3P68ssvdfq8hlBTU0M2NjY6vWODoXz33Xfk6uqq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\nxhhjJu3/A11nbl3i8AIoAAAAAElFTkSuQmCC\n",
"prompt_number": 26,
"text": [
"<rdkit.Chem.rdchem.Mol at 0x2f8e4b0>"
]
}
],
"prompt_number": 26
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pieces.children['[*]c1nc2c(ncn2C(C)C)c(Nc2ccc(C(=O)[O-])c(Cl)c2)n1'].children"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"prompt_number": 27,
"text": [
"{'[*]C(C)C': <rdkit.Chem.Recap.RecapHierarchyNode at 0x2f784d0>,\n",
" '[*]c1ccc(C(=O)[O-])c(Cl)c1': <rdkit.Chem.Recap.RecapHierarchyNode at 0x2f78410>,\n",
" '[*]c1nc2c(ncn2C(C)C)c([*])n1': <rdkit.Chem.Recap.RecapHierarchyNode at 0x2f78590>,\n",
" '[*]c1nc2c(ncn2[*])c(Nc2ccc(C(=O)[O-])c(Cl)c2)n1': <rdkit.Chem.Recap.RecapHierarchyNode at 0x2f786d0>}"
]
}
],
"prompt_number": 27
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Nodes also have parents.\n",
"Notice that the hierarchy is a network, not a tree -- each node can have multiple children and multiple parents"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pieces.children['[*]C(C)C'].parents"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"prompt_number": 28,
"text": [
"{'CC(C)C(CO)Nc1nc2c(ncn2C(C)C)c(Nc2ccc(C(=O)[O-])c(Cl)c2)n1': <rdkit.Chem.Recap.RecapHierarchyNode at 0x34b2cb0>,\n",
" '[*]c1nc(NC(CO)C(C)C)nc2c1ncn2C(C)C': <rdkit.Chem.Recap.RecapHierarchyNode at 0x34b2af8>,\n",
" '[*]c1nc2c(ncn2C(C)C)c(Nc2ccc(C(=O)[O-])c(Cl)c2)n1': <rdkit.Chem.Recap.RecapHierarchyNode at 0x34b2e10>,\n",
" '[*]c1nc2c(ncn2C(C)C)c([*])n1': <rdkit.Chem.Recap.RecapHierarchyNode at 0x34b2d60>}"
]
}
],
"prompt_number": 28
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"We can short-cut the hierarchy traversal with the `GetLeaves()` method:"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pieces.GetLeaves()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"prompt_number": 29,
"text": [
"{'[*]C(C)C': <rdkit.Chem.Recap.RecapHierarchyNode at 0x2f784d0>,\n",
" '[*]C(CO)C(C)C': <rdkit.Chem.Recap.RecapHierarchyNode at 0x2f78450>,\n",
" '[*]c1ccc(C(=O)[O-])c(Cl)c1': <rdkit.Chem.Recap.RecapHierarchyNode at 0x2f78410>,\n",
" '[*]c1nc2c(ncn2[*])c([*])n1': <rdkit.Chem.Recap.RecapHierarchyNode at 0x2f78610>}"
]
}
],
"prompt_number": 29
},
{
"cell_type": "code",
"collapsed": false,
"input": [],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 29
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"This document is copyright (C) 2012 by Greg Landrum\n",
"\n",
"This work is licensed under the Creative Commons Attribution-ShareAlike 3.0 License.\n",
"To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/3.0/ or send a letter to Creative Commons, 543 Howard Street, 5th Floor, San Francisco, California, 94105, USA.\n",
"\n",
"\n",
"The intent of this license is similar to that of the RDKit itself.\n",
"In simple words: \u201cDo whatever you want with it, but please give us some credit.\u201d"
]
}
],
"metadata": {}
}
]
}
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