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iwatobipen/espsim_with_cdk2_dataset.ipynb

Created December 10, 2021 13:25
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espsim_with_cdk2_dataset.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "c78a6079",
"metadata": {},
"outputs": [],
"source": [
"from rdkit import Chem\n",
"from rdkit.Chem import AllChem\n",
"from rdkit.Chem.Draw import IPythonConsole\n",
"from rdkit.Chem import rdFMCS\n",
"import py3Dmol\n",
"import espsim\n",
"from espsim import EmbedAlignConstrainedScore"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "51a95d3f",
"metadata": {},
"outputs": [],
"source": [
"mols = [m for m in Chem.SDMolSupplier('./cdk2.sdf', removeHs=False)]"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "8fe7e599",
"metadata": {},
"outputs": [],
"source": [
"def drawTwoMols(m1, m2,p=None, confId1=-1, confId2=-1, viewergrid=(1,2)):\n",
" if p is None:\n",
" p = py3Dmol.view(width=800, height=400, viewergrid=viewergrid)\n",
" p.removeAllModels(viewer=(0,0))\n",
" p.removeAllModels(viewer=(0,1)) \n",
" mb1=Chem.MolToMolBlock(m1, confId=confId1)\n",
" p.addModel(mb1, 'sdf', viewer=(0,0))\n",
" mb2=Chem.MolToMolBlock(m2, confId=confId2)\n",
" p.addModel(mb2, 'sdf', viewer=(0,1))\n",
" p.setStyle({'stick':{'radius':0.15}}, viewer=(0,0))\n",
" p.setStyle({'stick':{'radius':0.15}}, viewer=(0,1))\n",
" p.zoomTo(viewer=(0,0))\n",
" p.zoomTo(viewer=(0,1)) \n",
" return p"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "9c6bd27c",
"metadata": {},
"outputs": [],
"source": [
"p = drawTwoMols(mols[0], mols[1])"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "157da9cb",
"metadata": {},
"outputs": [
{
"data": {
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" <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
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"\tviewergrid_16391426587325096[0][1].addModel(\"ZINC03814459\\n RDKit 3D\\n\\n 30 32 0 0 1 0 0 0 0 0999 V2000\\n 3.2069 2.4332 0.1683 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.9680 1.3361 0.0191 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.0936 0.2661 -0.0051 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.8080 0.8502 0.1384 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.8933 2.2332 0.2504 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.7321 -0.0685 0.1386 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.0086 -1.3940 0.0148 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.2734 -1.7772 -0.1068 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.3866 -1.0536 -0.1367 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.4572 -3.1158 -0.2204 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.5735 0.3558 0.2686 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.5971 -0.6310 0.2422 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.9575 0.0650 0.3723 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.1165 -0.8888 0.6548 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.3322 -0.1496 0.1130 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.7364 0.9594 -0.7584 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.3578 0.6367 -0.8635 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.6300 3.4278 0.2204 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.9699 1.3070 -0.0571 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.3600 -3.4373 -0.5285 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6460 -3.6786 -0.4180 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.4556 -1.3123 1.0829 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.5595 -1.2189 -0.6765 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.9193 0.8386 1.1419 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.2043 -1.1389 1.7124 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.9777 -1.8177 0.0998 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.9676 -0.8188 -0.4679 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.9361 0.2761 0.9151 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.2028 1.0183 -1.7422 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.8426 1.9307 -0.2727 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 5 2 0\\n 1 2 1 0\\n 1 18 1 0\\n 2 3 1 0\\n 2 19 1 0\\n 3 9 1 0\\n 3 4 2 0\\n 4 5 1 0\\n 4 6 1 0\\n 6 7 2 0\\n 6 11 1 0\\n 7 8 1 0\\n 8 9 2 0\\n 8 10 1 0\\n 10 20 1 0\\n 10 21 1 0\\n 11 12 1 0\\n 12 13 1 0\\n 12 22 1 0\\n 12 23 1 0\\n 13 17 1 0\\n 13 14 1 0\\n 13 24 1 0\\n 14 15 1 0\\n 14 25 1 0\\n 14 26 1 0\\n 15 16 1 0\\n 15 27 1 0\\n 15 28 1 0\\n 16 17 1 0\\n 16 29 1 0\\n 16 30 1 0\\nM END\\n\",\"sdf\");\n",
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]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"p.show()"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "68c108f9",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'[#6]-&!@[#6](-&!@[#8]-&!@[#6]1:&@[#7]:&@[#6](:&@[#7]:&@[#6]2:&@[#6]:&@1:&@[#7]:&@[#6](:&@[#7]:&@2-&!@[#1])-&!@[#1])-&!@[#7](-&!@[#1])-&!@[#1])(-&!@[#1])-&!@[#1]'"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mcs = rdFMCS.FindMCS(mols[:2],completeRingsOnly=True, atomCompare=rdFMCS.AtomCompare.CompareElements)\n",
"mcs.smartsString"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "b29a60a5",
"metadata": {},
"outputs": [],
"source": [
"def getMCSmol(mol,mcs):\n",
" mcsp = Chem.MolFromSmarts(mcs.smartsString)\n",
" match = mol.GetSubstructMatch(mcsp)\n",
" match_smi = Chem.MolFragmentToSmiles(mol,atomsToUse=match,canonical=True)\n",
" return Chem.MolFromSmiles(match_smi)"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "1160af8a",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"RDKit WARNING: [22:24:18] Molecule does not have explicit Hs. Consider calling AddHs()\n",
"[22:24:18] Molecule does not have explicit Hs. Consider calling AddHs()\n"
]
}
],
"source": [
"mcsmol = getMCSmol(mols[0], mcs)\n",
"AllChem.AddHs(mcsmol)\n",
"AllChem.EmbedMolecule(mcsmol, AllChem.ETKDGv2())\n",
"core = AllChem.DeleteSubstructs(AllChem.ReplaceSidechains(mols[0],mcsmol),Chem.MolFromSmiles('*'))"
]
},
{
"cell_type": "code",
"execution_count": 9,
"id": "b93cea04",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[0.809231468849477] [0.39958657762640165]\n"
]
}
],
"source": [
"shapesim, espsim = EmbedAlignConstrainedScore(mols[0], [mols[1]], core\n",
" , prbNumConfs=mols[0].GetNumConformers()\n",
" , refNumConfs=mols[1].GetNumConformers())\n",
"print(shapesim, espsim)"
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "b5544ad0",
"metadata": {},
"outputs": [
{
"data": {
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"output_type": "display_data"
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{
"data": {
"text/plain": [
"<py3Dmol.view at 0x7f84c09c79d0>"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
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],
"source": [
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}
],
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