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": [
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       "\tviewergrid_16391426587325096[0][0].setStyle({\"stick\": {\"radius\": 0.15}});\n",
       "\tviewergrid_16391426587325096[0][1].setStyle({\"stick\": {\"radius\": 0.15}});\n",
       "\tviewergrid_16391426587325096[0][0].zoomTo();\n",
       "\tviewergrid_16391426587325096[0][1].zoomTo();\n",
       "viewergrid_16391426587325096[0][1].render();\n",
       "viewergrid_16391426587325096[0][0].render();\n",
       "});\n",
       "</script>"
      ]
     },
     "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": [
    {
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       "        <p id=\"3dmolwarning_16391426588176754\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the 3dmol extension: <br>\n",
       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
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      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "<py3Dmol.view at 0x7f84c09c79d0>"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "drawTwoMols(mols[0], mols[1])"
   ]
  }
 ],
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