cosmol.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "7b489aec-de5a-4d57-ad65-6e556569eb6c",
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem import AllChem\n",
    "from cosmolkit import EmbedParameters, MoleculeBatch\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "464bb0dd-3543-44dc-a932-fc509a87f1c2",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 3 μs, sys: 0 ns, total: 3 μs\n",
      "Wall time: 4.53 μs\n",
      "True\n"
     ]
    }
   ],
   "source": [
    "%time\n",
    "rdk_sdf = Chem.SDMolSupplier('cdk2.sdf')\n",
    "print(\"__getitem__\" in dir(rdk_sdf))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "68be9977-22db-407f-a637-2e9c9d631faa",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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",
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       "<table><tr><td colspan=\"2\" style=\"text-align: center;\"><image 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\"></td></tr>\n",
       "<tr><th style=\"text-align: right\">id</th><td style=\"text-align: left\">ZINC03814459</td></tr>\n",
       "<tr><th style=\"text-align: right\">Cluster</th><td style=\"text-align: left\">2</td></tr>\n",
       "<tr><th style=\"text-align: right\">MODEL.SOURCE</th><td style=\"text-align: left\">CORINA 3.44 0027  09.01.2008</td></tr>\n",
       "<tr><th style=\"text-align: right\">MODEL.CCRATIO</th><td style=\"text-align: left\">1</td></tr>\n",
       "<tr><th style=\"text-align: right\">s_st_Chirality_1</th><td style=\"text-align: left\">13_S_17_12_14_24</td></tr>\n",
       "<tr><th style=\"text-align: right\">r_mmffld_Potential_Energy-OPLS_2005</th><td style=\"text-align: left\">-67.4705</td></tr>\n",
       "<tr><th style=\"text-align: right\">r_mmffld_RMS_Derivative-OPLS_2005</th><td style=\"text-align: left\">9.48919e-05</td></tr>\n",
       "<tr><th style=\"text-align: right\">b_mmffld_Minimization_Converged-OPLS_2005</th><td style=\"text-align: left\">1</td></tr></table>"
      ],
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x77443dd1ff40>"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rdk_sdf[1]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "29ad2856-0252-4b68-a2b6-3cb1dcda6e0e",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 2 μs, sys: 0 ns, total: 2 μs\n",
      "Wall time: 3.34 μs\n"
     ]
    }
   ],
   "source": [
    "%time\n",
    "rdk_params = AllChem.ETKDGv3()\n",
    "for mol in rdk_sdf:\n",
    "    hmol = Chem.AddHs(mol)\n",
    "    AllChem.EmbedMolecule(hmol, rdk_params)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "f97fbc70-4d9a-4328-a0da-e20dfb7b4604",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 2 μs, sys: 0 ns, total: 2 μs\n",
      "Wall time: 3.34 μs\n"
     ]
    }
   ],
   "source": [
    "%time\n",
    "cosmol_sdf = MoleculeBatch.read_sdf('cdk2.sdf', sanitize=True, coordinate_dim=\"2d\")\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "9c1483b4-88a2-4e6d-b336-c237595b79ef",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'Nc1nc(OCC2CCC(=O)N2)c2nc[nH]c2n1'"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cosmol_sdf[2].to_smiles()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "782b161a-748b-4d63-af8b-607342142961",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 1e+03 ns, sys: 0 ns, total: 1e+03 ns\n",
      "Wall time: 3.1 μs\n"
     ]
    }
   ],
   "source": [
    "%time\n",
    "cos_params = EmbedParameters.etkdg_v3()\n",
    "embedded_mols = []\n",
    "for cos_mol in cosmol_sdf:\n",
    "    cos_mol.add_hydrogens_()\n",
    "    embedded = cos_mol.with_3d_conformer(cos_params)\n",
    "    embedded_mols.append(embedded)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "b74710ef-1ad8-41e3-a423-24f61ea87028",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[[ 3.59706665  1.40068263  0.78248951]\n",
      " [ 3.47140306 -0.04558058  0.37269855]\n",
      " [ 4.68308809 -0.4674032  -0.44992851]\n",
      " [ 2.23254933 -0.31278363 -0.38887202]\n",
      " [ 2.24338025 -0.75354752 -1.54779306]\n",
      " [ 0.92556748 -0.05354304  0.231482  ]\n",
      " [-0.15513888 -0.36878027 -0.64474239]\n",
      " [-1.48605446 -0.2051096  -0.27621191]\n",
      " [-2.45779706 -0.54019887 -1.19959407]\n",
      " [-3.7961813  -0.40087554 -0.89524538]\n",
      " [-4.50395837 -0.79834283 -1.97020606]\n",
      " [-3.64981423 -1.18993867 -2.95841013]\n",
      " [-2.40352882 -1.01998748 -2.4556846 ]\n",
      " [-4.10839979  0.07204562  0.33106939]\n",
      " [-3.16889262  0.40738425  1.25362671]\n",
      " [-1.86286314  0.26097808  0.9292148 ]\n",
      " [-3.58780367  0.89933761  2.52497328]\n",
      " [ 4.03926829  2.02945505 -0.02244835]\n",
      " [ 4.26752342  1.51581418  1.66311255]\n",
      " [ 2.61733124  1.79962548  1.04621236]\n",
      " [ 3.52284248 -0.66331623  1.30878053]\n",
      " [ 4.95427624  0.3137165  -1.21311808]\n",
      " [ 5.57181257 -0.61607835  0.19222686]\n",
      " [ 4.45891888 -1.38565414 -1.03359738]\n",
      " [ 0.81027035  0.99746415  0.55485708]\n",
      " [ 0.74899844 -0.65104688  1.16159941]\n",
      " [-5.55887984 -0.80288003 -2.0302632 ]\n",
      " [-3.9328534  -1.56030346 -3.94283118]\n",
      " [-3.92655704  1.89017795  2.63040437]\n",
      " [-3.54557414  0.24868882  3.33185728]]\n"
     ]
    }
   ],
   "source": [
    "print(embedded_mols[0].coordinates_3d())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "905bdd95-34bf-4da6-a2b6-5d113c003b1b",
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import DataStructs\n",
    "from rdkit.Chem import rdFingerprintGenerator\n",
    "from rdkit.Chem import Draw\n",
    "\n",
    "from cosmolkit import Fingerprint\n",
    "from cosmolkit import Molecule"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "84f2e628-365c-4cdf-bef8-064bb0bb362a",
   "metadata": {},
   "outputs": [],
   "source": [
    "fp_gen = rdFingerprintGenerator.GetMorganGenerator(radius=2, fpSize=2048)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "c8dc1ec3-2da7-47db-89a0-2ec0e1b9e9b5",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Nc1nc(OCC2CCCO2)c2nc[nH]c2n1\n",
      "Nc1nc(OCC2CCC(=O)N2)c2nc[nH]c2n1\n"
     ]
    }
   ],
   "source": [
    "smi1 = cosmol_sdf[1].to_smiles()\n",
    "smi2 = cosmol_sdf[2].to_smiles()\n",
    "print(f\"{smi1}\\n{smi2}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "09383edc-e3b1-4e65-bdb3-b57da4188338",
   "metadata": {},
   "outputs": [],
   "source": [
    "rd_mol1 = Chem.MolFromSmiles(smi1)\n",
    "rd_mol2 = Chem.MolFromSmiles(smi2)\n",
    "cos_mol1 = Molecule.from_smiles(smi1)\n",
    "cos_mol2 = Molecule.from_smiles(smi2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "9a396d4a-6f17-486b-a771-2f1e5690b64e",
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_tc_from_rdk(m1,m2):\n",
    "    fp1 = fp_gen.GetFingerprint(m1)\n",
    "    fp2 = fp_gen.GetFingerprint(m2)\n",
    "    return DataStructs.TanimotoSimilarity(fp1, fp2)\n",
    "\n",
    "def get_tc_from_csk(m1,m2):\n",
    "    fp1 = m1.fingerprint_morgan(radius=2, n_bits=2048)\n",
    "    fp2 = m2.fingerprint_morgan(radius=2, n_bits=2048)\n",
    "    return Fingerprint.tanimoto(fp1, fp2)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "21dd2f36-c2ef-4047-8c17-116aa04d3136",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0.5660377358490566"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "get_tc_from_rdk(rd_mol1, rd_mol2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "7912b70c-71a6-4f8c-ab70-dbf35439aa0f",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0.5660377358490566"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "get_tc_from_csk(cos_mol1, cos_mol2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "7dc27ae6-f811-4478-9a07-b87808446fbc",
   "metadata": {},
   "outputs": [],
   "source": [
    "for i in range(len(rdk_sdf)):\n",
    "    for j in range(i):\n",
    "        rd_m1 = rdk_sdf[i]\n",
    "        rd_m2 = rdk_sdf[j]\n",
    "        \n",
    "        cs_m1 = cosmol_sdf[i]\n",
    "        cs_m2 = cosmol_sdf[j]\n",
    "        rdk_tc = get_tc_from_rdk(rd_m1, rd_m2)\n",
    "        csk_tc = get_tc_from_csk(cs_m1, cs_m2)\n",
    "        #print(f\"Tc_RDKit : {rdk_tc:.3} Tc_Cosmol :{csk_tc:.3}\")\n",
    "        assert rdk_tc - csk_tc == 0.\n",
    "        #print(f\"####\")\n",
    "                "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "99a93805-fccf-43a9-8150-dce4ac1c9972",
   "metadata": {},
   "outputs": [],
   "source": [
    "from IPython.display import SVG\n",
    "from cosmolkit import Molecule\n",
    "mol = Molecule.from_smiles(\"c1ccccc1O\").with_2d_coordinates()\n",
    "\n",
    "svg = mol.to_svg(width=400, height=300)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "877afad2-b7a1-4f31-b3eb-2cd71161fe67",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/svg+xml": [
       "<svg xmlns=\"http://www.w3.org/2000/svg\" xmlns:rdkit=\"http://www.rdkit.org/xml\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" version=\"1.1\" baseProfile=\"full\" xml:space=\"preserve\" width=\"400px\" height=\"300px\" viewBox=\"0 0 400 300\">\n",
       "<!-- END OF HEADER -->\n",
       "<rect style=\"opacity:1.0;fill:#FFFFFF;stroke:none\" width=\"400.0\" height=\"300.0\" x=\"0.0\" y=\"0.0\"> </rect>\n",
       "<path class=\"bond-0 atom-0 atom-1\" d=\"M 181.1,242.3 L 74.5,242.3\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-1 atom-1 atom-2\" d=\"M 74.5,242.3 L 21.2,150.0\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-1 atom-1 atom-2\" d=\"M 83.7,226.3 L 39.7,150.0\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-2 atom-2 atom-3\" d=\"M 21.2,150.0 L 74.5,57.7\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-3 atom-3 atom-4\" d=\"M 74.5,57.7 L 181.1,57.7\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-3 atom-3 atom-4\" d=\"M 83.7,73.7 L 171.8,73.7\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-4 atom-4 atom-5\" d=\"M 181.1,57.7 L 234.3,150.0\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-5 atom-5 atom-6\" d=\"M 234.3,150.0 L 279.9,150.0\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-5 atom-5 atom-6\" d=\"M 279.9,150.0 L 325.4,150.0\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-6 atom-5 atom-0\" d=\"M 234.3,150.0 L 181.1,242.3\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-6 atom-5 atom-0\" d=\"M 215.9,150.0 L 171.8,226.3\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path d=\"M 175.7,242.3 L 181.1,242.3 L 183.7,237.7\" style=\"fill:none;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:10;stroke-opacity:1;\"/>\n",
       "<path d=\"M 79.8,242.3 L 74.5,242.3 L 71.9,237.7\" style=\"fill:none;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:10;stroke-opacity:1;\"/>\n",
       "<path d=\"M 23.9,154.6 L 21.2,150.0 L 23.9,145.4\" style=\"fill:none;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:10;stroke-opacity:1;\"/>\n",
       "<path d=\"M 71.9,62.3 L 74.5,57.7 L 79.8,57.7\" style=\"fill:none;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:10;stroke-opacity:1;\"/>\n",
       "<path d=\"M 175.7,57.7 L 181.1,57.7 L 183.7,62.3\" style=\"fill:none;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:10;stroke-opacity:1;\"/>\n",
       "<text x=\"328.9\" y=\"170.0\" class=\"atom-6\" style=\"font-size:40px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\">O</text>\n",
       "<text x=\"356.5\" y=\"170.0\" class=\"atom-6\" style=\"font-size:40px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\">H</text>\n",
       "</svg>"
      ],
      "text/plain": [
       "<IPython.core.display.SVG object>"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "SVG(svg)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2e0ff2cb-192d-4bd8-a6db-11a20578ba4c",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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