openeye_bug.ipynb

openeye_bug.ipynb

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     "name": "stdout",
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     "text": [
      "makecircular uses fp type: tb.GetFPType()=104\n",
      "makecircular uses fp type: tb.GetFPType()=104\n",
      "0.6721311211585999\n",
      "makefp uses fp type: tb.GetFPType()=104\n",
      "makefp uses fp type: tb.GetFPType()=104\n",
      "0.641791045665741\n"
     ]
    },
    {
     "ename": "AssertionError",
     "evalue": "",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mAssertionError\u001b[0m                            Traceback (most recent call last)",
      "Input \u001b[0;32mIn [1]\u001b[0m, in \u001b[0;36m<cell line: 65>\u001b[0;34m()\u001b[0m\n\u001b[1;32m     62\u001b[0m makefp_similarity \u001b[38;5;241m=\u001b[39m OETanimoto(fpa, fpb)\n\u001b[1;32m     63\u001b[0m \u001b[38;5;28mprint\u001b[39m(makefp_similarity)\n\u001b[0;32m---> 65\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m makefp_similarity \u001b[38;5;241m==\u001b[39m makecircular_similarity\n",
      "\u001b[0;31mAssertionError\u001b[0m: "
     ]
    }
   ],
   "source": [
    "import os\n",
    "import random\n",
    "os.environ[\"OE_LICENSE\"] = \"/home/ec2-user/oe_license.txt\"\n",
    "\n",
    "from openeye.oechem import (\n",
    "    OEGraphMol,\n",
    "    OESmilesToMol,\n",
    ")\n",
    "from openeye.oegraphsim import (\n",
    "    OEMakeCircularFP,\n",
    "    OEFPBondType_DefaultCircularBond,\n",
    "    OEFPAtomType_DefaultCircularAtom,\n",
    "    OEMakeFP,\n",
    "    OEFingerPrint,\n",
    "    OEFingerPrintType,\n",
    "    OETanimoto,\n",
    "    OEFPTypeParams\n",
    ")\n",
    "\n",
    "\n",
    "def makecircular(mol):\n",
    "    fp = OEFingerPrint()\n",
    "    numbits = 512\n",
    "    minradius = 0\n",
    "    maxradius = 5\n",
    "    atype = OEFPAtomType_DefaultCircularAtom\n",
    "    btype = OEFPBondType_DefaultCircularBond\n",
    "    \n",
    "    OEMakeCircularFP(\n",
    "        fp, mol, \n",
    "        numbits, minradius, maxradius, atype, btype\n",
    "    )\n",
    "    tb = fp.GetFPTypeBase()\n",
    "    \n",
    "    print(f\"makecircular uses fp type: tb.GetFPType()={tb.GetFPType()}\")\n",
    "    return fp\n",
    "\n",
    "def makefp(mol):\n",
    "    fp = OEFingerPrint()\n",
    "    fptype = OEFPTypeParams('Circular,ver=2.0.0,size=512,radius=0-5,atype=AtmNum|Arom|Chiral|FCharge|HCount|EqHalo,btype=Order')\n",
    "    OEMakeFP(fp, mol, fptype.GetFPType())\n",
    "    tb = fp.GetFPTypeBase()\n",
    "    print(f\"makefp uses fp type: tb.GetFPType()={tb.GetFPType()}\")\n",
    "    return fp\n",
    "\n",
    "\n",
    "def makemol(smiles):\n",
    "    mol = OEGraphMol()\n",
    "    OESmilesToMol(mol, smiles)\n",
    "    return mol\n",
    "\n",
    "\n",
    "fpa = makecircular(makemol('CCOCCCCc1ccc(C)cc1CNC'))\n",
    "fpb = makecircular(makemol('CCOCCCc1ccc(C)cc1CNC'))\n",
    "\n",
    "makecircular_similarity = OETanimoto(fpa, fpb)\n",
    "print(makecircular_similarity)\n",
    "\n",
    "fpa = makefp(makemol('CCOCCCCc1ccc(C)cc1CNC'))\n",
    "fpb = makefp(makemol('CCOCCCc1ccc(C)cc1CNC'))\n",
    "\n",
    "makefp_similarity = OETanimoto(fpa, fpb)\n",
    "print(makefp_similarity)\n",
    "\n",
    "assert makefp_similarity == makecircular_similarity"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "e4f0d30d-ec0f-4443-aa09-fbac0ca91ddf",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2021.2.0\n"
     ]
    }
   ],
   "source": [
    "import openeye\n",
    "print(openeye.__version__)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "db832aef-40fc-4590-9b52-9dffac90e5ac",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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