mnowotka/ws.ipnb

## ws.ipnb
{
 "metadata": {
  "name": "",
  "signature": "sha256:f784ff75e0dec53c6fef16fc487214e1f81833324cfa31e787b2ed105592c612"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "from chembl_webresource_client import *\n",
      "\n",
      "from lxml import etree\n",
      "import requests\n",
      "from IPython.display import Image\n",
      "from rdkit import Chem"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 1
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "compounds = CompoundResource()\n",
      "\n",
      "compounds.status()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 2,
       "text": [
        "True"
       ]
      }
     ],
     "prompt_number": 2
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "## Retrieve record(s) _via_ identifiers"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# ChEMBL ID (single hit)...\n",
      "\n",
      "c0 = compounds.get(\"CHEMBL554\") # lapatinib\n",
      "\n",
      "c0"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 3,
       "text": [
        "{u'acdBasicPka': 6.34,\n",
        " u'acdLogd': 6.26,\n",
        " u'acdLogp': 6.3,\n",
        " u'alogp': 6.04,\n",
        " u'chemblId': u'CHEMBL554',\n",
        " u'knownDrug': u'Yes',\n",
        " u'medChemFriendly': u'Yes',\n",
        " u'molecularFormula': u'C29H26ClFN4O4S',\n",
        " u'molecularWeight': 581.06,\n",
        " u'numRo5Violations': 2,\n",
        " u'passesRuleOfThree': u'No',\n",
        " u'preferredCompoundName': u'LAPATINIB',\n",
        " u'rotatableBonds': 11,\n",
        " u'smiles': u'CS(=O)(=O)CCNCc1oc(cc1)c2ccc3ncnc(Nc4ccc(OCc5cccc(F)c5)c(Cl)c4)c3c2',\n",
        " u'species': u'NEUTRAL',\n",
        " u'stdInChiKey': u'BCFGMOOMADDAQU-UHFFFAOYSA-N',\n",
        " u'synonyms': u'Lapatinib,SID103905568,Tykerb,SID103905567,SID50100107'}"
       ]
      }
     ],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# Structure...\n",
      "\n",
      "Chem.MolFromSmiles(c0[\"smiles\"])"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "png": 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lN3e6Inw6uRxgrO52Q/vefRewtlYswN62LXD8OHD2rDVWr179SAgCgI2NDY4f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\n",
       "prompt_number": 4,
       "text": [
        "<rdkit.Chem.rdchem.Mol at 0x10a632440>"
       ]
      }
     ],
     "prompt_number": 4
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# As XML...\n",
      "\n",
      "x = compounds.get(\"CHEMBL554\", frmt=\"xml\")\n",
      "r = etree.fromstring(x).getroottree()\n",
      "print(etree.tostring(r, pretty_print=True))\n",
      "print(r.xpath(\"/compound/smiles/text()\")[0])"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "<compound>\n",
        "  <smiles>CS(=O)(=O)CCNCc1oc(cc1)c2ccc3ncnc(Nc4ccc(OCc5cccc(F)c5)c(Cl)c4)c3c2</smiles>\n",
        "  <chemblId>CHEMBL554</chemblId>\n",
        "  <passesRuleOfThree>No</passesRuleOfThree>\n",
        "  <molecularWeight>581.06</molecularWeight>\n",
        "  <molecularFormula>C29H26ClFN4O4S</molecularFormula>\n",
        "  <acdLogp>6.30</acdLogp>\n",
        "  <knownDrug>Yes</knownDrug>\n",
        "  <stdInChiKey>BCFGMOOMADDAQU-UHFFFAOYSA-N</stdInChiKey>\n",
        "  <acdLogd>6.26</acdLogd>\n",
        "  <synonyms>Lapatinib,SID103905568,Tykerb,SID103905567,SID50100107</synonyms>\n",
        "  <medChemFriendly>Yes</medChemFriendly>\n",
        "  <rotatableBonds>11</rotatableBonds>\n",
        "  <alogp>6.04</alogp>\n",
        "  <preferredCompoundName>LAPATINIB</preferredCompoundName>\n",
        "  <numRo5Violations>2</numRo5Violations>\n",
        "  <species>NEUTRAL</species>\n",
        "  <acdBasicPka>6.34</acdBasicPka>\n",
        "</compound>\n",
        "\n",
        "CS(=O)(=O)CCNCc1oc(cc1)c2ccc3ncnc(Nc4ccc(OCc5cccc(F)c5)c(Cl)c4)c3c2\n"
       ]
      }
     ],
     "prompt_number": 5
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# Via InChIKey (single hit)...\n",
      "\n",
      "c1 = compounds.get(stdinchikey='BCFGMOOMADDAQU-UHFFFAOYSA-N')\n",
      "\n",
      "c1 == c0"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 6,
       "text": [
        "True"
       ]
      }
     ],
     "prompt_number": 6
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# Via SMILES (potentially multiple hits)...\n",
      "\n",
      "smiles = c0[\"smiles\"]\n",
      "\n",
      "c = compounds.get(smiles=smiles)\n",
      "\n",
      "len(c)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 7,
       "text": [
        "2"
       ]
      }
     ],
     "prompt_number": 7
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "[(x[\"chemblId\"], x[\"smiles\"]) for x in c]\n",
      "\n",
      "# Second is unstandardised PubChem compound"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 8,
       "text": [
        "[(u'CHEMBL554',\n",
        "  u'CS(=O)(=O)CCNCc1oc(cc1)c2ccc3ncnc(Nc4ccc(OCc5cccc(F)c5)c(Cl)c4)c3c2'),\n",
        " (u'CHEMBL1475148',\n",
        "  u'C[S+](=O)([O-])CCNCc1oc(cc1)c2ccc3ncnc(Nc4ccc(OCc5cccc(F)c5)c(Cl)c4)c3c2')]"
       ]
      }
     ],
     "prompt_number": 8
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "## Substructure-search (SMILES query)"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "query = \"c4ccc(Nc2ncnc3ccc(c1ccco1)cc23)cc4\"\n",
      "\n",
      "Chem.MolFromSmiles(query)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "png": 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ylpz84MednRkrLGTM3//Bj9+7p+hfX89dRmX27NnDjI2N2YEDB/gNosK9e/fY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\n6LT/AzHYpi0rc7USAAAAAElFTkSuQmCC\n",
       "prompt_number": 9,
       "text": [
        "<rdkit.Chem.rdchem.Mol at 0x10ae84d00>"
       ]
      }
     ],
     "prompt_number": 9
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "c = compounds.substructure(\"c4ccc(Nc2ncnc3ccc(c1ccco1)cc23)cc4\")\n",
      "\n",
      "len(c)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 10,
       "text": [
        "69"
       ]
      }
     ],
     "prompt_number": 10
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# Check Lapatinib is found...\n",
      "\n",
      "[x[\"smiles\"] for x in c if x[\"chemblId\"] == 'CHEMBL554'][0]"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 11,
       "text": [
        "u'CS(=O)(=O)CCNCc1oc(cc1)c2ccc3ncnc(Nc4ccc(OCc5cccc(F)c5)c(Cl)c4)c3c2'"
       ]
      }
     ],
     "prompt_number": 11
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "## Similarity search (SMILES query)"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "smiles = \"CS(=O)(=O)CCNCc1oc(cc1)c2ccc3ncnc(Nc4ccc(OCc5cccc(F)c5)c(Cl)c4)c3c2\""
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 12
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "c = compounds.similar_to(smiles, 0.90)\n",
      "\n",
      "c\n",
      "\n",
      "# XXX We should get some hits (see below)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 13,
       "text": [
        "404"
       ]
      }
     ],
     "prompt_number": 13
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# Try via 'raw' web service instead...\n",
      "\n",
      "r = requests.get(\"https://www.ebi.ac.uk/chemblws/compounds/similarity/{}/{}.json\".format(smiles, 90)).json()\n",
      "\n",
      "len(r['compounds'])"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 14,
       "text": [
        "21"
       ]
      }
     ],
     "prompt_number": 14
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "## Batch queries"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# Multiple ChEMBL IDs...\n",
      "\n",
      "c = compounds.get(['CHEMBL{}'.format(x) for x in range(1, 301)])\n",
      "\n",
      "len(c)\n",
      "\n",
      "# XXX The warnings aren't terribly helpful here"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:04 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:04 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:04 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:04 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:04 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:04 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:04 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:04 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:04 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:04 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:04 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:04 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:04 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:04 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:04 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:04 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:04 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:04 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:04 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:04 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:05 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:05 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:05 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:05 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:05 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:05 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:06 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:06 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:06 WARNING ] HttpConnectionPool is full, discarding connection: www.ebi.ac.uk\n"
       ]
      },
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 15,
       "text": [
        "300"
       ]
      }
     ],
     "prompt_number": 15
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# Remove 'misses' (i.e. where 404 is returned)...\n",
      "\n",
      "c = [x for x in c if not isinstance(x, int)]\n",
      "\n",
      "len(c)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 16,
       "text": [
        "170"
       ]
      }
     ],
     "prompt_number": 16
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "## Get salts for parent"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "cpds = compounds.forms(\"CHEMBL554\")\n",
      "\n",
      "cpds"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 17,
       "text": [
        "[{u'chemblId': u'CHEMBL554', u'parent': True},\n",
        " {u'chemblId': u'CHEMBL1201183', u'parent': False},\n",
        " {u'chemblId': u'CHEMBL1201179', u'parent': False},\n",
        " {u'chemblId': u'CHEMBL1076241', u'parent': False}]"
       ]
      }
     ],
     "prompt_number": 17
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "for cpd in [x for x in cpds if not x[\"parent\"]]:\n",
      "    \n",
      "    data = compounds.get(cpd[\"chemblId\"])\n",
      "    \n",
      "    if data == 404:\n",
      "        \n",
      "        logging.warn(\"{} downgraded?\".format(cpd[\"chemblId\"]))\n",
      "        \n",
      "        continue\n",
      "        \n",
      "    print(\"{} {}\".format(cpd[\"chemblId\"], data[\"smiles\"]))\n",
      "    \n",
      "# XXX Why is CHEMBL1201183 showing up?"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "[2014/May/12 14:40:06 WARNING ] CHEMBL1201183 downgraded?\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "CHEMBL1201179 O.Cc1ccc(cc1)S(=O)(=O)O.Cc2ccc(cc2)S(=O)(=O)O.CS(=O)(=O)CCNCc3oc(cc3)c4ccc5ncnc(Nc6ccc(OCc7cccc(F)c7)c(Cl)c6)c5c4\n",
        "CHEMBL1076241 Cc1ccc(cc1)S(=O)(=O)O.CS(=O)(=O)CCNCc2oc(cc2)c3ccc4ncnc(Nc5ccc(OCc6cccc(F)c6)c(Cl)c5)c4c3"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n"
       ]
      }
     ],
     "prompt_number": 18
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "## Drug mechanism of action"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "compounds.drug_mechnisms('CHEMBL1201179')"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 19,
       "text": [
        "[{u'chemblId': u'CHEMBL203',\n",
        "  u'mechanismOfAction': u'Epidermal growth factor receptor erbB1 inhibitor',\n",
        "  u'name': u'Epidermal growth factor receptor erbB1'},\n",
        " {u'chemblId': u'CHEMBL1824',\n",
        "  u'mechanismOfAction': u'Receptor protein-tyrosine kinase erbB-2 inhibitor',\n",
        "  u'name': u'Receptor protein-tyrosine kinase erbB-2'}]"
       ]
      }
     ],
     "prompt_number": 19
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "## Image query"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "png = compounds.image(\"CHEMBL554\")\n",
      "\n",
      "Image(png)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "png": 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Tp0+3mJiY4P0sHCGCDsBpH3zwwX6Pk5rV/5J+6qmnLDo62n77298e8DW2bNliaWlpFh4e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\ndeumPn36BLbS27V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       "prompt_number": 20,
       "text": [
        "<IPython.core.display.Image at 0x10adf4a90>"
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   ],
   "metadata": {}
  }
 ]
}