{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2009/05/07/me-is-having-bioclipsexmpprdf-fun.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/cprj5-xnk74", "url": "https://chem-bla-ics.linkedchemistry.info/2009/05/07/me-is-having-bioclipsexmpprdf-fun.html", "title": "/me is having Bioclipse/XMPP/RDF fun", "content_html": "

Johannes asked me what the Lipinski Rule of Five for\nfarnesol is, in reply to the matching XMPP cloud service.\nThanx to DBPedia for providing a machine readable form of the wikipedia entry:

\n\n

Here’s the solution (yes, suboptimal, but since we were hacking on XMPP support in\nBioclipse) which shows the structure in JChemPaint and Jmol\nas bonus (gist:107507):

\n\n
// Today, Johannes challenged me to use Bioclipse and XMPP to calculate the Lipinski Rule of Five for\n// http://en.wikipedia.org/wiki/Farnesol\nquery = \"Farnesol\"\n\n// Zero: clear the console\njs.clear();\njs.print(\"Query: \" + query + \"\\n\");\n\n// One: connect to the XMPP hive, and make contact with the CDK descriptor service here in Uppsala\nxmpp.connect();\nvar service = xmpp.getService(\"descriptor.ws1.bmc.uu.se\");\nservice.discoverSync(5000);\nservice.getFunctions();\nvar func = service.getFunction(\"LipinskiRuleOfFive\");\n\n// Two: take advantage of RDF, DBPedia\nstore = rdf.createStore()\nrdf.importURL(store, \"http://dbpedia.org/data/\" + query + \".rdf\")\nrdf.importURL(store, \"http://dbpedia.org/data/\" + query + \"/section1/Chembox_Identifiers.rdf\")\n\n// Three: run the SPARQL query and extract the SMILES from the List<List<String>>, and remove\n// the '@en' suffix\nvar sparql = \"PREFIX dbprop: <http://dbpedia.org/property/> SELECT ?o WHERE { ?s dbprop:smiles ?o }\"\nsmiles = rdf.sparql(store, sparql).get(0).get(0)\nsmiles = smiles.substring(0, smiles.length()-3)\n\n// Four: create a CML document\npropane = cdk.fromSMILES(smiles);\njs.print(\"Molecule SMILES: \" + smiles + \"\\n\");\n\n// Five: call the function\nresult = func.invokeSync(propane.getCML(), 900000);\ncmlReturned = xmpp.toString(result);\n\n// Six: tune the CML so that the Bioclipse CML reader is happy\ncmlReturned = cmlReturned.replace(\"xsd:int\", \"xsd:integer\")\n\n// Seven: extract the Lipinski Rule of Five score\npropertyList = cml.fromString(cmlReturned);\nvalue = propertyList.getPropertyElements().get(0).\n  getScalarElements().get(0).getValue()\njs.print(\"Lipinski Rule of Five: \" + value + \"\\n\")\n\n// Eight: while at it, let's create a 2D and open in JChemPaint\nservice = xmpp.getService(\"cdk.ws1.bmc.uu.se\");\nservice.discoverSync(5000);\nservice.getFunctions();\nfunc = service.getFunction(\"generate2Dcoordinates\");\nmol = cdk.fromSMILES(smiles)\nresult = func.invokeSync(mol.getCML(), 900000);\ncmlReturned = xmpp.toString(result);\nmol2d = cdk.fromCml(cmlReturned);\nui.open(mol2d)\n\n// Nine: oh, and a 3D model in Jmol\nfunc = service.getFunction(\"addExplicitHydrogens\");\nresult = func.invokeSync(mol.getCML(), 900000);\nmol = cdk.fromCml(xmpp.toString(result));\nfunc = service.getFunction(\"generate3Dcoordinates\");\nresult = func.invokeSync(mol.getCML(), 900000);\nmol3d = cdk.fromCml(xmpp.toString(result));\nfile = \"/Virtual/foo.cml\";\nui.remove(file)\ncdk.saveCML(mol3d, file);\nui.open(file)\n
", "summary": "Johannes asked me what the Lipinski Rule of Five for farnesol is, in reply to the matching XMPP cloud service. Thanx to DBPedia for providing a machine readable form of the wikipedia entry:", "date_published": "2009-05-07T00:00:00+00:00", "date_modified": "2009-05-07T00:00:00+00:00", "tags": ["bioclipse","rdf","xmpp"], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }