Egon Willighagen egonw
egonw
/ chebi mashup.js
Created
February 27, 2009 20:21
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| var ons = rdf.createStore() | |
| // output: RDFStore: 0 triples | |
| rdf.importURL(ons, | |
| "http://github.com/egonw/onssolubility/raw/master/ons.solubility.rdf/ons.rdf") | |
| // output: RDFStore: 1206 triples | |
| var results = rdf.sparql(ons, "PREFIX owl: <http://www.w3.org/2002/07/owl#> " + | |
| "PREFIX ons: <http://spreadsheet.google.com/plwwufp30hfq0udnEmRD1aQ/onto#> " + | |
| "SELECT DISTINCT ?same WHERE { " + |
egonw
/ Download and visualize Structures.js
Created
March 1, 2009 18:44
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| var ons = rdf.createStore() | |
| rdf.importURL(ons, | |
| "http://github.com/egonw/onssolubility/raw/master/ons.solubility.rdf/ons.rdf") | |
| var results = rdf.sparql(ons, "PREFIX ons: <http://spreadsheet.google.com/plwwufp30hfq0udnEmRD1aQ/onto#> " + | |
| "PREFIX chemblog: <http://blueobelisk.sourceforge.net/chemistryblogs/>" + | |
| "PREFIX dc: <http://purl.org/dc/elements/1.1/> " + | |
| "SELECT DISTINCT ?title ?smiles WHERE { " + | |
| " ?solvent dc:title ?title . " + | |
| " ?solvent chemblog:smiles ?smiles ." + |
egonw
/ gist:80816
Created
March 17, 2009 23:03
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| xmpp.connect(); | |
| service = xmpp.getService("descriptor.ws1.bmc.uu.se"); | |
| service.discoverSync(5000); | |
| service.getFunctions(); | |
| f = service.getFunction("XLogP"); | |
| ios = f.getIoSchemataSync(90000); | |
| // and it fails with: | |
| iof = xmpp.getIoFactory(ios); | |
egonw
/ gist:85566
Created
March 25, 2009 16:37
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| <rdf:RDF | |
| xmlns:mw="http://metware.sf.net/onto/#" | |
| xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" | |
| xmlns:owl="http://www.w3.org/2002/07/owl#" > | |
| <rdf:Description rdf:about="urn:lsid:localhost:net.sf.metware.beans.MetidMetabolitesAddonPubchemBean:297"> | |
| <owl:sameAs rdf:resource="urn:lsid:localhost:net.sf.metware.beans.MetidMetabolitesBean:16"/> | |
| <mw:PubChemCID>297</mw:PubChemCID> | |
| <rdf:type rdf:resource="http://metware.sf.net/onto/#PubChemExtras"/> | |
| </rdf:Description> | |
| <rdf:Description rdf:about="urn:lsid:localhost:net.sf.metware.beans.MetidMetabolitesBean:16"> |
egonw
/ Query the Blue Obelisk Descriptor Ontology.js
Created
April 15, 2009 18:34
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| var owl = rdf.createStore(); | |
| rdf.importURL(owl, | |
| "http://qsar.svn.sf.net/viewvc/qsar/trunk/qsar-dicts/descriptor-algorithms.owl?revision=210" | |
| ); | |
| // list of topological descriptors | |
| rdf.sparql(owl, | |
| "PREFIX qsar: <http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#> " + | |
| "SELECT ?s WHERE { ?s ?p qsar:topologicalDescriptor}" | |
| ); |
egonw
/ Calculates the XLogP for ethoxyethane using XMPP and the CDK.js
Created
April 15, 2009 19:48
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| // connect to the XMPP hive | |
| xmpp.connect(); | |
| // we are going to call the XLogP function of the descriptor service | |
| service = xmpp.getService("descriptor.ws1.bmc.uu.se"); | |
| service.discoverSync(5000); | |
| service.getFunctions(); | |
| f = service.getFunction("XLogP"); | |
| // we use Bioclipse to create a CML document, starting from a SMILES |
egonw
/ buildMolecule.js
Created
April 16, 2009 18:57
— forked from olas/buildmol
Build a molecule using Bioclipse script for JChemPaint
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| /******************************************************************************* | |
| * Bioclipse-script to iteratively build a molecule in JChemPaint | |
| * Author: Ola Spjuth | |
| * Author: Egon Willighagen | |
| ******************************************************************************/ | |
| //Start with a carbon and open in JCP | |
| mol=cdk.fromSMILES("C") | |
| mol2=cdk.generate2dCoordinates(mol) | |
| ui.open(mol2) |
egonw
/ Download Domoic Acid from PubChem.groovy
Created
April 17, 2009 14:44
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| import org.openscience.cdk.* | |
| import org.openscience.cdk.io.* | |
| import org.openscience.cdk.nonotify.* | |
| cid = 5282253 | |
| reader = new PCCompoundXMLReader( | |
| new URL( | |
| "http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=$cid&disopt=SaveXML" | |
| ).newInputStream() | |
| ) |
egonw
/ PubChem processing with the CDK
Created
May 4, 2009 07:54
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| 1. Get a copy of PubChem | |
| $ mkdir pubchem | |
| $ cd pubchem | |
| $ wget -r ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/CURRENT-Full/XML/ -c | |
| $ ln -s ftp.ncbi.nlm.nih.gov/pubchem/Compound/CURRENT-Full/XML XML | |
| 2. Set up MySQL | |
| CREATE TABLE IF NOT EXISTS `compounds` ( |
egonw
/ Calculates the TPSA for ethoxyethane using XMPP and the CDK.js
Created
May 6, 2009 09:56
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| // connect to the XMPP hive | |
| xmpp.connect(); | |
| // we are going to call the TPSA function of the descriptor service | |
| service = xmpp.getService("descriptor.ws1.bmc.uu.se"); | |
| service.discoverSync(5000); | |
| service.getFunctions(); | |
| f = service.getFunction("TPSA"); | |
| // we use Bioclipse to create a CML document, starting from a SMILES |