Egon Willighagen egonw
egonw
/ Bioclipse2 Script: Calculate Mass
Created
October 21, 2008 11:56
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| propane = cdk.fromSMILES("CCC"); | |
| cdk.calculateMass(propane) |
egonw
/ Bioclipse2 Script: create a new structure.js
Created
October 21, 2008 14:44
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| dimethylether = cdk.fromSMILES( "COC" ); | |
| cdk.addExplicitHydrogens( dimethylether ); | |
| cdk.generate3dCoordinates( dimethylether ); | |
| // save as CML | |
| cdk.saveCML( dimethylether, "/Virtual/dimethylether.cml" ); | |
| ui.open( "/Virtual/dimethylether.cml" ); // this should open a JmolEditor | |
| jmol.minimize(); |
egonw
/ Determine Chemical File Formats
Created
October 26, 2008 15:54
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| cdk.determineFormat("/DemoData/3D Structures/cml/alcohols/(2R,3R,4R,5S)-hexane-1,2,3,4,5,6-hexol.cml") | |
| cdk.determineFormat("/DemoData/3D Structures/mol/alcohols/(2R,3R,4R,5S)-hexane-1,2,3,4,5,6-hexol.mol") |
egonw
/ Invoke a XWS service (synchronous)
Created
November 4, 2008 19:23
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| xmpp.connect(); | |
| service = xmpp.getService("cdk.ws1.bmc.uu.se"); | |
| service.discoverSync(5000); | |
| service.getFunctions(); | |
| f = service.getFunction("calculateMass"); | |
| ios = f.getIoSchemataSync(90000); | |
| iof = xmpp.getIoFactory(ios); | |
| smiDoc = iof.createSmilesDocument(); | |
| smiDoc.setSmiles("CCC"); | |
| result = f.invokeSync(smiDoc.toString(), 900000); |
egonw
/ CDK Atom Typing Inspection
Created
November 12, 2008 15:35
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| ui.open( "/CDK Demo Scripts/propan-2-ol.cml" ) | |
| cdkMolecule1 = cdk.loadMolecule( "/CDK Demo Scripts/propan-2-ol.cml" ) | |
| cdkdebug.depictCDKAtomTypes( cdkMolecule1 ) |
egonw
/ sstructuredb test script.js
Created
November 17, 2008 10:13
— forked from jonalv/sstructuredb test script.js
Creates a local structure database and adds three molecules to it.
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| var dbName = "exampleScriptDB"; | |
| if ( structuredb.allDatabaseNames().contains(dbName) ) { | |
| structuredb.deleteDatabase(dbName); | |
| } | |
| structuredb.createDatabase(dbName); | |
| smiles = new Array("Cc1ccccc1", "CCO", "O=O"); | |
| names = new Array("toluene", "beer", "air"); |
egonw
/ Add Phenyl
Created
November 20, 2008 17:40
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| # just illustrative, and only works on a file only I have, but you get the idea | |
| ui.open("/PeptideMimetics/10.cml") | |
| oxygen = jcp.getModel().getAtomContainer().getAtom(11) | |
| jcp.addAtom("C", oxygen) | |
| newCarbon = jcp.getModel().getAtomContainer().getAtom(12) | |
| jcp.addPhenyl(newCarbon) |
egonw
/ Generate InChI and InChIKey.js
Created
December 8, 2008 10:37
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| mol = cdk.fromSMILES("C"); | |
| inchi1 = inchi.generate(mol); | |
| js.print(inchi1 + "\n"); | |
| js.print("Key: " + inchi1.getKey() + "\n"); |
egonw
/ gist:45495
Created
January 10, 2009 16:58
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| PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | |
| PREFIX dbpedia-owl: <http://dbpedia.org/ontology/> | |
| SELECT DISTINCT ?c WHERE { | |
| ?c a dbpedia-owl:ChemicalCompound | |
| } ORDER BY ?c LIMIT 1000 OFFSET 0 |
egonw
/ gist:47449
Created
January 15, 2009 15:43
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| xmpp.connect(); | |
| service = xmpp.getService("cdk.ws1.bmc.uu.se"); | |
| service.discoverSync(5000); | |
| service.getFunctions(); | |
| f = service.getFunction("TPSA"); | |
| result = f.invokeSync(cdk.fromSMILES("CC").CML, 5000); | |
| tpsaString = result.getTextContent() |
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