Egon Willighagen egonw

💭

I want peace and climate action

Open scientist teaching and doing research at Maastricht University.

egonw / Calculates the BCUT for ethoxyethane using XMPP and the CDK.js

Created May 6, 2009 10:05

	// connect to the XMPP hive
	xmpp.connect();

	// we are going to call the BCUT function of the descriptor service
	service = xmpp.getService("descriptor.ws1.bmc.uu.se");
	service.discoverSync(5000);
	service.getFunctions();
	f = service.getFunction("BCUT");

	// we use Bioclipse to create a CML document, starting from a SMILES

egonw / Calculates the RuleOfFive for ethoxyethane using XMPP and the CDK.js

Created May 6, 2009 10:25

	// connect to the XMPP hive
	xmpp.connect();

	// we are going to call the Lipinski Rule of Five function of the descriptor service
	service = xmpp.getService("descriptor.ws1.bmc.uu.se");
	service.discoverSync(5000);
	service.getFunctions();
	f = service.getFunction("LipinskiRuleOfFive");

	// we use Bioclipse to create a CML document, starting from a SMILES

egonw / Get RDF for methane using XMPP.js

Created May 6, 2009 11:03

	// connect to the XMPP hive
	xmpp.connect();

	// we are going to call the RDF bridge to http://rdf.openmolecule.net/
	service = xmpp.getService("rdf.ws1.bmc.uu.se");
	service.discoverSync(5000);
	service.getFunctions();
	func = service.getFunction("Bridge to RDF.OpenMolecules.net");

	// the input is a RDF description element of which only the rdf:about

egonw / Convert SMILES into CML.js

Created May 6, 2009 11:30

	// connect to the XMPP hive
	xmpp.connect();

	// we are going to call the SMILES2CML function of the descriptor service
	service = xmpp.getService("cdk.ws1.bmc.uu.se");
	service.discoverSync(5000);
	service.getFunctions();
	f = service.getFunction("SMILES2CML");

	// we use Bioclipse to create a CML document, starting from a SMILES

egonw / Generate 2D coordinates with CDK via an XMPP service.js

Created May 6, 2009 11:49

	// connect to the XMPP hive
	xmpp.connect();

	// we are going to call the generate2Dcoordinates function of the descriptor service
	service = xmpp.getService("cdk.ws1.bmc.uu.se");
	service.discoverSync(5000);
	service.getFunctions();
	f = service.getFunction("generate2Dcoordinates");

	// we use Bioclipse to create a CML document, starting from a SMILES

egonw / Generate 3D coordinates using the CDK via an XMPP service.js

Created May 6, 2009 11:54

	// connect to the XMPP hive
	xmpp.connect();

	// we are going to call the generate3Dcoordinates function of the descriptor service
	service = xmpp.getService("cdk.ws1.bmc.uu.se");
	service.discoverSync(5000);
	service.getFunctions();

	// we use Bioclipse to create a CML document, starting from a SMILES
	smiles = "COC(Br)(F)C";

egonw / gist:107507

Created May 6, 2009 12:56

We couldn’t find that file to show.

egonw / gist:110614

Created May 12, 2009 17:21

	mol = cdk.fromSMILES("C=C1C(=O)CC2CC1C2(C)(C)");
	mol = cdk.generate2dCoordinates(mol);
	ui.open(mol);
	jcp.setShowExplicitHydrogens(false)

	msSpectrum = medea.predictMassSpectrum(mol);
	spectrum.saveSpectrum(msSpectrum, "/Virtual/foo.cml", "cml");
	ui.open("/Virtual/foo.cml");

egonw / gist:114756

Created May 20, 2009 11:21

	$ git log
	commit e67014fc4a1040dd129a1e57d1994bed2831662b
	Author: shk3 <shk3@fcb5ba71-d80d-0410-8237-ba3920747fcc>
	Date: Wed May 20 09:47:15 2009 +0000

	now using dept and formula information

	git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10609 fcb5ba71-d80d-0410-8237-ba3920747fcc

	commit c3eb7a1653cd185dd447c0788c1cc1e97b18abcf

egonw / Validate the MetWare SKOS.js

Created May 25, 2009 14:22

	// analyze the MetWare SKOS

	js.clear();
	var armet = rdf.createStore();

	rdf.importURL(armet, "http://www.w3.org/TR/rdf-schema/rdfs-namespace");
	rdf.importURL(armet, "http://www.w3.org/2002/07/owl");
	rdf.importURL(armet, "http://www.w3.org/2004/02/skos/core");
	rdf.importFile(armet, "/OWL/MetWare/armet.skos", "RDF/XML");
	rdf.importFile(armet, "/OWL/MetWare/metware.skos", "RDF/XML");