Jonathan Alvarsson jonalv
jonalv
/ sstructuredb test script.js
Created
November 11, 2008 17:13
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| var dbName = "exampleScriptDB"; | |
| if ( structuredb.allDatabaseNames().contains(dbName) ) { | |
| structuredb.deleteDatabase(dbName); | |
| } | |
| toluene = cdk.fromSMILES("Cc1ccccc1"); | |
| ethanol = cdk.fromSMILES("CCO"); | |
| oxygen = cdk.fromSMILES("O=O"); | |
jonalv
/ sstructuredb test script.js
Created
February 4, 2009 12:42
— forked from egonw/sstructuredb test script.js
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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"); |
jonalv
/ sstructuredb test script.js
Created
February 4, 2009 12:43
— forked from egonw/sstructuredb test script.js
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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"); |
jonalv
/ gist:74367
Created
March 5, 2009 14:44
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| var file = "/Sample Data/SDF/borken.sdf"; | |
| iterator = cdk.createMoleculeIterator(file); | |
| var i = 0; | |
| js.print("\n"); | |
| var numberOff = cdk.numberOfEntriesInSDF(file); | |
| var molecules = cdk.createMoleculeList(); | |
| while ( iterator.hasNext() ) { | |
| m = iterator.next(); | |
| i++; |
jonalv
/ gist:84188
Created
March 24, 2009 16:17
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| mol = cdk.fromSMILES("C(C1C(C(C(C(O1)O)O)O)O)O"); | |
| mol = cdk.addExplicitHydrogens(mol); | |
| cdk.generate3dCoordinates(mol); | |
| fileName = "/Virtual/" + cdk.molecularFormula(mol) + ".cml"; | |
| cdk.saveMolecule(mol, fileName, true); | |
| ui.open(fileName); | |
| jmol.minimize(); | |
| jmol.run("move 0 360 90 -20 0 0 0 0 5"); |
jonalv
/ AbstractManagerMethodDispatcherTest.java
Created
April 29, 2009 15:42
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| package net.bioclipse.managers.tests; | |
| import static org.junit.Assert.assertEquals; | |
| import static org.junit.Assert.assertTrue; | |
| import java.io.ByteArrayInputStream; | |
| import java.lang.reflect.AccessibleObject; | |
| import java.lang.reflect.Method; | |
| import net.bioclipse.core.domain.BioList; |
jonalv
/ ITestManager.java
Created
April 29, 2009 15:47
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| package net.bioclipse.managers.tests; | |
| import java.util.List; | |
| import org.eclipse.core.resources.IFile; | |
| import net.bioclipse.core.domain.IBioObject; | |
| import net.bioclipse.jobs.BioclipseJob; | |
| import net.bioclipse.jobs.BioclipseJobUpdateHook; | |
| import net.bioclipse.managers.business.IBioclipseManager; |
jonalv
/ TestManager.java
Created
April 29, 2009 15:48
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| package net.bioclipse.managers.tests; | |
| import org.eclipse.core.resources.IFile; | |
| import org.eclipse.core.runtime.IProgressMonitor; | |
| import net.bioclipse.core.domain.BioObject; | |
| import net.bioclipse.core.domain.IBioObject; | |
| import net.bioclipse.jobs.BioclipseJob; | |
| import net.bioclipse.jobs.IPartialReturner; | |
| import net.bioclipse.managers.business.IBioclipseManager; |
jonalv
/ gist:124340
Created
June 5, 2009 15:51
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| Requested operation cannot be performed because it would invalidate the current configuration. See details for more information. | |
| Eclipse BIRT Report Runtime Feature (2.3.2.r232_v20081010-7k8E7fELFluav5n_2NEXh3W6B9_) requires feature "com.lowagie.itext (1.5.2)", or later version. | |
| Eclipse BIRT ODA JDBC Connection Profile Feature (2.3.2.r232_v20081010-67859cADAamA55V5A89) requires plug-in "org.eclipse.datatools.connectivity.sqm.core (1.0.1)", or later version. | |
| Eclipse XML Editors and Tools (3.0.4.v200811211541-7F2ENnCwum8W79A1UYNgSjOcFVJg) requires feature "org.eclipse.platform (3.4.0)", or compatible. | |
| WST Common UI (3.0.4.v200811200248-7C78ELhE8VrRVqtHp4iT8PuSwZ5W) requires feature "org.eclipse.platform (3.4.0)", or compatible. | |
| WST Common Core (3.0.4.v200811200248-7C7_EVNE_EkMNtRvY4V6o0) requires feature "org.eclipse.platform (3.4.0)", or compatible. | |
| WST XML Core (3.0.4.v200812040936-7A7NEH2E7QYGHOIsNrGpVX) requires feature "org.eclipse.platform (3.4.0)", or compatible. | |
| WST Common UI (3.0.5.v20090 |
jonalv
/ gist:130140
Created
June 15, 2009 14:43
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| ant | |
| Buildfile: build.xml | |
| runPerl: | |
| [exec] sh: /usr/bin/xpath: /usr/bin/perl: bad interpreter: No such file or directory | |
| [exec] sh: /usr/bin/xpath: /usr/bin/perl: bad interpreter: No such file or directory | |
| [exec] sh: /usr/bin/xpath: /usr/bin/perl: bad interpreter: No such file or directory | |
| [exec] sh: /usr/bin/xpath: /usr/bin/perl: bad interpreter: No such file or directory | |
| [exec] sh: /usr/bin/xpath: /usr/bin/perl: bad interpreter: No such file or directory | |
| [exec] sh: /usr/bin/xpath: /usr/bin/perl: bad interpreter: No such file or directory |
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