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Valentin Georgiev valyo

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@valyo
valyo / gist:6183060
Created August 8, 2013 09:16
!ENTRY org.eclipse.core.jobs 4 2 2013-08-08 11:15:01.115
!MESSAGE An internal error occurred during: "Decision Support Report".
!STACK 0
java.lang.IllegalAccessError: You requested the active parameter of type net.bioclipse.smartcyp.ds.SmartcypGenerator$Visibility, but it has not been registered yet. Did you make sure the IGeneratorParameter is registered, by registring the appropriate IGenerator? Alternatively, you can use getDefault() to query the default value for any parameter on the classpath.
at org.openscience.cdk.renderer.RendererModel.getParameter(RendererModel.java:152)
at org.openscience.cdk.renderer.RendererModel.set(RendererModel.java:205)
at net.bioclipse.ds.ui.ImageHelper.enableSelectedExternalGenerators(ImageHelper.java:191)
at net.bioclipse.ds.ui.ImageHelper.createImage(ImageHelper.java:136)
at net.bioclipse.ds.report.ReportHelper.createResultImage(ReportHelper.java:232)
at net.bioclipse.ds.report.ReportHelper.createBeanCollection(ReportHelper.j
@valyo
valyo / gist:4754453
Created February 11, 2013 13:35
Cannot complete the install because of a conflicting dependency.
Software being installed: Textm_feature 1.0.0.201302111420 (com.genettasoft.textm_feature.feature.group 1.0.0.201302111420)
Software currently installed: Bioclipse 2.6.0.v201212211322 (net.bioclipse.product 2.6.0.v201212211322)
Only one of the following can be installed at once:
OSGi System Bundle 3.8.1.v20120830-144521 (org.eclipse.osgi 3.8.1.v20120830-144521)
OSGi System Bundle 3.8.0.v20120529-1548 (org.eclipse.osgi 3.8.0.v20120529-1548)
Cannot satisfy dependency:
From: Textm_feature 1.0.0.201302111420 (com.genettasoft.textm_feature.feature.group 1.0.0.201302111420)
To: org.eclipse.osgi [3.8.0.v20120529-1548]
Cannot satisfy dependency:
@valyo
valyo / js
Created May 22, 2012 11:29
jonalv script
//======================
//Define properties
molfile="/drugbank/approved.sdf";
outFile="/drugbank/approved-res-sortInhib.sdf";
sortprop="growth inhibition"
//The models to run (use 'ds.getTests()' in Javascript Console to see available models)
screenmodel="screen.u251";
amesmodel="ames.hansen.r";
//======================
@valyo
valyo / bcr
Created May 21, 2012 09:23
bcr
Molceulce topoShape geomShape ATSp1 ATSp2 ATSp3 ATSp4 ATSp5 MDEC-11 MDEC-12 MDEC-13 MDEC-14 MDEC-22 MDEC-23 MDEC-24 MDEC-33 MDEC-34 MDEC-44 MDEO-11 MDEO-12 MDEO-22 MDEN-11 MDEN-12 MDEN-13 MDEN-22 MDEN-23 MDEN-33 TopoPSA SP-0 SP-1 SP-2 SP-3 SP-4 SP-5 SP-6 SP-7 VP-0 VP-1 VP-2 VP-3 VP-4 VP-5 VP-6 VP-7 VAdjMat SC-3 SC-4 SC-5 SC-6 VC-3 VC-4 VC-5 VC-6 ECCEN ATSc1 ATSc2 ATSc3 ATSc4 ATSc5 ATSm1 ATSm2 ATSm3 ATSm4 ATSm5 PetitjeanNumber C1SP1 C2SP1 C1SP2 C2SP2 C3SP2 C1SP3 C2SP3 C3SP3 C4SP3 Kier1 Kier2 Kier3 Zagreb SCH-3 SCH-4 SCH-5 SCH-6 SCH-7 VCH-3 VCH-4 VCH-5 VCH-6 VCH-7 WPATH WPOL SPC-4 SPC-5 SPC-6 VPC-4 VPC-5 VPC-6 fragC Wlambda1.unity Wlambda2.unity Wlambda3.unity Wnu1.unity Wnu2.unity Wgamma1.unity Wgamma2.unity Wgamma3.unity Weta1.unity Weta2.unity Weta3.unity WT.unity WA.unity WV.unity WK.unity WG.unity WD.unity LOBMAX LOBMIN PPSA-1 PPSA-2 PPSA-3 PNSA-1 PNSA-2 PNSA-3 DPSA-1 DPSA-2 DPSA-3 FPSA-1 FPSA-2 FPSA-3 FNSA-1 FNSA-2 FNSA-3 WPSA-1 WPSA-2 WPSA-3 WNSA-1 WNSA-2 WNSA-3 RPCG RNCG RPCS RNCS THSA TPSA RHSA RPSA to
@valyo
valyo / log
Created May 16, 2012 17:26
eclipse console output
at sun.org.mozilla.javascript.internal.InterpretedFunction.exec(InterpretedFunction.java:149)
at sun.org.mozilla.javascript.internal.Context.evaluateReader(Context.java:1169)
at com.sun.script.javascript.RhinoScriptEngine.eval(RhinoScriptEngine.java:149)
at com.sun.script.javascript.RhinoScriptEngine.eval(RhinoScriptEngine.java:167)
at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:247)
at net.bioclipse.jsexecution.execution.ScriptExecution.runRhinoScript(ScriptExecution.java:234)
at net.bioclipse.jsexecution.execution.ScriptExecution.access$0(ScriptExecution.java:185)
at net.bioclipse.jsexecution.execution.ScriptExecution$1.run(ScriptExecution.java:116)
at org.eclipse.core.internal.jobs.Worker.run(Worker.java:54)
@valyo
valyo / groovy code
Created April 20, 2012 14:46
Groovy code from Arvid
> qsar.getCategories()
[http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#topologicalDescriptor, http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#hybridDescriptor, http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#geometricalDescriptor, http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#constitutionalDescriptor, http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#electronicDescriptor]
getDescriptorIDs getDescriptorImplByID getDescriptorImpls getDescriptorImplsByProvider
> qsar.getDescriptorIDs()
[http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#chi1v, http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#numberOfAcidicGroups, http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#numberOfBasicGroups, http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#petitjeanShapeIndex, http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#autoCorrelationPolarizabilit
@valyo
valyo / BioclipseTeam.java
Created February 15, 2012 09:19
BioclipseTeam
public class BioclipseTeam {
private String[] players = new String[] {
"Ola Spjuth", "Martin Eklund", "Jonathan Alvarsson", "Arvid Berg", "Valentin Georgiev", "Klas Joensson" };
public String[] getTeam() {
return players;
}
}
@valyo
valyo / PrintBCPlayers.java
Created February 15, 2012 09:17
PrintBCPlayers
public abstract class PrintBCPlayers {
/**
* @param args
*/
public static void main(String[] args) {
// TODO Auto-generated method stub
BioclipseTeam bcteam = new BioclipseTeam();
String[] list = bcteam.getTeam();
printPlayers(list);
@valyo
valyo / "Updating Software" has encountered a problem
Created January 19, 2012 14:32
Configuration x86,win32.win32
An error occurred while collecting items to be installed
session context was:(profile=Bioclipse, phase=org.eclipse.equinox.internal.p2.engine.phases.Collect, operand=, action=).
No repository found containing: osgi.bundle,net.bioclipse.gist,2.5.0.201201181553
No repository found containing: osgi.bundle,net.bioclipse.scripting,2.5.0.201201181553
No repository found containing: osgi.bundle,net.bioclipse.scripting.ui,2.5.0.201201181553
No repository found containing: osgi.bundle,net.bioclipse.usermanager,2.5.0.201201181213
No repository found containing: binary,net.bioclipse.product.executable.win32.win32.x86,2.5.0.201201181553
@valyo
valyo / Using Bioclipse Scripting Language
Created January 11, 2012 09:19
ds=qsar.calculate(mols,dlist);
09:55:18.490 DEBUG [net.bioclipse.qsar.business.QsarManager] Calculate impl: org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor for mol: CDKMolecule:C22H36NO2
09:55:18.491 DEBUG [net.bioclipse.qsar.business.QsarManager] Calculate impl: org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor for mol: CDKMolecule:C22H36NO2
09:55:18.491 DEBUG [net.bioclipse.qsar.business.QsarManager] Parameter: key='type', value='unity'
09:55:18.491 DEBUG [net.bioclipse.qsar.business.QsarManager] Calculate impl: org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor for mol: CDKMolecule:C22H36NO2
09:55:18.491 DEBUG [net.bioclipse.qsar.business.QsarManager] Calculate impl: org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor for mol: CDKMolecule:C22H36NO2
09:55:18.491 DEBUG [net.bioclipse.qsar.business.QsarManager] Calculate impl: org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor for mol: CDKMolecule:C22H36NO2
09:55:18.491 DEBUG [net.bioclip