error during molecuar weight search

Hi,


I have a DB (Biometa) with all Markush structures removed using


Instant-JChem and now I want to find all structures less or equal than


500 Dalton, by searching MW < 500.001. Please also check with less


or larger than and scroll through the structures. The error only


occurs with Real numbers, not with Integers and we are back at the IEEE 754


floating point discussion from last time. There is no less or equal, so I have to put some X.0001 in there.





I get a hidden error in module Clean2D which I can not see,


and an out of memory error (which is not true) there is 1GByte left


and I have plenty of heap memory free 250 MByte.





Instant JChem Version: 2.1 (build: 071002) JChem Version: 3.2.11 Marvin


Version: 4.1.13 (build date: 2007-9-20) Java: 1.5.0_11; Java HotSpot(TM) Client


VM 1.5.0_11-b03 System: Windows XP version 5.1 running on x86;


Cp1252; en_US (instantjchem)


Tobias





error in clean2D





java.lang.OutOfMemoryError: unable to create new native thread


at java.lang.Thread.start0(Native Method)


at java.lang.Thread.start(Unknown Source)


at chemaxon.marvin.common.swing.MolPanel.initCursor(MolPanel.java:5037)


at chemaxon.marvin.common.swing.MolPanel.initCursor(MolPanel.java:5016)


at chemaxon.marvin.common.swing.MolPanel.endHourglass(MolPanel.java:3671)


at chemaxon.marvin.common.swing.MolPanel.molLoaded(MolPanel.java:4472)


at chemaxon.marvin.view.swing.ViewPanel.molLoaded(ViewPanel.java:2599)


at chemaxon.marvin.view.swing.ViewPanel.setM(ViewPanel.java:1657)


at chemaxon.marvin.beans.MViewPane.setM(MViewPane.java:462)


at com.im.ijc.renderers.impl.StructureRenderer.getWidgetCellRendererComponent(StructureRenderer.java:262)


at com.im.ijc.renderers.impl.StructureRenderer.getTableCellRendererComponent(StructureRenderer.java:190)


at javax.swing.JTable.prepareRenderer(Unknown Source)


at javax.swing.plaf.basic.BasicTableUI.paintCell(Unknown Source)


at javax.swing.plaf.basic.BasicTableUI.paintCells(Unknown Source)


at javax.swing.plaf.basic.BasicTableUI.paint(Unknown Source)


at javax.swing.plaf.ComponentUI.update(Unknown Source)


at javax.swing.JComponent.paintComponent(Unknown Source)


at javax.swing.JComponent.paint(Unknown Source)


at javax.swing.JComponent.paintChildren(Unknown Source)


at javax.swing.JComponent.paint(Unknown Source)


at javax.swing.JViewport.paint(Unknown Source)


at javax.swing.JComponent.paintChildren(Unknown Source)


at javax.swing.JComponent.paint(Unknown Source)


at javax.swing.JComponent.paintChildren(Unknown Source)


at javax.swing.JComponent.paint(Unknown Source)


at javax.swing.JComponent.paintChildren(Unknown Source)


at javax.swing.JComponent.paint(Unknown Source)


at javax.swing.JComponent.paintChildren(Unknown Source)


at javax.swing.JComponent.paint(Unknown Source)


at javax.swing.JComponent.paintChildren(Unknown Source)


at javax.swing.JComponent.paint(Unknown Source)


at javax.swing.JComponent.paintChildren(Unknown Source)


at javax.swing.JComponent.paint(Unknown Source)


at javax.swing.JComponent.paintChildren(Unknown Source)


at javax.swing.JComponent.paint(Unknown Source)


at javax.swing.JComponent.paintChildren(Unknown Source)


at javax.swing.JComponent.paint(Unknown Source)


at org.netbeans.core.windows.view.ui.MultiSplitPane.paint(MultiSplitPane.java:294)


at javax.swing.JComponent.paintChildren(Unknown Source)


at javax.swing.JComponent.paint(Unknown Source)


at org.netbeans.core.windows.view.ui.MultiSplitPane.paint(MultiSplitPane.java:294)


at javax.swing.JComponent.paintChildren(Unknown Source)


at javax.swing.JComponent.paint(Unknown Source)


at javax.swing.JComponent.paintChildren(Unknown Source)


at javax.swing.JComponent.paint(Unknown Source)


at javax.swing.JLayeredPane.paint(Unknown Source)


at javax.swing.JComponent.paintChildren(Unknown Source)


at javax.swing.JComponent.paint(Unknown Source)


at javax.swing.JComponent.paintChildren(Unknown Source)


at javax.swing.JComponent.paint(Unknown Source)


at javax.swing.JComponent.paintChildren(Unknown Source)


at javax.swing.JComponent.paint(Unknown Source)


at javax.swing.JLayeredPane.paint(Unknown Source)


at javax.swing.JComponent.paintChildren(Unknown Source)


at javax.swing.JComponent.paint(Unknown Source)


at java.awt.GraphicsCallback$PaintCallback.run(Unknown Source)


at sun.awt.SunGraphicsCallback.runOneComponent(Unknown Source)


at sun.awt.SunGraphicsCallback.runComponents(Unknown Source)


at java.awt.Container.paint(Unknown Source)


at org.netbeans.core.windows.view.ui.MainWindow.paint(MainWindow.java:507)


at sun.awt.RepaintArea.paintComponent(Unknown Source)


at sun.awt.RepaintArea.paint(Unknown Source)


at sun.awt.windows.WComponentPeer.handleEvent(Unknown Source)


at java.awt.Component.dispatchEventImpl(Unknown Source)


at java.awt.Container.dispatchEventImpl(Unknown Source)


at java.awt.Window.dispatchEventImpl(Unknown Source)


at java.awt.Component.dispatchEvent(Unknown Source)


at java.awt.EventQueue.dispatchEvent(Unknown Source)


at java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)


at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)


at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)


at java.awt.Dialog$1.run(Unknown Source)


at java.awt.Dialog$2.run(Unknown Source)


at java.security.AccessController.doPrivileged(Native Method)


at java.awt.Dialog.show(Unknown Source)


at org.netbeans.core.windows.services.NbPresenter.superShow(NbPresenter.java:812)


at org.netbeans.core.windows.services.NbPresenter.doShow(NbPresenter.java:846)


at org.netbeans.core.windows.services.NbPresenter.run(NbPresenter.java:834)


at org.netbeans.core.windows.services.NbPresenter.run(NbPresenter.java:82)


at org.openide.util.Mutex.doEventAccess(Mutex.java:1201)


at org.openide.util.Mutex.readAccess(Mutex.java:220)


at org.netbeans.core.windows.services.NbPresenter.show(NbPresenter.java:819)


at java.awt.Component.show(Unknown Source)


at java.awt.Component.setVisible(Unknown Source)


at org.netbeans.core.NotifyExcPanel.updateState(NotifyExcPanel.java:355)


at org.netbeans.core.NotifyExcPanel.access$400(NotifyExcPanel.java:68)


at org.netbeans.core.NotifyExcPanel$2.run(NotifyExcPanel.java:287)


at java.awt.event.InvocationEvent.dispatch(Unknown Source)


at java.awt.EventQueue.dispatchEvent(Unknown Source)


at java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)


at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)


at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)


at java.awt.Dialog$1.run(Unknown Source)


at java.awt.Dialog$2.run(Unknown Source)


at java.security.AccessController.doPrivileged(Native Method)


at java.awt.Dialog.show(Unknown Source)


at javax.swing.JOptionPane.showOptionDialog(Unknown Source)


at chemaxon.marvin.common.swing.modules.ExceptionFrame.runErrorDialog(ExceptionFrame.java:136)


at chemaxon.marvin.common.swing.modules.ExceptionFrame.run(ExceptionFrame.java:114)


at java.awt.event.InvocationEvent.dispatch(Unknown Source)


at java.awt.EventQueue.dispatchEvent(Unknown Source)


at java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)


at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)


at java.awt.EventDispatchThread.pumpEvents(Unknown Source)


at java.awt.EventDispatchThread.pumpEvents(Unknown Source)


at java.awt.EventDispatchThread.run(Unknown Source)

HI,


I found out I did not remove Markush structures,


so they were still in.


Tobias

TobiasKind wrote:

HI, I found out I did not remove Markush structures, so they were still in. Tobias

Thisis not the reason for this error and removing the Markushs does not solve the problem!


Tobias