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error during molecuar weight search

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TobiasKind Joined: 26 Jan 2005 Posts: 354 Back to top	Post subject: error during molecuar weight search Posted: Sat Oct 13, 2007 2:41 am  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)
TobiasKind Joined: 26 Jan 2005 Posts: 354 Back to top	Post subject: Posted: Sat Oct 13, 2007 9:12 am  HI, I found out I did not remove Markush structures, so they were still in. Tobias
TobiasKind Joined: 26 Jan 2005 Posts: 354 Back to top	Post subject: Posted: Tue Oct 23, 2007 11:39 pm  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
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