Can not reopen Marvin generated files with n-group

Hello,

I have an issue with n-numerated groups (SRU polymer):

- I draw a structure with a numbered group ("multiple group") and save the file.

The File can be reopened after closing Marvin sketch

- I open the same file and change the group to a SRU-polymer with index n and save again

I get an error when I try to reopen it after closing.

Can anyone reproduce?

 

Operating System OS X 10.9.1

Version MarvinSketch 6.2.0

 

ERROR: 

Unknown error.

 

STACK TRACE:

java.lang.NullPointerException

at chemaxon.struc.sgroup.RepeatingUnitSgroup.calcConnectingCrossingBond(RepeatingUnitSgroup.java:480)

at chemaxon.struc.sgroup.RepeatingUnitSgroup.addCrossingBonds(RepeatingUnitSgroup.java:782)

at chemaxon.marvin.io.formats.cml.BondReader.processBondCorrespondence(BondReader.java:439)

at chemaxon.marvin.io.formats.cml.CMLImport.readMol0(CMLImport.java:503)

at chemaxon.marvin.io.formats.cml.CMLImport.readMol00(CMLImport.java:414)

at chemaxon.marvin.io.formats.cml.CMLImport.readMolecule(CMLImport.java:376)

at chemaxon.marvin.io.formats.cml.MrvImport.readChemicalStruct(MrvImport.java:366)

at chemaxon.marvin.io.formats.cml.MrvImport.readMDocument(MrvImport.java:223)

at chemaxon.marvin.io.formats.cml.MrvImport.readMRV(MrvImport.java:168)

at chemaxon.marvin.io.formats.cml.MrvImport.readDocument(MrvImport.java:106)

at chemaxon.marvin.io.MRecordImporter.readMol(MRecordImporter.java:712)

at chemaxon.marvin.io.MRecordImporter.readMol(MRecordImporter.java:684)

at chemaxon.marvin.io.MRecordImporter.readMol0(MRecordImporter.java:592)

at chemaxon.marvin.io.MRecordImporter.readMol(MRecordImporter.java:509)

at chemaxon.formats.MolImporter.readMol(MolImporter.java:823)

at chemaxon.formats.MolImporter.read(MolImporter.java:710)

at chemaxon.formats.MolImporter.read(MolImporter.java:680)

at chemaxon.common.swing.io.input.FileLoader.readSelectedMoleculesFromFile(FileLoader.java:169)

at chemaxon.common.swing.io.input.FileLoader.importStructures(FileLoader.java:86)

at chemaxon.common.swing.io.input.FileLoader.doOpenFile(FileLoader.java:70)

at chemaxon.common.swing.io.input.FileLoader.openFileWithDialog(FileLoader.java:60)

at chemaxon.common.swing.io.input.FileLoader.openFile(FileLoader.java:47)

at chemaxon.marvin.sketch.swing.SketchPanel.fileOpen(SketchPanel.java:7054)

at chemaxon.marvin.common.swing.MolPanel.openMolfile(MolPanel.java:4395)

at chemaxon.marvin.sketch.swing.SketchPanel.setMol(SketchPanel.java:4756)

at chemaxon.marvin.beans.MSketchPane.setMol(MSketchPane.java:383)

at chemaxon.marvin.Sketch.main0(Sketch.java:737)

at chemaxon.marvin.Sketch.main(Sketch.java:586)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

at java.lang.reflect.Method.invoke(Method.java:597)

at com.exe4j.runtime.LauncherEngine.launch(Unknown Source)

at com.install4j.runtime.launcher.MacLauncher.main(Unknown Source)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

at java.lang.reflect.Method.invoke(Method.java:597)

at apple.launcher.LaunchRunner.run(LaunchRunner.java:116)

at apple.launcher.LaunchRunner.callMain(LaunchRunner.java:51)

at apple.launcher.JavaApplicationLauncher.launch(JavaApplicationLauncher.java:52)

I have tried the above mentioned procedure on a windows computer at work. Here is the result:

 

ERROR:

Error during molecule display: java.lang.NullPointerException

Cannot load structures from PF sulfonat - n generic.mrv.

 

STACK TRACE:

java.lang.NullPointerException

                at chemaxon.struc.sgroup.RepeatingUnitSgroup.calcConnectingCrossingBond(RepeatingUnitSgroup.java:480)

                at chemaxon.struc.sgroup.RepeatingUnitSgroup.addCrossingBonds(RepeatingUnitSgroup.java:782)

                at chemaxon.marvin.io.formats.cml.BondReader.processBondCorrespondence(BondReader.java:439)

                at chemaxon.marvin.io.formats.cml.CMLImport.readMol0(CMLImport.java:503)

                at chemaxon.marvin.io.formats.cml.CMLImport.readMol00(CMLImport.java:414)

                at chemaxon.marvin.io.formats.cml.CMLImport.readMolecule(CMLImport.java:376)

                at chemaxon.marvin.io.formats.cml.MrvImport.readChemicalStruct(MrvImport.java:366)

                at chemaxon.marvin.io.formats.cml.MrvImport.readMDocument(MrvImport.java:223)

                at chemaxon.marvin.io.formats.cml.MrvImport.readMRV(MrvImport.java:168)

                at chemaxon.marvin.io.formats.cml.MrvImport.readDocument(MrvImport.java:106)

                at chemaxon.marvin.io.MRecordImporter.readDoc(MRecordImporter.java:756)

                at chemaxon.marvin.io.MRecordImporter.readDoc(MRecordImporter.java:741)

                at chemaxon.marvin.io.MRecordImporter.readDoc0(MRecordImporter.java:483)

                at chemaxon.marvin.io.MRecordImporter.readDoc(MRecordImporter.java:427)

                at chemaxon.formats.MolImporter.readDoc(MolImporter.java:786)

                at chemaxon.formats.MolImporter.nextDoc(MolImporter.java:728)

                at chemaxon.marvin.view.MDocStorage.readDoc(MDocStorage.java:2801)

                at chemaxon.marvin.view.MDocStorage.tryToExtend(MDocStorage.java:935)

                at chemaxon.marvin.view.MDocStorage.getMainDoc(MDocStorage.java:850)

                at chemaxon.marvin.view.MDocStorage.getMainDoc(MDocStorage.java:814)

                at chemaxon.marvin.view.swing.TableSupport$11.run(TableSupport.java:707)

                at chemaxon.marvin.view.swing.TableSupport.setDocSource(TableSupport.java:730)

                at chemaxon.marvin.view.swing.TableSupport.access$600(TableSupport.java:68)

                at chemaxon.marvin.view.swing.TableSupport$UpdateTask.run0(TableSupport.java:232)

                at chemaxon.marvin.view.swing.TableSupport$UpdateTask.run(TableSupport.java:217)

                at chemaxon.marvin.view.SequentialScheduler$CmpRunnable.run(SequentialScheduler.java:55)

                at chemaxon.marvin.view.SequentialScheduler$1.run(SequentialScheduler.java:220)

Hello,

 

thank you for the report.

I could not reproduce the issue on my computer, could you send us the mrv file that causes this issue?

Peter

gezapeti wrote:

Hello,   thank you for the report. I could not reproduce the issue on my computer, could you send us the mrv file that causes this issue? Peter

of course. thank you for you reply

Hi,

 

This is a bug, we will fix it soon. The problem is that we handle it poorly, when an sgroup is arranged as perfectly vertical atoms.

 

I'm sorry for the inconvenience.

dzatonyi wrote:

Hi,   This is a bug, we will fix it soon. The problem is that we handle it poorly, when an sgroup is arranged as perfectly vertical atoms.   I'm sorry for the inconvenience.

thank you for your help