chemaxon.formats.MolFormatException with own names

Hi,

i used

molconvert name C8H16O2-stereoisomers.smi > C8H16O2-stereoisomers-names.txt
molconvert smiles C8H16O2-stereoisomers-names.txt > C8H16O2-stereoisomers-struc2name.smi

and got the following exception, I attached all two files.

One of the errors was: 2-[(1R)-1-(propan-2-yloxy)ethoxy]prop-1-ene

Tobias

-----------

chemaxon.formats.MolFormatException
    at chemaxon.marvin.io.formats.name.nameimport.IUPACNameReader.importName(IUPACNameReader.java:60)
    at chemaxon.marvin.io.formats.name.NameImport.readMol(NameImport.java:39)
    at chemaxon.marvin.io.MRecordImporter.readDoc(MRecordImporter.java:170)
    at chemaxon.marvin.common.swing.modules.EditMolfileFrame.doImport(EditMolfileFrame.java:624)
    at chemaxon.marvin.common.swing.modules.EditMolfileFrame$1.run(EditMolfileFrame.java:875)
    at java.lang.Thread.run(Unknown Source)
    at chemaxon.marvin.common.swing.modules.EditMolfileFrame$ImportAction.actionPerformed(EditMolfileFrame.java:873)
    at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
    at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
    at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
    at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
    at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
    at java.awt.Component.processMouseEvent(Unknown Source)
    at javax.swing.JComponent.processMouseEvent(Unknown Source)
    at java.awt.Component.processEvent(Unknown Source)
    at java.awt.Container.processEvent(Unknown Source)
    at java.awt.Component.dispatchEventImpl(Unknown Source)
    at java.awt.Container.dispatchEventImpl(Unknown Source)
    at java.awt.Component.dispatchEvent(Unknown Source)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
    at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
    at java.awt.LightweightDispatcher.dispatchEvent(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.pumpOneEventForFilters(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForFilter(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)
Caused by: java.lang.NullPointerException
    at chemaxon.marvin.io.formats.name.nameimport.parse.IUPACParserCore.addStereoDataToParents(IUPACParserCore.java:1154)
    at chemaxon.marvin.io.formats.name.nameimport.parse.IUPACParserCore.addStereoDataToParents(IUPACParserCore.java:1121)
    at chemaxon.marvin.io.formats.name.nameimport.parse.IUPACParserCore.handleCloseBracket(IUPACParserCore.java:278)
    at chemaxon.marvin.io.formats.name.nameimport.parse.IUPACParserCore.parseTokens(IUPACParserCore.java:187)
    at chemaxon.marvin.io.formats.name.nameimport.parse.IUPACParserCore.parseTokens(IUPACParserCore.java:116)
    at chemaxon.marvin.io.formats.name.nameimport.IUPACNameReader.importSystematicName(IUPACNameReader.java:103)
    at chemaxon.marvin.io.formats.name.nameimport.IUPACNameReader.importSingleName(IUPACNameReader.java:93)
    at chemaxon.marvin.io.formats.name.nameimport.IUPACNameReader.importName(IUPACNameReader.java:54)
    ... 31 more

 

Dear Tobias,

A new version (5.2.2) of Marvin will be released in a few days. In that, some problems are already fixed, and we will work on fixing the others to the next version.

Thanks for the report,

Veréb Rita

Hi,

thanks alot, I will try again in the future.

Tobias

 

Hi,

...five days later, I used Marvin 5.2.2

I get the following error with Name to Structure:

{[(2Z)-2-ethylidenepentyl]oxy}methanol
{[(2E)-2-ethylidenepentyl]oxy}methanol

Please see the full import file from above, so these are Marvin created names.

C8H16O2-stereoisomers-names.txt:1659: error: Unrecognized element type "D"

chemaxon.formats.MolFormatException: Unrecognized element type "D"
at chemaxon.marvin.io.formats.name.nameimport.IUPACNameReader.importName(IUPACNameReader.java:63)
at chemaxon.marvin.io.formats.name.NameImport.readMol(NameImport.java:47)
at chemaxon.marvin.io.MRecordImporter.readDoc(MRecordImporter.java:375)
at chemaxon.marvin.io.MRecordImporter.readDoc(MRecordImporter.java:356)
at chemaxon.marvin.io.MRecordImporter.readDoc(MRecordImporter.java:168)
at chemaxon.marvin.common.swing.modules.EditMolfileFrame.doImport(EditMolfileFrame.java:603)
at chemaxon.marvin.common.swing.modules.EditMolfileFrame$ImportAction$1.run(EditMolfileFrame.java:846)
at java.lang.Thread.run(Unknown Source)
at chemaxon.marvin.common.swing.modules.EditMolfileFrame$ImportAction.actionPerformed(EditMolfileFrame.java:844)
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(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.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(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)
Caused by: java.lang.RuntimeException: Unrecognized element type "D"
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at chemaxon.marvin.util.JavaLangUtil.newThrowable(JavaLangUtil.java:76)
at chemaxon.marvin.util.JavaLangUtil.newRuntimeException(JavaLangUtil.java:30)
at chemaxon.marvin.io.formats.name.nameimport.parse.data.Structure.buildMolecule(Structure.java:453)
at chemaxon.marvin.io.formats.name.nameimport.parse.data.Structure.addLigand(Structure.java:1241)
at chemaxon.marvin.io.formats.name.nameimport.parse.data.Structure.connectLigands(Structure.java:1175)
at chemaxon.marvin.io.formats.name.nameimport.parse.data.Structure.buildMolecule(Structure.java:477)
at chemaxon.marvin.io.formats.name.nameimport.parse.data.Structure.addLigand(Structure.java:1241)
at chemaxon.marvin.io.formats.name.nameimport.parse.data.Structure.connectLigands(Structure.java:1175)
at chemaxon.marvin.io.formats.name.nameimport.parse.data.Structure.buildMolecule(Structure.java:477)
at chemaxon.marvin.io.formats.name.nameimport.parse.data.Structure.getMolecule(Structure.java:570)
at chemaxon.marvin.io.formats.name.nameimport.IUPACNameReader.importSystematicName(IUPACNameReader.java:110)
at chemaxon.marvin.io.formats.name.nameimport.IUPACNameReader.importSingleName(IUPACNameReader.java:99)
at chemaxon.marvin.io.formats.name.nameimport.IUPACNameReader.importName(IUPACNameReader.java:57)
... 33 more
Caused by: chemaxon.formats.MolFormatException: Unrecognized element type "D"
at chemaxon.marvin.io.formats.smiles.SmilesImport.readSymbolAndAddAtom(SmilesImport.java:1232)
at chemaxon.marvin.io.formats.smiles.SmilesImport.readMol0(SmilesImport.java:687)
at chemaxon.marvin.io.formats.smiles.SmilesImport.readMol(SmilesImport.java:534)
at chemaxon.marvin.io.formats.smiles.CxsmilesImport.readMol(CxsmilesImport.java:36)
at chemaxon.marvin.io.formats.smiles.SmilesImport.readMol(SmilesImport.java:492)
at chemaxon.marvin.io.formats.name.nameimport.Util.readMol(Util.java:207)
at chemaxon.marvin.io.formats.name.nameimport.parse.data.Structure.readMol(Structure.java:2205)
at chemaxon.marvin.io.formats.name.nameimport.parse.data.SimpleStructure.getMol(SimpleStructure.java:153)
at chemaxon.marvin.io.formats.name.nameimport.parse.data.Structure.buildMolecule(Structure.java:451)
... 43 more

Tobias

 

Dear Tobias,

the 5.2.2 version was nearly released, when you have sent the files, so unfortunately the most fixes couldn't appear in it. We fixed many problems since the release, it will appear in the next patch (in a couple weeks).

Thanks for you patience,

Rita Veréb

 

Dear Tobias,

now all the problems with molecule generating in the given file is already fixed, most of the fixes are already released, the other will be released with 5.3. We have a minor problem with the name generation (some cis/trans data is ignored during the name generation). This part is waiting for other developments, but we are already working on the problem.

 

Best regards,

 Rita Vereb