Aromatic, Double, Triple Bond Perception in Gaussian Output

Hello.  I was wondering JChem could perceive aromatic, double, and triple bonds from Gaussian output?  I figure that JChem must have to perceive bond order already in order to import other types of file formats (e.g., .pdb).  Thanks!

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Hi Steven,

The import of Gaussian output can be used with the same option "b" which is defined for Gaussian cube format. It  tries to guess bond types from atom distances and valence rules.

More information is available in the documentation of file formats:

https://docs.chemaxon.com/display/FF/Gaussian+Cube+import+and+export+options

Best regards,

Zsuzsa

Thanks for the response.  Is there any way to force Marvin to infer bond orders from cube files?  Or is this functionality only available in the Java API?  Thanks.

-&

Hi Steven,

I have moved your question to the Marvin forum, my colleagues from the Marvin team will answer your question soon.

Best regards,

Zsuzsa

Dear Steven,

   Marvin does not support the setting of any export parameters in case of saving the structure. Everything is saved with the default values.

Regards:
Balázs 

Hello.  I get an Exception when I try to read a G09 .cube file (both with the Marvin application and the MolImporter Java API).  This is the stack trace:

ERROR:
Read error after molecule 0:
0.000000 - integer expected at position: 167

STACK TRACE:
chemaxon.formats.MolFormatException: 0.000000 - integer expected at position: 167
 at chemaxon.marvin.modules.mprop.VolumetricData$Parser.readInteger(VolumetricData.java:253)
 at chemaxon.marvin.modules.mprop.VolumetricData$Parser.parseAxes(VolumetricData.java:201)
 at chemaxon.marvin.modules.mprop.VolumetricData$Parser.parseVolumetricData(VolumetricData.java:182)
 at chemaxon.marvin.modules.mprop.VolumetricData.<init>(VolumetricData.java:79)
 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
 at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
 at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
 at java.lang.reflect.Constructor.newInstance(Constructor.java:408)
 at chemaxon.marvin.io.MPropHandler.createScalar(MPropHandler.java:145)
 at chemaxon.marvin.io.formats.gaussian.CubeRecordReader.nextRecord(CubeRecordReader.java:144)
 at chemaxon.marvin.io.formats.gaussian.CubeRecordReader.nextRecord(CubeRecordReader.java:68)
 at chemaxon.marvin.io.MRecordImporter.startReadingNext(MRecordImporter.java:1029)
 at chemaxon.marvin.io.MRecordImporter.readRecord(MRecordImporter.java:673)
 at chemaxon.marvin.io.MRecordImporter.readDoc0(MRecordImporter.java:480)
 at chemaxon.marvin.io.MRecordImporter.readDoc(MRecordImporter.java:430)
 at chemaxon.formats.MolImporter.readDoc(MolImporter.java:844)
 at chemaxon.formats.MolImporter.nextDoc(MolImporter.java:784)
 at chemaxon.marvin.view.MDocStorage.readDoc(MDocStorage.java:2809)
 at chemaxon.marvin.view.MDocStorage.tryToExtend(MDocStorage.java:938)
 at chemaxon.marvin.view.MDocStorage.getMainDoc(MDocStorage.java:853)
 at chemaxon.marvin.view.MDocStorage.getMainDoc(MDocStorage.java:817)
 at chemaxon.marvin.view.swing.TableSupport$11.run(TableSupport.java:710)
 at chemaxon.marvin.view.swing.TableSupport.setDocSource(TableSupport.java:733)
 at chemaxon.marvin.view.swing.TableSupport.access$600(TableSupport.java:71)
 at chemaxon.marvin.view.swing.TableSupport$UpdateTask.run0(TableSupport.java:235)
 at chemaxon.marvin.view.swing.TableSupport$UpdateTask.run(TableSupport.java:220)
 at chemaxon.marvin.view.SequentialScheduler$CmpRunnable.run(SequentialScheduler.java:55)
 at chemaxon.marvin.view.SequentialScheduler$1.run(SequentialScheduler.java:220)

-&

Dear Steven,

can you attach the file that causes the exception, or send it by e-mail if it is confidential?

Thank you,

Zsuzsa