Problems reading molfile and sdf files of a molecule

User d27b99d458

20-02-2013 16:18:45

 


 


                 Hello!


 


                 I am trying to calculate the number of fragments in a molecule (cxcalc fragmentcount), but I just obtain the following error:


                    ' chemaxon.formats.MolFormatException: Attachment point handling is not supported for S-groups with more than 2 crossing bonds'


                  I cannot also view the molecule in the marvin view.


                   The molfile that I have tested is attached to this post.


 


                                                    Thank you in advance,


 


                                                              Raquel

ChemAxon 5fc3e8d7d0

25-02-2013 11:42:30


Dear Raquel,



Use the import option "mol:Fsg".
http://www.chemaxon.com/marvin/help/formats/mol-csmol-doc.html#ioptions


For example:


   cxcalc fragmentcount mol_error.mol{mol:Fsg}


or


   mview mol_error.mol{mol:Fsg}




After import those s-groups will be ungroupped that have more than 2 attachment points.


 


Best regards,


Laszlo

User d27b99d458

26-02-2013 09:15:52

 


 


      Thank you for the answer, but I still have problems in two molecules when I run the command to a sdf file with several molecules:


       Some features of OS(O)(=O)=O.[#6]N([#6])C(=O)COC1=CC2=C(CC[[email protected]@H](C2)NC[[email protected]](O)C2=CC=C(O)C(CCO)=C2)C=C1 cannot be converted to the given format. Try mrv format.


 


Some features of [#6]CCCCCCC\C=C/CCCCCCCC(=O)OCCOCC(OCCO)C1OCC(OCCO)C1OCCO cannot be converted to the given format. Try mrv format.


          Any idea where they come from?

 


                           Thank you!

User d27b99d458

26-02-2013 10:53:44

 


 


 


                       And in a certain point of the file, the program breaks with the folowwing error:


 



java.lang.RuntimeException: sgroups[0] == null in clonecopy


        at chemaxon.struc.Molecule.clonecopySgroups(Unknown Source)


        at chemaxon.struc.Molecule.clonecopy(Unknown Source)


        at chemaxon.struc.Molecule.cloneMolecule(Unknown Source)


        at chemaxon.struc.Molecule.cloneMoleculeWithDocument(Unknown Source)


        at chemaxon.calculator.CalculatorLogger.log(CalculatorLogger.java:124)


        at chemaxon.calculator.CalculatorLogger.log(CalculatorLogger.java:113)


        at chemaxon.marvin.Calculator.outputError(Calculator.java:1924)


        at chemaxon.marvin.Calculator.outputOnlyPlugin(Calculator.java:1793)


        at chemaxon.marvin.Calculator.consume(Calculator.java:1724)


        at chemaxon.marvin.Calculator.run(Calculator.java:1444)


        at chemaxon.marvin.Calculator.run(Calculator.java:1345)


        at chemaxon.marvin.Calculator.main(Calculator.java:2023)




              

User d27b99d458

26-02-2013 15:17:29

 


 


 


               This is the sdf file of the molecule that gives this error...


 


                           Thanks,


 


                           Raquel

ChemAxon d26931946c

26-02-2013 15:59:29

Dear Raquel,



The attached file contains two SuperatomSgroups (abbreviations) and they both containing all the atoms of the molecule and we can't represent this correctly. 

Thank for reporting this issue, we will fix it.

You may try to delete the Sgroups from the file by removing all the lines starting with "M S**".

We're sorry for the inconvenience.

Best regards,

Peter

ChemAxon d26931946c

07-03-2013 09:28:50

Dear Raquel,


 


I would like to inform you that we managed to fix the bug.


The fix will be available in Marvin 6.0. We're planning to release it in May, 2013.


 


Best  regards,


Peter

User d27b99d458

07-03-2013 09:49:51

Hello!


 


Thank you for notifying me! I will be waiting for the new version.


 


Best regards,


 


Raquel