Problems reading molfile and sdf files of a molecule

                 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

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

      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[C@@H](C2)NC[C@H](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.

                           Thank you!

                       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)

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

                           Thanks,

                           Raquel

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

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

Hello!

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

Best regards,

Raquel