Rgdecomp: output problem (converted to smiles)

When I try to use rgdecomp; I can have my output in SDF or in mrv; but when I try to have it in smiles (default) I have this error:

Exception in thread "main" java.lang.IllegalArgumentException:
Some features of Br cannot be converted to smiles. Use the cxsmiles, smarts or cxsmarts format.
        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(Unknown Source)
        at chemaxon.marvin.util.JavaLangUtil.newIllegalArgumentException(Unknown Source)
        at chemaxon.struc.Molecule.toFormat(Unknown Source)
        at chemaxon.jchem.RGDecomp.decomp(RGDecomp.java:541)
        at chemaxon.jchem.RGDecomp.runDecomp(RGDecomp.java:405)
        at chemaxon.jchem.RGDecomp.run(RGDecomp.java:303)
        at chemaxon.jchem.RGDecomp.main(RGDecomp.java:606)
Caused by: chemaxon.marvin.io.MolExportException:
Some features of Br cannot be converted to smiles. Use the cxsmiles, smarts or cxsmarts format.
        at chemaxon.marvin.io.formats.smiles.SmilesExport.throwMolExportExceptionSMILES(Unknown Source)
        at chemaxon.marvin.io.formats.smiles.SmilesExport.toSMILES(Unknown Source)
        at chemaxon.marvin.io.formats.smiles.SmilesExport.convert(Unknown Source)
        at chemaxon.struc.Molecule.exportToObject(Unknown Source)
        at chemaxon.struc.Molecule.exportToObject(Unknown Source)
        at chemaxon.struc.Molecule.exportToFormat(Unknown Source)

What is the problem?

Thanks for your help

Lionel

I must had that I have this error with the JChem versions 5.4.x.x; but nor with the 5.3.3 version

Hi,

It must be because of the new representation of the explicit attachment point is possible to represent in smiles.

You may use cxsmiles (ChemAxon extended smiles) instead, or use a different attachment point representation.

See the -a parameter:

  -a, --attachment-symbol <N|P|A|M|L>  attachment symbol on ligands:
                                       N: none
                                       P: R-group attachment 
                                       A: any-atom (default)
                                       M: atom map
                                       L: atom label
                                       R: atom label with 'R' prefix

http://www.chemaxon.com/jchem/doc/user/RGroupDecomposition.html#usage

  -a, --attachment-symbol <N|P|A|M|L>  attachment symbol on ligands:
                                       N: none
                                       P: R-group attachment 
                                       A: any-atom (default)
                                       M: atom map
                                       L: atom label
                                       R: atom label with 'R' prefix

Thanks for your fast response!

After some change in the -a parameter; only attachment P is not support in smile...

So, I will try to use other attachement symbol;

thanks for your help

Lionel