Markushcount question

Hi,


I have to files which give me a number of possible structures.


one is coded as R1 = x.y,z the other one as R1 = L{x,y,z}.


In mview I get Markush library size = 390625 (~ 10^6) only for the file with L (see attachement).





Otherwise I get the error:


chemaxon.enumeration.ExpansionException: Circular dependency in order graph.


Cycle atom indexes: 11 9


at chemaxon.enumeration.ExpansionHelper.findExpansionSequence(ExpansionHelper.java:158)


at chemaxon.enumeration.ExpansionCounter.createExpansionGraph0(ExpansionCounter.java:737)


at chemaxon.enumeration.ExpansionCounter.createExpansionGraph(ExpansionCounter.java:689)


at chemaxon.enumeration.ExpansionCounter.countExpansions(ExpansionCounter.java:538)


at chemaxon.marvin.calculations.MarkushEnumerationPlugin.run(MarkushEnumerationPlugin.java:501)


at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(CalculatorPluginManager.java:175)


at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(CalculatorPluginManager.java:159)


at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(CalculatorPluginManager.java:108)


at chemaxon.marvin.plugin.CalculatorPluginManager.callback(CalculatorPluginManager.java:76)


at chemaxon.marvin.plugin.PluginManager.callback(PluginManager.java:87)


at chemaxon.marvin.common.swing.MolPanel.run(MolPanel.java:2105)


at java.lang.Thread.run(Unknown Source)








What is wrong? According to the help it seems fine.


Tobias





Idea: Depth-First

Hi Tobias,





Your first Markush structure is not well-formed. The Rgroup that it contains is not an atomlist but an R1 atom itself. It seems to be an atomlist only because it has a label (mrvAlias):

Code:

elementType="R"             rgroupRef="1"             attachmentPoint="1"             mrvAlias="H, F, Cl, Br, I"

(You can see the difference by erasing the "mrvAlias=..." line from the file.)





So this is a real circular reference to R1 from inside the R1 definition.





Best regards,


Tamás

One remark: if you use an atom list as in your -2 files then the R-group notation is not needed, you can just as well replace your R1 atoms by the atom list itself.





Or, you can use an R-group definition by putting the different atoms in different R-group members, as in the attached -3 file.

Hello Tamas and Nora,


thank you for your comments and help.


Tobias