I understand how position and frequency variation can be used, independently. What I do not know how to do is how to use them at the same time. Let's say, I select two contiguous atoms, and do position variation for a substituent. It works. Then I select again the same two atoms for repetition, but when doing markush enumeration, I get:
Error during molecule display: java.lang.ArrayIndexOutOfBondsException: Array index out of range: 2
I attach the file.
Is it then possible to do the two things at the same time?
I have found a bug in our clonecopy mechanism which seems to be the direct cause of this problem.
We are working on the solution and will let you know when it is fixed. Thanks for the report.
The clonecopy bug has been fixed and the correction will be available in the 5.4 release.
However, your input molecule is also incorrect: only the two non-central atoms of the multicenter are contained in the repeating unit. I have fixed this, the new molecule is attached. Using this, enumeration in the 5.4 Marvin will give you all of the 6 enumerates:
cxcalc enumerations position_and_frequency_variation_fixed.mrv -f smiles