The CMLHandler has a small bug in the CML convention
handling. If convention is instantiated in the child
element, then it is not reset when returning to parent
elements. Here is an example:
<list convention="aa">
<molecule id="1">
<bond convention="bb"> ... </bond>
</molecule>
<molecule id="2">
...
</molecule>
</list>
The problem is that the convention "bb" (from a bond
element of the molecule 1) will be active in the
molecule 2.
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There is no easy way to test this, but I think I've
uploaded a fix for this problem. Please confirm that it
is fixed. Being optimistic I've closed the bug, but open
it again when it still does not work. BTW, how did you
find the bug? Can we use that to make a regression test?