Hi all,
I'm trying to calculate the rmsd between two molecules I've aligned. I
couldn't find any tools for it in the CDK so I tried using
AtomMappingTools.mapAtomsOfAlignedStructures to match the atoms so I
could calculate it by hand. The function seems to work when applied to
two copies of the same molecule but it just threw a
NullPointerException when applied to two different molecules. Is this
a known issue? The exception is thrown in the line
for (int i = 0; i < list.size(); i++) {
so clearly the list returned from
UniversalIsomorphismTester.getSubgraphAtomsMap can be null, and this
is not handled. Why it would be null I cannot guess: that does not
make sense.
Is this a known bug? Is there another way to find the rmsd between two
molecules in CDK?
Regards,
Thomas
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