[Cdk-devel] ModelBuilder3d/aromaticity detection

[Stefan K. <ste...@eb...>]

Dear co-developers,
two comments which might be important for the upcoming release:
1. I fixed the ModelBuilder3d - all tests except one work (will look at this 
tomorrow). The reason were changes in the fingerprinter, apart from the 
ill-fated changes in the modelbuilder itself, which I fixed earlier. I can 
only ask everybody to run tests (I know I might have missed that myself). I 
added a test case to the TemplateHandler3DTest, which tests the fingerprints 
for stability.
2. While working on this, I found the fingerprinter is always doing 
aromaticity detection. While I think we do not yet have a solution for "a 
detection if needed only", the class should at least have an option to switch 
this off. Worse, when running the ModelBuilder3DTests with a slight change, I 
get errors "org.openscience.cdk.exception.NoSuchAtomTypeException: The 
AtomType Csp2 could not be found". It looks like the aromaticity detection 
(now?) relies on atom typing, but atom typing fails on aromatic carbons. This 
sounds alarming for me. If you want to test, change line 171 of 
TemplateHandler3D from BitSet ringSystemFingerprint = new 
Fingerprinter().getFingerprint(queryRingSystem);
to BitSet ringSystemFingerprint = new 
Fingerprinter().getFingerprint(ringSystems); and run the ModelBuilder3D 
tests. four of them fail with this problem.
Stefan