I tried to read particular ChEbi molfiles, created with Marvin. This failed, it turned out that these molfiles contain bond types > 4.
An example is this appropriately Christmas tree-like compound http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:51730
According to the CTFfile spec, the bond types go up to 8.
1 = Single, 2 = Double,
3 = Triple, 4 = Aromatic,
5 = Single or Double,
6 = Single or Aromatic,
7 = Double or Aromatic, 8 = Any
However, MDLV200Reader stops at 4, and you end up with null bonds in the atomcontainer if the bond type is 5-8.
Is it okay if I create a patch for this? I think the CDK should support these peculiar bond types, so we'd need some new IBond.Orders.
The patch should be easy but I don't know if there are objections as these bond types look somewhat odd.
If CDK doesn't accept the bonds, a clear error should be thrown.