#976 Error in converting cdx files with functional group aliases

[Matthias Budzynski]

In some cases, functional groups are not converted correctly from cdx files in which they are represented by an alias instead of having all bonds drawn explicitly.

The attached cdx file contains three structures of 1,3-substituted benzenes. Using Open Babel 2.4.0, the command "obabel -icdx test.cdx -ocan" yields the following result:

c1cccc(c1)C(F)(F)F
c1cccc(c1)C(Cl)(Cl)Cl
IC(c1cccc(c1)C(I)(I)I)(I)I

The only structure converted correctly is the one with all bonds drawn explicitly. For the other structures, possibly dependent on orientation, one of the two functional groups is missing. Note that this happens both when the bond is drawn to the "C" in the alias, or, in a less correct representation, to the halogen. I could also reproduce this behavior for other functional groups, such as CN.