#919 MDLV2000Reader G group reading

[Loren Lenzen]

It is my understanding that the MDL spec requires all elements to be listed in the atom group. Therefore, the atoms in a G group do not need to (and probably should not) replace those in the atom group using replaceAtomByAtom method. After commenting out the G group reader if statement from the MDLV2000Reader class two things happened: 1. I stopped getting atom type R exceptions. 2. My substructure searches actually worked.

I see that this bug was reported a while back but it still exists in 1.2.2

[Egon Willighagen]

John, can you comment?

[John May]

Hmmm not sure...

Group Abbreviation [ISIS/Desktop - not used in current products]

aaa: Atom number
ppp: Atom number
x: Abbreviation label
Abbreviation is required for compatibility with previous versions of ISIS/Desktop, which allowed
abbreviations with only one attachment. The attachment is denoted by two atom numbers, aaa and
ppp. All of the atoms on the aaa side of the bond formed by aaa-ppp are abbreviated. The coordinates
of the abbreviation are the coordinates of aaa. The text of the abbreviation is on the following line (x...).
In current versions of ISIS, abbreviations can have any number of attachments and are written out using
the Sgroup appendixes. However, any ISIS abbreviations that do have one attachment are also written
out in the old style, again for compatibility with older ISIS versions, but this behavior might not be
supported in future versions.

The preferred way of doing this now is with Sgroups Abbreviations which we do support. What I should do is make the Group property set that.