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#424 MDL Mol file reader problem with g in the property block
If I load a mdl mol file which contains the g option in
the property block will that molecule not be parsed
correctly. It only replaces the one connected atom and
with a pseudo atom:
Example see attached file. If I write this molecule to
a file again it has only replace the N to a NO2 but
there are now 2 O's to much!
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Thomas, I added the JUnit test for the attached file, but
does not check the bug yet. Please update that, thanx!
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This is pending a decision to move IFragmentAtom into the interfaces
module.
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State needs to be further explored; IFragmentAtom is in the interfaces module, and the unit test for this bug report does not fail. However, I do not see use if IFragmentAtom in the MDLV2000Reader either...
This won't make it into the 1.2.0 release.
John, can you comment on this bug report?
The group tag is currently ignored since we don't have the semantics to correctly represent the grouping. Resolving this would involve handling MDL SGroups (Substructure Groups) correctly which would be a very large patch including polymers/mixtures etc. This would be useful but I would move this to feature request for enhancement.
Just to add to that, the problem here no longer exists since the group is ignored the N is not converted to NO2.
i.e. < 1.5.x C[N+](=O)[O-] as attached was being converted to C[NO2](=O)[O-] instead of C[NO2] > 1.5.x C[N+](=O)[O-] as attached is left alone