#424 MDL Mol file reader problem with g in the property block

master
open
John May
5
2015-01-01
2006-10-30
thomaskuhn
No

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!

Discussion

  • thomaskuhn

    thomaskuhn - 2006-10-30
     
  • Egon Willighagen

    Logged In: YES
    user_id=25678

    Thomas, I added the JUnit test for the attached file, but
    does not check the bug yet. Please update that, thanx!

     
  • Egon Willighagen

    Logged In: YES
    user_id=25678
    Originator: NO

    This is pending a decision to move IFragmentAtom into the interfaces
    module.

     
  • Egon Willighagen

    Logged In: YES
    user_id=25678
    Originator: NO

    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...

     
  • Egon Willighagen

    This won't make it into the 1.2.0 release.

     
  • Egon Willighagen

    John, can you comment on this bug report?

     
  • Egon Willighagen

    • assigned_to: John May
     
  • John May

    John May - 2015-01-01

    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.

     
  • John May

    John May - 2015-01-01

    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