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#155 charge and isotope support in MOL V3000 format

closed
Bob Hanson
5
2009-04-09
2009-04-09
Angel Herraez
No

The MOL V3000 specification allows for atomic charge and mass. It would be nice to have Jmol recognize those values, both go in each atom line (after the coordinates).
The string "CHG=" is followed by the atomic charge (same values as for MOL V2000: 0 = uncharged, 1 = +3, 2 = +2, 3 = +1,
4 = doublet radical, 5 = -1, 6 = -2, 7 = -3)
The string "MASS=" is followed by the atomic mass of the isotope (if not specified, defaults to natural abundant isotope)
The alanine files in SVN Jmol-datafiles/V3000 can be used for testing.

Discussion

  • Angel Herraez
    Angel Herraez
    2009-04-09

    Correction: the charge range is the same as in V2000, but V3000 does not use the codes, but directly the charge vale, e.g.
    "CHG=1"
    "CHG=-1"
    as seen in the alanine example.
    Looking at V3000Reader.java, it seems that charge is already implemented, but it fails (see bug #2747323)

     
  • Bob Hanson
    Bob Hanson
    2009-04-09

    calling this a bug and implementing in Jmol 11.7.32 and 11.6.21

     
  • Bob Hanson
    Bob Hanson
    2009-04-09

    • assigned_to: nobody --> hansonr
    • status: open --> closed