JChem 3.1.3 and Marvin 4.0.3 released

news · 16 years ago
The new JChem 3.1.3 includes the Marvin 4.0.3. Please run through the list of the most important changes:
  • Bugfixes:
    • Minor bugfixes in MarvinSpace
    • In mol file export
  • Import/Export:
    • IUPAC InChi support
    • MDL Molfiles, RGfiles etc.: Implicit H is stored as attached data when needed.
    • Improved PDB import.
    • Hydrogenize bug fixed: tetrahedral geometry of alcohol Oxygen atom is now maintained.
    • Volumetric data import/export for CUBE files (not processed by Marvin)
  • Implemented trivalent doublet and quartet. (RAD3_DOUBLET, RAD3_QUARTET)
  • Applets:
    • New methods: MSketch.getSelectedMol, MSketch.getMolMass, MSketch.getMolExactMass, MSketch.getMolFormula, MView.getMolMass, MView.getMolExactMass, MView.getMolFormula, JMSketch.getMolMass, JMSketch.getMolExactMass, JMSketch.getMolFormula, JMView.getMolMass, JMView.getMolExactMass, JMView.getMolFormula
    • New sketcher parameter: undetachByX.
  • MarvinSpace beta, includes public API:
    • Dynamic loading of JOGL libraries.
    • Better handling of PDB files including not standard complient variants.
    • Save graphic scene as PNG image file.
    • Basic Gaussian Cube file support.
    • Improved User Interface.
  • Plugin:
    • New parameter in ResonancePlugin: take major contributors (-m, --mcontrib).
    • New parameter in TautomerizationPlugin: take dominant tautomers (--d, --dominants).
    • Bugfix in Tautomerization Plugin.
  • S-group names can contain almost any ascii character.
  • Bugfixes:
    • Hydrogenize bug fixed: tetrahedral geometry of alcohol O is now maintained.
    • Minor bugfixes in aromatization, in 2D cleaning and in molconverter.