v4

December 11, 2007: Marvin 4.1.14

  • API:

  • Fixed bugs:

    • Import/export:

      • There was a critical property based smiles export bug

      • There was a NullPointerException in Parity (forum topic)

    • GUI:

      • Plugin options panel could not be closed using only the keyboard after running the calculation

      • Edited molecule was not updated in viewer by closing the sketcher.

      • Rotating a group in expanded form removed the group definition.

      • Update isotope number in selection by D and T shortcuts.

      • Type-over atom D did not work.

      • In OS X, the scroll down button of sketcher scrollbar was covered by window resize button. (forum topic)

      • Fix a small refreshing problem in MarvinSpace.

      • Quick setting of component visibility on mouse drag in MarvinSpace.

    • Calculator Plugins:

      • Bugfix in the pKa plugin.

    • Misc:

      • Bugfix in the maximum common substructure search.

September 18, 2007: Marvin 4.1.13

  • API:

  • Bugfixes:

    • Change frames to dialogs to avoid focus problem of model dialogs. (forum topic)

    • "Any" bond was invisible in OS X. (forum topic)

    • ElementalAnalyser and ElementalAnalyserPlugin: scientifically correct rounding of molecular weight (mass)

    • CleanUtil.arrangeComponents() bug for reactions containing Sgroups. (forum topic)

    • Bug in abbreviated group visibility.

    • Correcting a bug of getting the most frequent natural isotope of Hydrogen. It returned 0, though the correct result is 1.

    • Marvin Beans batch files accept 40 parameters. (forum topic)

    • MarvinSpace: lone pair visibility correction.

August 17, 2007: Marvin 4.1.12

  • Improvement in IUPAC name export. Very significant performance increase for large molecules, fixing about half the previously existing naming failures (due to timeouts) for typical datasets. New export option to setup naming timeout.

  • Bugfixes:

    • Redo bug fixed.

    • Bugfix in Clean 2D

    • Fix bug by flipping.

    • MolAtoms were not selected when selectionChanged property change event invoked.

July 23, 2007: Marvin 4.1.11

  • GUI:

    • Text box improvement: its highlighting color is lighter than other highlighting colors because dark colors obscured the text for short strings.

  • API:

  • Bugfixes:

    • IUPAC Naming: fixed timeout errors.

    • Fixing bug "Phosphorus loses chirality after explicit-H-removal"

  • Calculator plugins:

July 6, 2007: Marvin 4.1.10

  • Bugfix in displaying of pKa calculation results in command line (cxcalc).

June 26, 2007: Marvin 4.1.9

  • GUI:

    • Remove small blue corners in MarvinView (except in tables).

    • Hide dashed line in bond forming electron flow arrows.

    • Fixing undo and copying error in reactions.

  • API:

  • IUPAC name generation improvements, in particular for ions.

  • Bugfixes:

    • Fixing arrow initialization problem in RxnMolecule clean.

    • In PDB export, the -c option did not work properly.

    • Empty field parsing bugfix in Smiles import.

May 17, 2007: Marvin 4.1.8

  • Import/export:

    • Image export option ("noatsym") to hide atom symbols in 3D mode.

    • SUBSTRUCTURE section is also generated in mol2

    • Bugfix in MRV import: absolute stereo flag could not be set.

    • Fix superatom S-group export bug in MRV export.

  • GUI:

    • Fix NullPointerException by displaying MViewPane with menubar.

    • Graphical reaction arrows.

    • Bugfix in arrow drawing.

  • API:chemaxon.marvin.util.MPainterUtil

        is deprecated, use

      chemaxon.marvin.MolPrinter

      • Bugfixes:

        • LP chirality fix

        • Bugfix in CleanUtil

        • Minor bugfixes in calculation plugins

      April 13, 2007: Marvin 4.1.7

      • IUPAC name generator, for interactive and batch naming

      • Bugfixes:

        • In Graph invariant.

        • Arrow mirroring bugfixes.

        • Infinite loop fix in Parity.

        • Converting to "base64:gzip:mrv" did not work.

        • Exception by missing atom list definition fixed.

        • ArrayIndexOutOfBoundsException in RxnMolecule.removeNode()

        • Non-transformable polyline point highlighting fix

        • InChi import/export works also in Java Web Start

      March 14, 2007: Marvin 4.1.6

      • Import/Export:

        • RDfile properties can be hierarchized or flattened.

        • Data sgroup improvements in MRV import/export.

        • Bugfix in MRV export.

        • Bugfixes in MolImporter.

        • Bugfixes in Peptide import.

        • Bad EOL (End Of Line) characters in the output of the InChi export was fixed.

      • GUI:

        • Double-clicking at selection unselects selected atoms.

        • Bugfix in printing: Texts components covered each others on the printed view table.

        • Removed unnecessary confirmation dialog by closing viewer detached sketch frame.

        • Deleting problem of multiple is solved.

        • Corrected the wrong location of plus sign in reactions.

      • API:

      • Bugfixes:

        • Bugfixes in Clean 2D.

        • Bugfixes in aromatization.

        • Fix parity error during H removal.

        • Potential deadlocks are fixed in MarvinSketch initalization.

        • Bugfix in Parity.

        • Bugfixes in calculator plugins (Tautomerization,pKa,Ionizer).

      January 9, 2007: Marvin 4.1.5

      Bugfixes:

      • Import/Export:

        • EMF/PDF creating does not drop HeadlessException in headless mode.

        • Fix EMF export bug (structure was invisible if canvas contained any text box).

        • Problem with both super atom and data sgroups in mol import.

        • ArrayIndexOutOfBoundsException in unique SMILES export.

      • Plugins:

        • In Tautomerization.

        • In Charge.

        • In pKa.

        • In PolarGroups.

      • Parity error during H removal.

      • Abbrev group problem with Me3SiO.

      December 7, 2006: Marvin 4.1.4

      • GUI:

        • Fix endless loop by rings join.

        • Exception in custom amino acid loading is fixed.

      • API:

      • Plugins:

        • Bugfix in MSA calculation.

        • Acceptor count and donor count is displayed on the plugin result window.

        • Bugfix in Major Microspecies calculation.

        • Minor bugfixes in pKa calculation.

        • Improved canonical tautomer generation.

      • Fixing broken peptide snake.

      • Bugfix in peptide import/export

      • Fixing minor bugs in clean 3D

      • Minor bugfix in Parity

      November 17, 2006: Marvin 4.1.3

      • API:

        • implicitizeHydrogens(int) is final. Subclasses should implement implicitizeHydrogens(int, MolAtom[]) instead.

      • Plugins:

      • MarvinSpace

        • Available in MarvinView as an optional 3D structure viewer.

        • Enhanced secondary structure visualization

        • Charmm pdb file support for both structures and crystals

        • Charmm Slab visualization

      October 16, 2006: Marvin 4.1.2

      • Import/Export:

        • InChi import can load structures without AuxInfo.

        • PDB import:

          • multi model proteins

          • nucleic acid backbone

          • non-standard pdb file related changes (missing mandatory blocks etc.)

          • charmm pdb ATOm record support

          • new class for Water molecules

          • support for DOD and TIP3 water

          • recognition of water H (even when it's denoted by O)

          • H-O-H bonds

      • GUI:

        • Improved display performance for large structures.

        • Bugfix in 3D rotation: Front atoms did not follow mouse movement.

        • Atom/bond coloring bug for abbreviated groups is fixed.

        • CxSmiles conversion in Edit Source window is fixed.

        • Marvin applications uses user's home as default directory in the File Open dialog.

      • New methods in API: JMSketch.undo(), JMSketch.redo(), MSketchPane.undo() and MSketchPane.redo()

      • MarvinSpace 1.3.2:

        • Charmm grid support

        • Displaying bonds in water molecules

        • Secondary structure visualization of nucleic acids

      • Others:

        • New S-group types: MIX (mixtures) and COM (components).

        • Daylight style mapping, mapping style guessing

        • Bugfix in Parity

      September 8, 2006: Marvin 4.1.1

      • Changes in MarvinSpace 1.3.1

      • Bugfixes:

        • Import/export:

          • In SMARTS import

          • In CxSmiles import/export

          • In 3D cleaning

        • Calculator plugins:

          • In pKa calculation

          • In logP calculation

          • in logD calculation

        • GUI:

          • Bugfix in pseudo atom display

          • Out of memory error by dearomatizing huge view tables

          • Minor bugs in loading/saving journal styles settings

        • Valence check bug

      August 4, 2006: Marvin 4.1

      May 25, 2006: Marvin 4.0.6

      • Bugfixes:

        • In aromatization.

        • In ionizer.

        • In Marvin Beans installer.

        • NullPointerException at refreshing empty cells in view table

      March 24, 2006: Marvin 4.0.5

      • Import/Export:

        • Minor bugfixes in SMILES and in SMARTS import.

        • Atom value in molfile.

        • Bugfix in PDB import.

        • Fix RXN incompatibility in MDLCompressor and in MolImporter.

      • GUI:

        • Speed-up slow viewer/sketcher performance on very large structures.

        • Shortcut for clear screen.

      • Plugins:

        • Adding the dot-disconnected molecule formula calculation to Elemental Analysis.

      • MarvinSpace:

        • Proper handling of H and LP on hetero groups.

        • Bond order perception.

      January 23, 2006: Marvin 4.0.4

      • Import/Export:

        • Non-ASCII characters are escaped in MRV import/export.

        • SMILES fields can be separated with TAB separators.

        • Slow image export bug fixed.

        • Minor bugs fixed in CML import.

        • Bugfixes in PDB import. Note, that PDB import is no longer compatible with the original implementation which is still applied for XYZ files. See release notes.

        • Bugfix in the SMILES import of aromatic bonds.

        • Minor CxSmiles import/export bug.

      • API:

        • Skin parameter/menu is denied in MViewPane and in MSketchPane. It is available ony in Marvin applets/applications.

        • Giving of the encoding in MolConverter was changed. Both input and output encoding can be specified.

      • GUI Bugfixes:

        • Link node drawing problem.

        • Copy from R-group definition did not work.

        • Last page of the view table was not printed if there were empty cells.

        • PropertyChangeEvent was not invoked when molecule was changed.

        • Down wedge looked like Up wedge on the toolbar.

        • Pseudo atom exception in sketcher.

        • Missing attachment point option in popup menu.

        • Right click raises exception for reactions with abbrev. groups.

        • Opening molfile with embedded groups caused exception.

      • Other Bugfixes:

        • Minor bugs in Calculator Plugins.

        • Clean 2D produced zero coordinates.

        • Edit source bullet import bug.

        • Potential deadlock at the closing of a MarvinSketch applet.

        • H removal throws exception on Markush structures.

        • Bug in Molecule.clone().

      November 10, 2005: Marvin 4.0.3

      • Bugfixes:

        • Minor bugfixes in MarvinSpace

        • In mol file export

      November 4, 2005: Marvin 4.0.2

      • Import/Export:

        • IUPAC InChi

        • 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.

        • Bugfixes.

      • Plugin:

      • Sgroup 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.

      August 19, 2005: Marvin 4.0.1

      • Trivalent radicals are displayed and their MRV import is fixed.

      • Bugfixes in cxsmiles, in 2D cleaning and in parity calculation.

      August 8, 2005: Marvin 4.0