December 11, 2007: Marvin 4.1.14

• API:

  • MDocument.simplifyMolecule()

• 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:

  • Background color settings for MolPrinter: MolPrinter.setBackgroundColor(java.awt.Color). (forum topic)

• 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:

  • Clear undo queue: MSketchPane.clearHistory().

  • New property to set default save format: defaultSaveFormat

• Bugfixes:

  • IUPAC Naming: fixed timeout errors.

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

• Calculator plugins:

  • Added dominant tautomer distribution calculation to Tautomeriztion plugin

    • cxcalc: dominanttautomerdistribution calculation

    • Related changes in TautomerizationPlugin API

  • Maximum allowed lenght of the tautomerization path can be set in Tautomeriztion plugin

    • See options of the tautomers calculation in cxcalc

    • New method in TautomerizationPlugin API: setMaximumTautomerizationPathLength(int)

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:

  • New image export option to display atom numbers.

  • New PropertyChangeEvent to indicate when selection changes.

  • New method in the MolPrinter class to set display options.

  • In the chemaxon.marvin.util.MolExportModule class, the optionSign2 field is replaced by getOptionSign() method.

• 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:

  • MarvinPane.setEnabled(boolean) is implemented.

  • MViewPane.setDraggable(boolean) allows or denies drag operation in cells.

  • New property change event in MarvinView: selectedIndex

  • Molecule.draw is deprecated, use chemaxon.marvin.util.MPainterUtil instead of that.

  • New MarvinSketch applet parameter: buttonmenubar

  • Text Box improvements

• 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:

  • MarvinView drops events by opening/closing detached sketcher/viewer.

  • New methods: ConformerPlugin.getEnergy(), ConformerPlugin.getEnergy(int).

• 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:

  • New option added to conformer plugin to set the conformer diversity limit. API: setDiversity(double)

  • New option added to pKa plugin to handle the acid/base state depending on the submitted micro state. API: setpKaPrefix(int), getpKaValues(int, int)

• 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

• Import/Export:

  • EMF export

  • Preliminary Mol2 import/export

  • Image export: atom and bond set colors, wire thickness, stick thicknessball radius, daylight down wedge, anybond style and atom mapping visibility can be specified.

  • Molecule and document properties with special data types (not only strings) are exported and imported in MRV, SDfiles and RDfiles. Supported data types: boolean, int, double, int[], Molecule, MDocument.

  • molconvert: optionally skips molecule on error and continues with the next molecule (option -g) (default: as before, exits on error).

• R-groups:

  • the maximum R-group number is increased to 32767 (from 32), the minimum is decreased to 0 (from 1). R0-R32767 are saved in MRV and V3 Molfiles. In V2 Molfiles, only R1-R999 are saved. The values of following constants are changed: MolAtom.RGROUP_MAX=32767, RgMolecule.RG_ID_MASK, RG_ID2_OFF, RG_ID2_MASK, RG_RESTH.

  • RgMolecule.indexOf(CNode), indexOf(CEdge), getNode(int) and getEdge(int) are applied to the graph union instead of the root structure.

• GUI:

  • Integration of MarvinSketch and MarvinSpace:

    • 3 Dimensional structure building: allows to modify ligand in the binding pocket.

    • Visualization of plugin results: 3D structure display, colored molecular surfaces.

  • Save options in viewer.

  • Viewer handles huge SD files.

  • Journal based drawing style templates

  • Multipage molecular documents

• Plugins:

  • Plugins are grouped

  • Added OrbitalElectronegativityPlugin to Charge group

  • Added StereoisomerPlugin to Isomers group

  • Added ConformerPlugin and MolecularDynamicsPlugin to Conformation group

  • Added GeometryPlugin and MSAPlugin (3D molecular surface area calculation - methods: van der Waals, solvent accessible) to Geometry group

  • Improved calculation methods in several plugins (pKa, logP, logD, etc.)

  • Possibility to save multimolecular plugin results from GUI (e.g. conformers)

• License handling: added graphical license handler interface

  • press the 'Manage license keys' button on the Edit / Preferences / Licenses tab, in MarvinSketch or MarvinView, or else

  • use the license command line script

• MarvinSpace 1.3

  • Ribbon representation of protein secondary structure

  • Interactive editing of molecules/ligands in MarvinSketch

  • Copy/Cut/Paste, Drag&Drop functions

  • High resolution image export in various formats (PNG, BMP, Targa, JPG), arbitrary size

  • New coloring types: secondary structure, rainbow, b-factor (temperature factor), SETOR residue colors, color palettes

  • Interactive change of the isovalue of Gaussian Cube surfaces

  • Enhanced selection tools: binding pocket, residues etc.

  • Enhanced labels (colors, size, placement), more built in types (e.g. residue labels, secondary structure label)

  • Improved error handling, out of memory does not terminate

  • Progress bar, better feedback about processes

• API changes:

  • Added Molecule.cloneMoleculeWithDocument(): clones the molecule with its non-molecular data (graphics objects: polylines, arrows; electron flows; text boxes).

  • Added Molecule.arrangeComponents(): avoids overlapping components (reaction components, R-group definitions) by translations.

  • Added MolImporter.skipRecord(), nextDoc(), getRecordCount(), getRecordCountMax(), estimateNumRecords(), seekRecord(int), isRewindable().

  • Sgroup.setGUIStateRecursively returns true if the state was changed.

  • CGraph became abstract, MoleculeGraph(parent) and Molecule(parent) constructors removed to avoid confusion with copy constructors.

  • The implementation of seeking in MolImporter required the extension of the molecule/document import interfaces:
    MolImportIface.isSkippingSupported(), skipMol() and MDocumentImportIface.getGlobalProperties() must be implemented.

  • The implementation of the sticky midpoints of MPolylines required incompatible changes in the graphics classes:
    MPoint.getX(), getY(), getZ(), setLocation(DPoint3) and setXYZ(double, double, double) are replaced by getLocation(CTransform3D) and setLocation(DPoint3, CTransform3D), MObject.calcCenter(DPoint3), transform(CTransform3D, int) and getPointRef(int) are replaced by by calcCenter(DPoint3, CTransform3D), transform(CTransform3D, int, CTransform3D) and getPointRef(int, CTransform3D).

• Applet/bean parameter changes:

  • Toolbar templates are not handled together with the other templates appearing in their own window. Toolbar template sets can be specified using the new ttmpls parameter, the old tmpls parameter is used only for other template sets.

• Deprecation:

  • bondWidth property/applet parameter is replaced by bondSpacing

  • RxnMolecule.getStructureCount, getStructure, addStructure, removeStructure methods are replaced by getComponentCount, getComponent, addComponent and removeComponent.

• AWT applets have been removed from Marvin Applets package.

• .NET support in Marvin Beans.

• Bugfixes:

  • Molecule.calcHybridization() assigns HS_S to hydrogen atoms.

  • Fixed potential memory leaks in Marvin applets.

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:

  • New parameter in ResonancePlugin: take major contributors (-m, --mcontrib).

  • New parameter in TautomerizationPlugin: take dominant tautomers (--d, --dominants).

  • Bugfix in TautomerizationPlugin.

• 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

• MarvinSpace 1.0-alpha is released as part of Marvin 4.0.
  MarvinSpace is a 3D molecular structure visualization tool for displaying macromolecules, protein-ligand complexes as well as small molecules.
  Release notes: At present MarvinSpace is available as standalone desktop application and as Java Applet. Java Beans and the public API will be released later. See also Known Issues.

• Import/export

  • Link node outer bonds imported and exported in CML, MRV and MDL.

  • MRV: atom and bond set colors are stored, animation of a chemical process can be stored. Parity is stored in 0D.

  • CML: MRV tags and attributes are no longer supported but they can be imported. If you have a CML document that is created by an older Marvin, it is recommended to save that in MRV format!

  • RDfiles with missing "M END"s are also imported.

  • MS BMP image format (only export).

  • SDF import: reading sdf-s containing empty structures

  • Atom types are read in case insensitive manner in mol/sdf import.

  • cxsmiles import/export: Pseudo atom types

  • SMILES import/export: Handling of radicals and unusual valences

  • Support for localized encoding of structure files.

• Double bond with a wiggly bond neighbour are treated as unspecified E/Z configuration.

• Improved unique smiles canonicalization

• Improvements in chirality calculation

• Clean wedges function

• GUI:

  • New templates in MarvinSketch: Aromatics, Bridged Polycycles, Bicycles, Crown Ethers, Cycloalkanes, Fullerenes

  • My Templates are available in the MarvinSketch applet (only in Swing).

  • Wrap long data fields in MarvinView

  • Shortcut + SHIFT click: automatically ungroup abbreviated groups

  • View implied lone pairs

  • Improved rendering quality

  • Attach data to atoms (Data S-groups)

  • Drawing of h<n>, D<n>, s<n>, s*, rb<n>, rb*, u query properties

• Plugins

  • Calculator plugin handling is completely rewritten:

    • Dynamical loading of plugins and parameter panels based on configuration by PluginFactory

    • Separated graphical plugin result display: CalculatorPluginDisplay

    • Graphical parameter panels are generated from XML: <plugin class name>Parameters.xml if exists, otherwise asked from the display class: CalculatorPluginDisplay.getParameterPanel()

    • Configuration files calc.properties (Calculator) and plugins.properties (MarvinSketch, MarvinView) together with the parameter panel configuration XMLs and custom plugin JARs are placed in the xjars directory under Marvin root.

    • CalculatorOutput used by Calculator is renamed: CalculatorPluginOutput (and subclasses are found automatically by the following naming convention: output class name = <plugin class name>Output)

    • CalculatorPlugin API is slightly changed.

    • A custom plugin example with test application is added.

  • Added MRV result molecule output to cxcalc.

  • Added options JPEG / PNG image save and copy & paste image to chart result display in MarvinSketch / MarvinView.

  • Changes in specific plugin calculations:

    • Added IsoelectricPointPlugin.

    • Added TautomerizationPlugin and ResonancePlugin.

    • Added microspecies distribution calculation (msdistr) to cxcalc.

    • New topological properties in TopologyAnalyser and TopologyAnalyserPlugin:
      asymmetricAtomCount(), balabanIndex(), carboRingCount(), carboaromaticRingCount(), cyclomaticNumber(), distanceCount(int atom, int distance), distanceDegree(int atom), eccentricity(int atom), hararyIndex(), hyperWienerIndex(), isAsymmetricAtom(), isConnected(), isConnected(int atom1, int atom2), plattIndex(), randicIndex(), shortestPath(int atom1, int atom2), stericEffectIndex(), szegedIndex(), wienerIndex(), wienerPolarity().

• API

  • PeriodicSystem: new radius functions getAtomicRadius(int z), getCovalentRadius(int z), getVanDerWaalsRadius(int z).

  • MSketchPane: new methods isCloseEnabled(), setCloseEnabled(boolean), getMrvWithSettings(), setMrvWithSettings(String), getImage(scale), getImage(size), getBoundRectSize().

  • MoleculeGraph.getLocalParity(int) to calculate local parity of an atom

  • Incompatible API changes:

    • MarvinPane.setAtomSymbolsVisible(boolean) applies to 3D molecules only; atom symbols are always visible in 2D.