July 27, 2005: Marvin 3.5.9

  • Improved aromatization

  • Svg export gives UTF-8 encoded output.

  • Bugfixes:

    • In CmlImport

    • In 3D cleaning

    • In dearomatization

June 29, 2005: Marvin 3.5.8

  • Bugfixes:

    • In plugin calculations.

    • In parity.

    • In 3D cleaning.

    • In displaying of implicit hydrogens

May 28, 2005: Marvin 3.5.7

  • Minor bugfixes in plugin calculations.

May 17, 2005: Marvin 3.5.6

  • R/S and canonical smiles calculation speedup.

  • 3D:

    • Improved 3D cleaning efficiency.

    • New Clean3D options. Time limit in the 3D cleaning process.

  • Bugfixes:

    • The R/S label is not displayed on the first atom of the structure.

    • Fonts are not scaled on the printed page.

    • Bug fixes in R/S calculation.

    • Implicit hydrogen hides upper bond.

    • Bug fix in cxsmiles export.

March 29, 2005: Marvin 3.5.5

  • Plugins: logP calculation is supplemented with metal fragments.

  • Bugfixes:

    • RGfile import with nonstandard header.

    • Fixing bugs according to the user's response and improvement of pKa calculation quality.

January 31, 2005: Marvin 3.5.4

  • Smarts import: atom expressions of type [C,c] are imported as [#6].

  • Bugfix: 3D cleaning can cause Java 1.4.2_06 VM to crash.

January 24, 2005: Marvin 3.5.3

  • Bugfix: Import of SMILES containing atoms with "unspecified atomic number" (*) is fixed.

January 11, 2005: Marvin 3.5.2

  • Colored MarvinView labels at celular level

  • Bugfixes:

    • Error in extended SMILES export

    • NullPointerException at adding new structure to My Templates

    • Error in drawing multiple groups

November 29, 2004: Marvin 3.5.1

November 5, 2004: Marvin 3.5

August 16, 2004: Marvin 3.4.3

  • New applet parameter: molChanged0 to evaluate a JavaScript code when the molecule is loaded.

  • Bugfixes: NullPointerException in shapely color mode, deadlock in MarvinSketch applet.

August 5, 2004: Marvin 3.4.2

  • Bugfixes: memory leak and deadlock in sketcher bean.

July 29, 2004: Marvin 3.4.1

  • Reaction AutoMapper class API is available.

  • Calculator Plugin API usage examples in class headers.

  • Atom symbol/label font can be changed using the atomFont applet parameter.

July 1, 2004: Marvin 3.4

  • Import/Export

    • New formats: ChemAxon Extended SMILES and SMARTS, Gaussian Cube.

    • Full support of SMARTS. Added features:

      • Recursive SMARTS $()

      • Logical expressions in atom and bond: high and low priority "and"(& and ;), "or" (,) and "not" (!).

      • Degree atom query property (D)

      • Implicit hydrogens atom query property (h)

      • Chiral or unspecified atoms @?, @@?

      • Ring bond query property (@)

      • Conditional directional bonds: /?,\?

    • CML and Marvin Document Format fix: atom aliases and query strings are imported and exported.

    • MDL Molfiles: S-group parent list (M SPL in V2, PARENT in V3) and expansion information (M SDS EXP in V2, ESTATE in V3) are stored.

    • Incompatible API change in the MolImportIface interface: molecule import modules must implement the createMol() method.

    • MolConverter and MolExporter fix: created text files are in the local text format (instead of unix) if the useSysEOL boolean argument is true. The molconvert program writes OS dependent end of lines always.

  • S-groups

    • Embedded S-group support (in MDL Molfiles and Marvin Document Format).

    • API changes in Sgroup, SuperatomSgroup, and MultipleSgroup: the copy and the newInstance methods are replaced by copy constructors and cloneSgroup.

  • Other

    • Line thickness can be set for wireframe mode using the wireThickness applet parameter and the MarvinPane.setWireThickness bean method.

    • Line thickness for graphics line, polyline, rectangle and text box objects can be set using MPolyline.setThickness.

March 9, 2004: Marvin 3.3.3

February 4, 2004: Marvin 3.3.2

  • Bugfixes: in SMILES import.

January 29, 2004: Marvin 3.3.1

  • Mac OS X: MarvinSketch and MarvinView applications use the screen menu bar.

  • Bugfix in the drawing of R-group attachment points.

January 14, 2004: Marvin 3.3

  • Atom and bond sets

    • Colorable bond sets are introduced, see the bondSet and bondSetColor applet parameters, the MView.setBondSetColor() applet method and the MarvinPane.setBondSetColor() bean method.

    • Atom and bond set coloring can be used together with other color schemes. Atoms and bonds in set 0 are displayed in Monochrome, CPK, Shapely or Group color scheme, but other sets are displayed with atom/bond set colors if the value of the setColoringEnabled applet parameter is true (default).

    • Deprecation:

      • Use the atomSet applet parameter instead of set, atomSetColor instead of setColor and the MView.setAtomSetColor() and MarvinPane.setBondSetColor() methods instead of setSetColor.

      • Use colorScheme="mono" and setColoringEnabled=true settings instead of the deprecated "atomset" color scheme.

  • Import/export:

    • Marvin Document file format

    • Multiple Sgroup support for MDL molfiles

    • New image export option to switch off antialiasing: noantialias.

    • CML improvements: support of CML2 atom/bond attributes (instead of the deprecated builtins), reactions, stereochemistry, residues. Because of efficiency reasons, deprecated CML-1 data types are not supported any more.

    • Base64 encoding/decoding.

    • Import options for input files are specified in braces instead of parentheses ("file{options}") to avoid conflicts with ugly SMILES strings ending with a branch specification. For backward compatibility, parentheses still work after filenames (but not after SMILES strings).

  • 3D:

    • Analitic gradients implemented in Dreiding forcefield for optimization and Clean 3D

  • Document editing with graphics objects in sketcher

    • The MDocument class stores the molecule and other graphics objects like polylines and rectangles. The document can be saved in Marvin Document format.

  • Calculator plugins

    • Support electrolite concentration is taken into account in logP and logD calculations.

    • Concentration of K, Na and Cl ions can be adjusted in the range of 0 - 0.25 mol/l.

    • logP calculation of zwitterionic compounds also have been improved with considering distance correction factors.

    • pKa calculation have been extended to carbon-bases. Now basic pKa estimation of Indole derivatives available. Both acidic and basic pKa values are displayed. Microspecies distribution is shown on chart.

    • Accuracy of pKa calculations is improved for heterocyclic compounds.

    • Calculation of polar surface area (PSA) based on 2D topological (TPSA) information of molecules are available.

  • Others:

    • Recognition of more than four hundred chemical abbreviations.

    • Help documents can be specified by applet parameters: sketchHelp, sketchQuickHelp, viewHelp, viewQuickHelp.

    • Molecule.draw paints the molecule to a graphics context.

    • Standard residue names returned by MolAtom.residueSymbolOf(int) are not all upper case, only the first letter ("Ala" instead of "ALA").

    • Marvin GUI: Set the visibility of the atom chirality (R/S) labels from View/Misc menu.

    • Double click in Windows operating systems opens chemical files with the MarvinView application.

    • Deprecation: SketchMolecule (replaced by MDocument), SuperAtom.updateSgroupCrossings() (replaced by Sgroup.findCrossingBonds())

    • Incompatible change: chemaxon.struc.sgroup.Contractable interface removed, Expandable changed. This change was required because MDL's incomplete multiple group expansion had to be simulated for proper molfile export.

  • Bugfixes: in MViewPanel.setParams, in Dreiding forcefield, PDB import, atom lists in V3 molfiles, resize of MViewPanel and MSketchPanel, R-logic, etc.

July 28, 2003: Marvin 3.2

June 30, 2003: Marvin 3.1.4

  • RDfiles containing internal and external regnos: the first molecule or reaction type property is supposed to be the main structure.

  • API changes

    • Removed the broken RxnMolecule.moveReactionArrow method.

  • Calculator plugins:

    • logP: New atom types.

    • pKa:

      • Hydrogen bound defined between aromatic carboxyl and phenolic hidroxyl groups in pKa plugin.

      • Calculation of the sulphonamid acid molecules were improved.

      • In calculation of third order amins strain is considered.

June 2, 2003: Marvin 3.1.3

  • Molecule file formats:

    • Extended reaction files: AGENTS are imported and exported (in a non-standard way, because MDL's standard format does not support them).

    • SMILES import: error checking improved.

    • PDB import/export: bonds of standard residues are not exported and not guessed from coordinates at import. Full atom names (including remoteness indicator and branch designator) are imported and exported.

  • 2D and 3D:

    • Background color, rendering style and navigation mode are stored separately for 2D and 3D. Cleaning a molecule in 3D also switches automatically to the 3D parameter set in that cell. Cleaning in 2D switches back to the 2D parameters.

    • clean2dOpts and clean3dOpts parameters.

May 6, 2003: Marvin 3.1.2

  • MDL import/export improvements:

  • S-groups: automatic contraction after import in sketcher and viewer.

  • API changes:

  • Bugfixes: R-logic bug.

April 30, 2003: Marvin 3.1.1

  • JRE bug workaround (inappropriate lines were drawn on the Marvin panel).

April 29, 2003: Marvin 3.1

  • Applets

    • Java 1.0 compatibility is no longer maintained. The minimum Java VM version required to run the applets is 1.1 (Netscape 4.06, MSIE 4 or later version).

    • The Swing version of the unsigned applets are no longer available. Use the signed applets instead. To unsign signed jar files, see the FAQ.

    • The deprecated installer for Marvin Applets is no longer maintained. The set of downloadable Marvin Applets packages has been reduced.

  • Plugins:

    • New plugin: Atom polarizability

    • Chart display in logD plugin

  • Molecule import/export improvements:

    • SMILES:

    • PDB: residues are imported as Sgroups, Sgroups are exported as residues.

    • Molfiles:

      • Sgroups are also imported as (PDB) residues. As a consequence, the PDB-specific coloring styles, "shapely" and "group", are also applicable to molfiles containing Sgroups.

      • Extended (V3) molfile export.

      • Changes in V2 format:

        • 3D molecule coordinates are stored in Angstrom units. The unit can be specified as an import option.

        • Illegal atom map values (from molfiles generated by the IDBS ChemXtra data cartridge) are not considered to be error at import.

  • API changes

March 21, 2003: Marvin 3.0.2

  • Bugfixes: contracted S-groups are automatically expanded before exporting in molecule file formats (PDB, SMILES, XYZ, ...)

March 17, 2003: Marvin 3.0.1

  • RGfile import/export: root structure can be a reaction.
    Note that mixing RGfiles and Rxnfiles is not possible in a standard way so these files can only be imported by Marvin.

  • PDB import: HETATM records are recognized.

  • Bugfixes: Invisible atom symbols at image export in Molecule.toObject(String), Sgroup export in MDL formats, Sgroup-related NullPointerException in viewer.

February 10, 2003: Marvin 3.0

  • 3D cleaning.

  • New applet paremeters and bean properties

  • API improvements and simplifications:

    • chemaxon.struc:

      • CGraph and Molecule are not thread safe any more but their methods became 20-30% faster.

      • Created the SelectionMolecule class for molecule selections, removed the CGraph.selection field.

      • Created the MoleculeGraph class as the direct ancestor of SelectionMolecule and Molecule.

      • RgMolecule and RxnMolecule changes:

        • Nodes and edges are only stored in subgraphs (root structure, R-groups, product/reactant/agent structures).

        • The graph union is returned by the MoleculeGraph.getGraphUnion() method.

        • Methods like getNodeCount(), getEdgeCount(), getNode(i), getEdge(i) call the root structure's corresponding method in RgMolecule or the graph union's method in RxnMolecule.

      • CGraph.findFrags() and CGraph.findFrags(boolean) are replaced by CGraph.findFrags(Class) and Molecule.findFrags()

      • CGraph.cloneNodes() and cloneEdges() renamed to getNodeVector, getEdgeVector.

      • CGraph.reallyContains(CEdge) and countRealEdges() removed.

      • CGraph.getSSSR() returns an int[][] array instead of CEdge[][]

      • The MolAtom.flags, MolAtom.countFlags and MolBond.flags fields became private.

    • Molecule import/export:

    • Initialization file saving:

    • Other bean related changes

  • Template button title is specified using the abbreviation SDF property instead of title.

  • Bugfix: in Rxnfile import