Improved aromatization

Svg export gives UTF-8 encoded output.

Bugfixes:

• In CmlImport

• In 3D cleaning

• In dearomatization

Bugfixes:

• In plugin calculations.

• In parity.

• In 3D cleaning.

• In displaying of implicit hydrogens

Minor bugfixes in plugin calculations.

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.

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.

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.

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

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

Extended SMILES export: d option to write C/T info for ring double bonds.

API:

• New methods: JMView.isEmpty(), MView.isEmpty, JMSketch.isEmpty(), JMSketch.getAtomCount(), JMSketch.isAtomSelected, MSketch.isEmpty(), MSketch.getAtomCount, MSketch.isAtomSelected().

Plugins:

• TopologyAnalyserPlugin is available: calculates molecule properties from topology like number of various ring types, rotatable bonds.

• Calculation of molecular polarizability is available in PolarizabilityPlugin.

• Improved pKa and logP predictions.Test Results

• Added calculation of aromatic system and aromatic ring total charges in ChargePlugin.

Import/export:

• Link nodes are imported and exported in MDL molfiles and MRV/CML. See also the related API changes.

• MDL Molfiles:

  • Usg import option to ungroup all S-groups.

  • Atom coordinates are not rescaled in 2D V2 molfiles if the b import/export option is used with 0 argument.

  • MdlCompressor can compress Rxnfiles.

• SMARTS import: d option for Daylight-conform meaning of "H". Importing ambiguous SMARTS gets a warning message when not using this option.

• MRV (Marvin Document) and CML:

  • reaction arrow type is stored (default, resonance, retrosynthetic or equilibrium), see also the API changes.

  • valence is imported and exported

• Image export:

  • Options for displaying chiral structures.

  • Automatic generation of atom coordinates for 0D molecules.

API:

• New methods and functions:

  • MolAtom methods related to link nodes: getMaxRepetitions(), setMaxRepetitions(int), getMinRepetitions(), setMinRepetitions(int), isLinkNode().

  • RxnMolecule methods for accessing reaction arrow type: getReactionArrowType(), getReactionArrowTypeName(), setReactionArrowType(int), setReactionArrowType(String).

  • MSketch, JMSketch, MView and JMView applet methods

    • for accessing molecule properties: getMolProperty(String), setMolProperty(String, String), getMolPropertyCount(), getMolPropertyKey(int), getMProperty(int, String), setMProperty(int, String, String), getMPropertyCount(int), getMPropertyKey(int, int),

    • for accessing extra atom label and alias strings: setAtomAlias(int, String), getAtomAlias(int), setAtomExtraLabel(), getAtomExtraLabel(int), setAtomAlias(int, int, String), getAtomAlias(int, int), setAtomExtraLabel(int, int, String), getAtomExtraLabel(int, int).

  • Added JavaScript functions in marvin.js to get JVM and GUI ("awt" or "swing"): marvin_get_jvm() and marvin_get_gui().

• Changes:

  • Valence is not a query property any more, use MolAtom.setValenceProp(v) and getValenceProp() instead of setQProp("v", v) and getQPropAsInt("v").

  • The simpView applet parameter and MSketchPane.setSimpView(int) are deprecated, the simpView = 2 setting is removed. Use bondDraggedAlong and MSketchPane.setBondDraggedAlong(boolean) instead.

  • Serialization: DPoint3 and CTransform3D became Externalizable.

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

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

Bugfixes: memory leak and deadlock in sketcher bean.

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.

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.

MDL Molfile import: S-groups are contracted by default. Importing in expanded form; use the Xsg option.

Abbreviated groups: Abbreviations are given a priority over the element symbols. New abbreviations in the default abbeviated group list.

Improved pK_a, logP, logD calculation.

New methods in MolPrinter: getChiralitySupport(), getExplicitH(), isAtomSymbolsVisible(), isEzVisible(), setAtomSymbolsVisible(), setChiralitySupport(), setExplicitH(), setEzVisible().

Marvin Applets: Workaround for browsers without Java - JavaScript communication.

Mac friendly shortcuts for Cut, Copy and Paste.

Bugfixes:

• In MolConverter

• In the opening of the edit source window.

Bugfixes: in SMILES import.

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

Bugfix in the drawing of R-group attachment points.

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.

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

• Accuracy of pK_a 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.

Enhanced stereochemical representation support in extended molfiles.

Improved Charge and pKa calculation.

Bugfixes:

• In SMILES q option.

• In flip.

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.

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.

MDL import/export improvements:

• Extended reaction file import/export ("rxn:V3").

• Rgroups are supported in extended molfile import/export.

• RDfiles: Molecule and reaction type properties ($MFMT and $RFMT) are also imported and exported. Use the Molecule.getPropertyObject function to get such properties.

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

API changes:

• MoleculeGraph.calcCenter returns the geometrical center instead of the center of mass.

Bugfixes: R-logic bug.

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

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:

  • Data fields can be imported from multi-column files.

  • Better error checking at import: exception is thrown if a ring is formed from two neighboring atoms.

• 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

• New RgMolecule method: RgMolecule.addRgroupsTo.

• New flag RxnMolecule.RGROUPED for the getStructure(flags, f) method.

• New methods related to explicit Hydrogen removal: MoleculeGraph.calcDehydrogenizedGrinv, implicitizeHydrogens, MolAtom.isImplicitizableH.

• The protected removeNode(..., boolean changeNodes) and removeEdge(..., boolean changeNodes) methods in CGraph, MoleculeGraph, Molecule, etc. are replaced by removeNode(int i, int cleanupFlags), removeNode(CNode node, int cleanupFlags), removeEdge(int i, int cleanupFlags), removeEdge(CEdge edge, int cleanupFlags).

• Removed the malfunctioning RxnMolecule(parent) and RgMolecule(parent) constructors.

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

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.

3D cleaning.

New applet paremeters and bean properties

• detachable paremeter in the viewer.

• atomSymbolsVisible parameter instead of labels which became deprecated.

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:

  • MolExportModule.convert(Molecule) and close() throw MolExportException instead of IOException.

  • MolImporter.read() and importMol(byte[]) returns RgMolecule object only if R-groups are present.

• Initialization file saving:

  • MarvinSketch and MarvinView has a common initialization file in the $HOME/.chemaxon subdirectory.

  • MarvinPane.saveIni(), loadIni(), getIniFile() and setIniFile() are removed and replaced by UserSettings.save(String), UserSettings.tryToLoad(), and DotfileUtil.setDotDirName(String).

• Other bean related changes

  • Buttons and checkboxes in molecule cells can fire java.awt.event.ActionEvents and java.awt.event.ItemEvents as javax.swing.AbstractButton objects.

  • MViewPane.getCanvasComponent is deprecated. Use MViewPane.getVisibleCellComponent.

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

Bugfix: in Rxnfile import