Changes, new parameters, upgrade problems

• Marvin 3.3.2
  • Bugfixes: in SMILES import.
• Marvin 3.3.1
  • Mac OS X: MarvinSketch and MarvinView applications use the Mac OS X menu bar.
  • Bugfix in the drawing of R-group attachment points.
• 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 parantheses ("file{options}") to avoid conflicts with ugly SMILES strings ending with a branch specification. For backward compatibility, parantheses 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.
• Marvin 3.2
  • Enhanced stereochemical representation support in extended molfiles.
  • Improved Charge and pKa calculation.
  • Bugfixes:
    • In SMILES q option.
    • In flip.
• 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.
• 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.
• Marvin 3.1.2
  • 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.
• Marvin 3.1.1
  • JRE bug workaround (inappropriate lines were drawn on the Marvin panel).
• 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:
      • 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.
• Marvin 3.0.2
  • Bugfixes: contracted S-groups are automatically expanded before exporting in molecule file formats (PDB, SMILES, XYZ, ...)
• 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.
• Marvin 3.0
  • 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 ActionEvents and ItemEvents as 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
• Marvin 2.10.5
  • atomMappingVisible is a new applet/bean parameter and property.
  • Bugfixes: Copy and Copy as smiles bugs under Mac. Hotkey bug in swing version of Marvin applets at Java 1.4.
• Marvin 2.10.4
  • skin applet/bean parameter and new menu option (only in SWING).
  • Improved SD file import (DTn fields).
  • Bugfix: NoSuchMethodError at drawing R-group definition in AWT mode (if Java version is earlier than 1.2).
• Marvin 2.10.3
  • grinv is a new applet/bean parameter and property.
  • Bugfix: in SDfile import.
• Marvin 2.10.2
  • Bugfixes:
    • Improved printing layout of MView tables.
    • Improvements in Copy / Paste of reactions.
    • Fixed calculation of molecule bounds.
• Marvin 2.10.1
  • Molweight calculation.
  • Handling agents of reactions.
  • Bugfix: MolConvert.convert() cleans imported SMILES.
• Marvin 2.10 (2.9.13)
  • Signed Marvin applets
  • Open, save, cut and paste can be used with signed applets. Examples can be launched by selecting "Signed applets".
  • Marvin applications with Java Web Start
    • Examples for using the MarvinSketch and the MarvinView applications via Internet.
  • New applet/bean parameters
  • valenceErrorVisible applet/bean parameter and property in MarvinSketch. Its value can be also modified from menu: View/Misc/Valence Errors.
  • reactionErrorVisible applet/bean parameter and propert in MarvinSketch. It can also be set from menu: View/Misc/Reaction Errors.
• Marvin 2.9.12
  • Import/Export
    • CML import and better export.
    • Atom map support for Rxnfiles and reaction SMILES.
    • Atom label font size and double bond width can be set for image export using the atsiz and bondw options.
    • If an error occurs while reading a multi-molecule file (an SDfile for example), the remaining parts of the current molecule can be skipped and the file pointer can be positioned to the next one.
      • MolImportIface interface changed, the skipToNext() method introduced
      • MolImporter.skipToNext()
  • Stereochemistry
    • chiralitySupport applet/bean parameter
    • ezVisible applet/bean parameter
  • Other new applet/bean parameters and properties
    • popupMenusEnabled bean property
    • atomNumbersVisible applet/bean parameter
  • Other API changes
    • The MolAtom.SELECTED and VALENCE_ERROR constants are not public any more, they are replaced by the isSelected, setSelected, hasValenceError and setValenceError methods.
    • deprecated methods removed: MolAtom.getAbbrev() and abbrevOf() replaced by getSymbol() and symbolOf()
    • CNode.copy(CNode), MolAtom.copy(CNode) does not copy the edges, CNode.clone() became abstract, MolAtom.clone() does not clone the edges.
  • Fixed: memory leak and printing problems with Java Plugin, atom lists in molfile, bugs during reaction drawing, MarvinView stdin reading, etc.
• Marvin 2.9.11
  • SMARTS improvements: "a" (aromatic) and "A" (aliphatic) atom primitives recognized even outside of brackets, ":" (aromatic bond) symbol recognized at file format recognition.
  • New importConv option (c) to automatically clean up the molecule.
  • Image export improvements
    • scale option
    • getImageSize method
  • bondWidth applet parameter and setBondWidth bean method.
  • API changes
    • Molecule.toFormat, toBinFormat, toObject, MolExportModule.open and MolExportModule.parseOption throw IllegalArgumentException instead of IOException if bad format string was specified
    • "mag" property renamed to "scale", setMag, getMag, maxMag methods became deprecated (MSketchPane, MSketch, JMSketch, MolPrinter) and replaced by setScale, getScale, maxScale
  • Fixed: delayed printing, image export option parsing, cml:A, etc.
• Marvin 2.9.10
  • Occassional NullPointerException in MolInputStream.canBeJTF() fixed.
• Marvin 2.9.9
  • Extra templates can be specified using the xtmpls parameter.
  • New importConv option (H) to add/remove explicit Hydrogen atoms.
  • Common aromatization and explicit Hydrogen addition/removal options for molecule export modules: a, +a, -a, H, +H, -H
  • Incompatibilities:
    • In PdbExport, Hydrogens are added with the common "H" option instead of "h".
    • MolExportModule.getOptions() became protected
• Marvin 2.9.8
  • Apache Batik 1.1.1 classes needed for SVG export are included with Marvin Beans and Applications
• Marvin 2.9.7
  • Image export:
    • Scalable Vector Graphics (svg) format.
    • Implicit Hydrogen display options can be specified for the MolConverter utility and the toObject and toBinFormat methods.
  • MViewPane.applyRotationMatrix, applyRotationMatrixes: methods to apply the viewing transformation on the atomic coordinates appearing in the molfile
• Marvin 2.9.6
  • No autoscale is the default in the sketcher.
• Marvin 2.9.3
  • MView applet: atom sets can be selected for different coloring, using the setN.M parameters.
  • MolPanel changes:
    • autoScale property was added, it can be accessed via setAutoScale() and getAutoScale() methods.
  • SketchPanel improvements:
    • Autoscale is avaible both in AWT and Swing versions.
    • depending on the autoScale property automatic scaling is done when loading molecules
    • The select all function can be triggered by Ctrl+A.
    • Bug fixes.
• Marvin 2.9.2
  • New applet and bean methods:
    • getTabScale(i) to query the magnification in a cell
    • getBestTabScale(i) to query the best magnification value for a cell
    • getBestTabScale() to query the smallest best scale value
  • MViewPane bean only:
    • autoTabScale property enables automatic uniform scaling of cells.
• Marvin 2.9.1
  • MarvinView improvements
    • JavaScript code can be called at image click in the applet using the "js:javascript" syntax.
    • Use tabScale to set the magnification in the molecule cells (instead of automatic scaling), use winScale to set the magnification in the zoom windows (same as the old mag parameter).
    • Many molecules in one cell. Molecules coming from multi-molecule files are merged into one molecule object containing atom sets if MULTISET is specified as the first import option in the mol parameter. To display only the specified sets, use the showSets applet parameter, the MView.setSetVisible() applet method or the MarvinPane.setInvisibleSets bean method.
    • Atom set colors can be changed using the setColor applet parameters, the MView.setSetColor() applet method or the MarvinPane.setSetColor() bean method.
    • "Shapely" and "Group" color schemes (for PDB input).
  • Class library changes
    • MULTISET can also be passed to the MolImporter constructor through the option string
    • The newInstance() method of CGraph, Molecule, etc. became public.
  • PDB
    • Residue symbol is imported for standard residues.
    • Residue sequence number is imported.
    • New export and import options.
    • Export does not hydrogenize the molecule automatically, use the h option for this.
• Marvin 2.9
  • Rxnfile, RDfile and Reaction SMILES import/export
  • Molecule.getComment() and setComment() methods
  • New MarvinSketch applet parameter and bean methods: reactionSupport, getReactionSupport(), setReactionSupport().
  • MolExportModule API changed: the open method has a return value
• Marvin 2.8.4
  • Default value of the "format" property is "DEFAULT" instead of null
• Marvin 2.8.3
  • Beans:
    • List of properties to save/load to/from the initialization file (~/.mview, ~/.msketch) can be set using the setIniProps method.
    • Beans can be used in applets that cannot access to disk files:
      • Ini file is not loaded automatically, only when sketchPane.loadIni() or viewPane.loadIni() is called.
      • Ini file is not saved automatically, only if the value of the saveIniEnabled property is true.
  • The dispopts applet parameter is deprecated, use implicitH, explicitH or navmode instead.
• Marvin 2.8.1
  • New bean methods and applet parameters for customizing 3D rendering: stickThickness, ballRadius.
  • java.awt.Image objects can be created from molecules using mol.toObject("image");
  • API for import module creation (MolImportIface).
  • Import file format can be specified, by writing "filename(format:)" or "filename(format:options)" in the mol applet parameter, or in the command line of molconvert, msketch or mview.
  • MSketchPane: setMol(File, String) method added, where string can contain the import options, in one of the following forms: "format:options", "format:", "options". The old setMol(File) method removed. MViewPane: setM(int, File, String) added.
  • MolExportModule.sbuf field renamed to stringBuffer.
  • MolAtom.getAbbrev() and abbrevOf are deprecated, use getSymbol() and symbolOf() instead.
• Marvin 2.8
  • New 3D rendering mode: sticks.
  • Display quality can be controlled with an applet parameter.
  • Molecule import/export:
    • New XYZ import options: bond length cut-off (f...) and maximum number of connections (C4,H1,Cl1)
    • Automatic dearomatization after molecule loading.
    • All export modules recognize the "a", "+a" (aromatize) and "-a" (dearomatize) options. Example: "smiles:a"
  • Class library, beans
    • Molecule.aromatize()
    • Bugfix: MViewPane.getCellCount() returns the total number of cells, not just the number of visible cells.
    • PropertyChangeEvents generated when the molecule is changed in the sketcher or viewer component.
    • Event handling fix: PropertyChangeEvent source is the the bean component, not the internal SketchPanel or ViewPanel.
• Marvin 2.7.11
  • New rendering style: "ball & stick".
  • Class library, beans:
    • New image export options: rendering style and color scheme.
    • Image export options must be separated by commas in format descriptor strings.
    • Molecule.toBinFormat method to convert molecules into binary formats such as JPEG/PNG/PPM.
    • The type of the rendering, colorScheme, implicitH, downWedge, navmode properties in PropertyChange events is String just like the argument type of their set methods. (Previously, the two types did not match.)
• Marvin 2.7.9
  • Binary export formats: GZIP, JPEG, PNG, PPM
  • User defined export module creation by overriding chemaxon/marvin/util/MolExportModule.
• Marvin 2.7.6
  • Text field (T) component for MView tables.
  • cacheMols applet parameter for caching loaded molecules.
  • loadMols applet parameter for preloading molecules.
  • Molecule.getProperty(key) is not case sensitive.
• Marvin 2.7.5: Optional spin vector.
• Marvin 2.7
  • File formats
    • New: XYZ import
    • New: Extended Molfile (V3.0) import.
    • CML export options changed, cml:1 -> cml, cml:0 -> cml:A, cml:A writes three coordinates for each atom even if the molecule is 2D (so Jmol can read the file)
  • MView applet:
    • Animated XYZ files can be displayed
    • New parameters: animFPS, animDelay, animSync.
  • MarvinSketch Applet/Bean:
    • New: File/New menu item in the bean. If your application using the bean has a File/New Window menu item, then File/New should be moved to File/New/Clear current, and File/New Window should be moved to File/New/New Window. See the MarvinSketch application source (marvinbeans/examples/sketch/chemaxon/marvin/Sketch.java) for details.
    • "Visual fragment placement" can be disabled: use the simpView parameter or the View/Misc/Object in Hand option if you do not like to see what you are doing.
    • Bond length related changes.
  • Class library:
    • Changes related to atomic coordinates and transformations
      • New: CTransform3D class for general 3D transformations (like in Java3D)
      • Molecule.rot(...), tra(...), magnify(...) removed, use transform(CTransform3D T) instead
      • Atom coordinates became absolute
      • Molecule.getO() and setO() replaced by getLocation() and setLocation()
      • Molecule.getCenter() renamed to calcCenter(), and it calculates center of mass instead of geometrical center
      • New:Molecule.moveTo(location)
    • CGraph.indexOf changes
      • Splitted into two methods, indexOf(CNode atom) and indexOf(CEdge bond)
      • Speed improvement. CNode and CEdge has an index field that contains the object's index in its parent graph. Calling the parent graph's indexOf method returns the value of this field. The index is only searched (in the old way) when the CGraph is not the direct parent.
    • Valence rules
      • New: MolAtom.ionChargeOf(Z)
      • MolAtom.negoxOf(Z, boolean) removed, negOxOf(Z), posOxOf(Z) created instead
    • SDF properties
      • "name" and "informat" are no longer stored in the properties hashtable, they became fields of Molecule
      • Molecule.getProperties() removed
      • Molecule.clearForImport() -> clearForImport(name)
      • New methods in Molecule: getName, setName, getInputFormat, setInputFormat, getPropertyCount(), getPropertyKey(n), getPropertyKeys()
    • Bond length related changes.
  • API simplification: internal bond length of Marvin fixed to be MolBond.CCLENGTH
    • bondlen, rescaling applet/bean parameters, setBondlen, getBondlen, setRescaling, getRescaling methods removed, use MSketch.getMol("mol:b=XXX") instead of <param NAME="bondlen" VALUE="XXX">
    • The bondlen argument of Molecule.clean(dim, bondlen, opts) removed, use clean(dim, opts)
    • MolBond.DEFAULT_LENGTH renamed to MolBond.CCLENGTH
    • MolBond.getDesiredLengthRatio() removed, use the new dimension dependent Molecule.getDesiredLength(bond) method instead
    • MolAtom.covalentRadiusOf(Z) -> covalentRadiusOf(Z, bondOrder)
• Marvin 2.6
  • The "style" applet parameter renamed to " rendering because of a conflict with a Netscape keyword. The getStyle, setStyle methods of the beans are also renamed to getRendering, setRendering.
  • New rendering style: "Wireframe with Knobs".
  • Atoms can be highlighted in the MView/JMView applets by specifying a selection.
  • All query atoms and extra bond types can be enabled by omitting the queryAtoms, atomStrings, and extraBonds parameters.
  • "Cis or Unspecified" and "Trans or Unspecified" bond types; "ctu" in extraBonds.
  • Cleaning options can be specified using the cleanOpts applet parameter.
  • Optional down wedge bond orientation (MDL or Daylight) using the downWedge parameter.
  • New MView/JMView applet methods:
    • getAtomCount(moleculeIndex) to query the number of atoms in a molecule cell
    • isSelected(moleculeIndex, atomIndex) to query whether the specified atom is selected or not
    • selectAtom(moleculeIndex, atomIndex, select) to (un)select an atom
    • selectAllAtoms(moleculeIndex, select) to (un)select all atoms
  • Real scrolling in MView!
    • The applet is scrollable if visibleRows is less than rows or visibleCols is less than cols.
    • The names of the layouti and parami parameters changed to layout and param for the molecule cells, layoutH and paramH for the optional header.
    • The scroll parameter ceased to exist.
  • Class library:
    • RgMolecule for R-groups
    • Thread safe API for molecules
    • New methods in CGraph: getCtab(), getBtab(), fragments(), findFrag(), getFragIds(), getLock(), getParent(), etc.
    • New methods in CNode: getLigand(i), getEdge(i), getEdgeCount()
    • CNode.findFrag() and CGraph.fuseFrag() removed
    • CGraph.getEdge(i), CGraph.getNode(i), Molecule.getAtomArray() created; CGraph.getEdges(), CGraph.getNodes(), Molecule.getAtoms(), Molecule.getBonds() removed
    • Molecule.reuseAtom(Z, i) and Molecule.endReuse(na) created, MolAtom.reuse(Z, mol, i) removed
    • The two-argument MolAtom.setCharge method removed. Instead of a.setCharge(charge, false), use a.setCharge(charge); a.setFlags(0, MolAtom.FIX_CHARGE);
• Marvin 2.5
  • SMILES import
  • Class library:
    • CGraph.fuseFrag(CNode a) has only one argument.
    • CGraph.removeNode and removeEdge instead of remove and removeRef; removeEdge leaves edge.node1 and edge.node2 unchanged (they were set to null in removeRef).
    • MolBond.setFlags(int flags, int mask) method introduced.
    • Stereochemistry: double bonds can also be UP/DOWN (not just CIS/TRANS); CIS and TRANS information can also be stored (not just EITHER). The MolBond.getStereo and setStereo methods and the UP, DOWN, EITHER constants ceased to exists, the STEREO1_UP, STEREO1_DOWN, STEREO1_EITHER, STEREO2_CIS, STEREO2_TRANS, STEREO2_EITHER, STEREO_CARE flags introduced instead.
    • MolBond.getTopology/setTopology ceased to exist, the TOPOLOGY_RING, TOPOLOGY_CHAIN flags introduced instead.
• Marvin 2.4.2
  • Scrolling in the MView and JMView applets. See the visibleRows parameter.
• Marvin 2.4
  • Structures are colorful by default. Colorization can be disabled by setting colors=mono, both in the sketcher and the viewer.
  • Spacefill rendering can be enabled instead of wireframe by using the style parameter.
  • Atom labels can be hidden with the labels parameter.
  • Up/down and cis/trans either bonds
  • Classes in chemaxon/beans moved to chemaxon/marvin/beans. The MarvinSketch bean is chemaxon.marvin.beans.MSketchPane, the MarvinView bean is chemaxon.marvin.beans.MViewPane.
• Marvin 2.3.1 The basic applet tag for MSketch and MView is simplified, and also generalized to work with or without Sun's Java Plugin.
• Marvin 2.3
  • New file format: PDB (for simple, non-macro molecules)
  • Changes in template handling
    • The four template sets that come with Marvin became default. Templates only have to be specified as applet parameter if you need a different template set.
    • Templates moved to directory chemaxon/marvin/templates/ (from templates/).
    • File extension changed to .t (from .cssdf).
      This change was required because of a Netscape restriction related to the loading of JAR file resources.
    • The JAR files marvin.jar and jmarvin.jar contain chemaxon/marvin/templates/generic.t, so the firewall problem ceased for the generic template set.
      If needed, the additional templates may also be put into the JARs by the user with the JAR utility (part of Sun's JDK). However, doing this increases the JAR size with a noticable amount.
  • The MolImport module moved into marvin.jar because of the firewall problem.
• Marvin 2.2
  1. New query bond types: "single or double", "single or aromatic", "double or aromatic", "chain" and "ring".
  2. SMARTS export handles the heteroatom (Q in molfile) type intelligently.
  3. The heteroatom and the any atom types are specified in the queryAtoms parameter. The anyatom parameter became deprecated but is still present for backward compatibility, with slightly changed behaviour. Specifying anyatom with any value (empty string also) is equivalent to specifying "any,hetero" in queryAtoms.
  4. Cell selection in MarvinView can be controlled using the selectable parameter.
  5. New methods in MarvinSketch: getBondlen. getMag, getPiece, getRescaling. New method in MarvinView: setSelectedIndex, The setDispopts method ceased to exist. Display options can be set using the dispopts applet parameter only.
  6. In Marvin 2.2 and later, the Java classes come only in packaged forms: marvin.jar and marvin.zip. It means that support is ceased for those archaic Java-compatible browsers that cannot handle the ARCHIVE option in the applet tag (Netscape 2 and MS Explorer 3). Reasons:
     1. Under certain circumstances, some Netscape versions try to load the class files one by one instead of using marvin.jar. The simplest way to keep Netscape from doing so is to remove the class files.
     2. Most of our users don't understand what ARCHIVE is, and don't use it properly. The consequence is a significantly increased download time.
        From now, a missing ARCHIVE option cannot be left unnoticed, because Marvin will simply not run. Much better than turning your user's hair gray.
     3. Marvin is rarely tested in the oldest (and buggiest) browsers.

     If you are absolutely sure that you want your Marvin page work with Netscape 2 and MS Explorer 3 too, you must unpack marvin.zip manually. However, we do not recommend this, because you will probably do something wrong. For example, once you will upgrade Marvin and forget to unpack the new marvin.zip. Mixing two different versions will result in malfunction.

• Marvin 2.1.5: Molecules in MarvinView are only editable if the editable applet parameter is set.
• Marvin 2.1.1
  • getCellCount() method in MarvinView.
  • The anchor parameter in the layout also sets label alignment.
• Marvin 2.1
  1. CML (XML) export.
  2. The getSelectedIndex() method in MarvinView.
  3. Default value of the rescaling parameter in MarvinSketch is changed to "mag" because generally this value is the most useful.
  4. The MarvinView-only package ceased to exist, the new Edit/Structure function made it irrelevant.
• Marvin 2.0
  1. Templates in MarvinSketch: From now on templates are stored in SDfiles (.sdf) or compressed SDfiles (.cssdf). The template file can be optionally compressed with GZIP, but the applet will only work in Java 1.1 compatible browsers in that case. The tmplmol, tmplpar, and ntmpls parameters no longer exist and are replaced by the much more easy to use tmpls parameters. The unit rotation angle can be specified as a new Marvin-specific property M MRV PHI in the template molecule files (instead of the tmplpar parameters).
  2. Applet tags changed: Rewrite your applet tags according to the last solution in MarvinSketch Example 1. This applet tag can load the AWT and the Swing applets as well.
     Note that the file &{marvinjar}; is not packaged now (its name caused too many problems), so you must rewrite your applet tags, otherwise the download time with MS Explorer will not be optimal.
  3. New in MarvinSketch: The menubar parameter enables or disables the menu bar in the Swing sketcher.
  4. New in MarvinView: Molecules start rotating in 3D automatically if you set the animate parameter in MarvinView.
  5. New in MarvinView: Border between cells in molecule tables.
  6. Change in MarvinView: From now the colors can be specified in the same way as in MarvinSketch. Molecule background is molbg, normal table background is bgcolor. (Previously, bgcolor was also the molecule background.)
  7. JavaScripter applet ceased to exist.
     Its functionality is moved into a MarvinView module that is automatically loaded at the first js: action.
     

     In the past, JavaScripter was required because scripting applets are not cached by older browsers (namely Netscape 3). An applet that has the MAYSCRIPT attribute is loaded from the net for each page that contains it. In Netscape 4 and later, there is no such problem. On the other hand, a bug (or feature?) in Netscape 4.6 makes the use of JavaScripter impossible as a separate applet. That's why we merged the two applets now.

  8. New: Three new molecule file formats: "sybyl" (the SybylImport and SybylExport modules), "xyz" (XyzExport), and "pov" (PovExport).
  9. New and changed: The "implicitH" option in the dispopts applet parameter instead of the showH parameter which ceased to exist.
     • "off" -> "implicitH=off"
     • "term" -> "implicitH=heteroterm" (because "term" ceased to exist)
     • "hetero" -> "implicitH=hetero"
     • "heteroterm" -> "implicitH=heteroterm" (default)
     • "all" -> "implicitH=all"
     New features: if you want the explicit H atoms to be invisible, use "explicitH=off" (default: "all").
     If you have 3D molecules, use "dim=3" for MarvinView, to let him know that you want 3D rotation as the default mouse drag action.
• Marvin 1.3
  1. New: The atomStrings parameter enables the usage of atom aliases and SMARTS strings in the sketcher.
  2. Incompatible change: The setAtoms, setNoatoms, setNobonds methods, and the atoms, noatoms, nobonds applet parameters ceased to exist and replaced by elements, anyatom, queryAtoms, and extraBonds.
  3. New: The new detach parameter makes it possible to detach the sketcher from the web page immediately when the applet is loaded.
  4. Recommended: In molfiles and compressed molfiles written directly in HTML, you should end all the molfile lines with backslash and also a real newline character like here:

     ...
     000Wun+V70\
     iuzV000W60\
     iuzVGS2W60\
     K72WGS2W60\
     ...
     	

     Omitting the real newlines like in "000Wun+V70\iuzV000W60\iuzVGS2W60\K72WGS2W60\", seemed to be safe so far, while the Marvin applets were tested only in Sun, Netscape, Symantec, and Microsoft JVM's. The reason for discontinuing this practice is that the AppletViewer in Kaffe 1.0b3 has problems if you write more than one molfile lines in one HTML line.
  5. Removed: Backward compatibility with the old style (1.0-1.1) usage of getMol() and getM() removed. It didn't work with MSIE anyway.
• Marvin 1.2
  1. Incompatible change: MSketch.getMol(x) and MView.getM(n,x).

     In Marvin 1.1.4 and before, x was a boolean variable specifying the format of the generated molfile: MDL mol (false) or compressed mol (true).

     From version 1.2, x is a format descriptor string to ease the introduction of new molecule file formats as Marvin evolves. MDL molfile format is denoted by the string "mol", compressed mol is "csmol", SMILES is "smiles".

  2. New: The preload applet parameter.

     "Extra features" are planned to be available as external modules in future releases of Marvin. External modules are downloaded only when needed. In Marvin 1.2.3, MDL mol, compressed mol and SMILES export are external modules.

     The problem is that older browsers such as Netscape 3, cannot load the external modules when the module is needed by a public method which is called from JavaScript. So if you want your web page containing Marvin to work perfectly with earlier releases of Netscape than 4, then you should preload all the modules which may be needed by JavaScript calls.

     For example, if you are using MSketch.getMol("smiles") on your page, then you should also have the following applet parameter:
     <param NAME="preload" VALUE="SmilesExport">.