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Marvin Suite Changelog

What's new in Marvin Suite 24.1.1

Mar 6, 2024
  • Bugfixes:
  • CXSMILES export adds incorrect cis/trans flag to the structure
  • E/Z stereo information is handled incorrectly in case of InChi keys

New in Marvin Suite 23.17.0 (Jan 9, 2024)

  • Bugfixes:
  • Opening up an MRV file in MarvinView throws an error

New in Marvin Suite 23.14.0 (Nov 16, 2023)

  • Bugfixes:
  • MarvinSketch does not open structure files on macOS.

New in Marvin Suite 23.13.0 (Oct 6, 2023)

  • Bug fixes:
  • Analysis Box was miscalculating values in certain cases

New in Marvin Suite 23.12.0 (Aug 30, 2023)

  • Bugfixes:
  • Phenyl abbreviated group was sprouted incorrectly, when placed in expanded state
  • Improvements:
  • Analysis Box can be placed even if multiple fragments are selected, with the same restriction that exist for single fragment selection

New in Marvin Suite 23.10.0 (Jul 6, 2023)

  • Bundled Java has been updated to Eclipse Adoptium OpenJDK 17.0.7+7

New in Marvin Suite 23.9.0 (Jun 29, 2023)

  • Bug fixes:
  • Leading number was rendered in subscript by automatic label formatting

New in Marvin Suite 23.8.0 (Jun 1, 2023)

  • Improvements:
  • Change in CT File export: Label formatting is no longer exported in CT File formats in accordance with the corresponding file format specification

New in Marvin Suite 23.4.0 (Mar 13, 2023)

  • Bug fixes:
  • Pasting a structure with aromatic nitrogens in SMILES resulted in an incorrect number of hydrogens.
  • Placing an expanded Glu or Asp on the canvas resulted in an incorrect structure.
  • The source output in CXON was incorrect when it contained a contracted abbreviated group.

New in Marvin Suite 23.3.0 (Feb 24, 2023)

  • Improvements:
  • The look and feel of MarvinSketch has been harmonized across the different operating systems.

New in Marvin Suite 23.1.0 (Jan 26, 2023)

  • Improvements:
  • Bundled Java has been updated to Eclipse Adoptium Java 11.0.17.
  • The look and feel of MarvinSketch has been harmonized across the different operating systems.

New in Marvin Suite 22.20.0 (Nov 24, 2022)

  • Bug fixes:
  • MarvinSketch failed to start when the applied license was near its expiration date.

New in Marvin Suite 22.19.0 (Oct 27, 2022)

  • Bug fixes:
  • In rare cases, turning on the grid view resulted in an error.
  • Improvements:
  • The "typing support" of homology groups was extended and unified. For example, previously one could type chk to insert an Alkyl atom, but could not type alkyl to achieve the same result. Now all aliases of all homology groups are handled uniformly.
  • A new tool button was added to the Markush toolbar that makes it easier to draw homology groups. This toolbar is not shown by default in MarvinSketch, but can be shown through View > Toolbars > Markush.
  • Nihonium, Flerovium, Moscovium, and Livermorium are now classified as metals.

New in Marvin Suite 21.18.0 (Dec 3, 2021)

  • As of version 21.18, MarvinSketch automatically collects anonymous usage data and information from academic and non-commercial users. We use the data exclusively to analyze and enhance the user experience and trends as a whole to improve our product. For more information, see our EULA.

New in Marvin Suite 20.16.0 (Jul 21, 2020)

  • New features:
  • It is now possible to initiate structure searches through MarvinSketch in Google Patents and Google Scholar.
  • Improvements:
  • When importing mdl rxn and extended mdl rxn files, the reaction components are ordered automatically.
  • Bugfixes:
  • Drag and dropping an .rxn or .smiles file that contains a reaction caused an error.
  • In some cases, electrons were painted twice or were positioned incorrectly when the contents of the canvas were rendered into an image.
  • Copyright and version number information were missing from the splash screen of MarvinSketch.

New in Marvin Suite 20.15.0 (Jul 6, 2020)

  • Improvements:
  • A new API option for converting and fixing reactions has been added.
  • It is now possible to copy the contents of the canvas as PDF, including MRV source as metadata.
  • Bugfixes:
  • When the scaling percentage was set to higher values, the Marvin applications did not open in the correct position. This problem is fixed, and the application now always opens in the center of the screen, regardless of scaling or display size.

New in Marvin Suite 20.14.0 (Jun 23, 2020)

  • Improvements:
  • New API option for setting chirality label font size has been added.
  • The downwedge_mdl and downwedge_daylight legacy formats are now supported.
  • Bugfixes:
  • When the structure was present on the clipboard in only MDLCT format, pasting it into MarvinSketch was not possible.
  • Formatting the source of an mrv with arbitrary indentations that contains a reaction sign and trying to open it in MarvinSketch, resulted in duplicated reaction signs.
  • Dockable toolbars could not be pinned to their designated new place.
  • The IUPAC numbering displayed in MarvinSketch and when using the "cxsmiles:+numbering" format option was incorrect for some fused ring systems.

New in Marvin Suite 20.11.0 (Apr 20, 2020)

  • Improvements:
  • Now, when a bond tool is active and the cursor is over an atom, a gray-colored feedback appears in the selected bond type. Pressing the Shift key changes the direction of the bond.
  • Bugfixes:
  • When the canvas was not empty, pasting a reaction arrow in SMILES or SMARTS format resulted in an error.

New in Marvin Suite 20.6.0 (Feb 28, 2020)

  • Improvements:
  • Grid visibility is now kept between sessions.
  • It is now possible to choose between full structure search and substructure search through a dialog box when initiating a Reaxys search.
  • Bugfixes:
  • In some cases, during template handling, improper user privileges were set on files/directories which resulted in an error.
  • When a reaction arrow was present on the canvas, group creation with the Create Group tool resulted in an exception.

New in Marvin Suite 20.2.0 (Jan 21, 2020)

  • IMPROVEMENTS:
  • Toolbar:
  • "Search Online" toolbar is available with Chemicalize and Reaxys® search possibility.
  • Menu:
  • View > Color > Monochrome option is applied for every item on the canvas (such as map number, attached data, value, query properties etc.) which the user does not color explicitly.
  • "Regenerate Bonds" action is no longer available in MarvinSketch and MarvinView.
  • "Clean Wedge Bonds" action is removed from Structure>Clean 2D menu.
  • Bugfixes:
  • When View>Stereo>R/S labels> "All" or "All possible" option was set, and there were closed S-groups in the structure, the calculation froze and stereo labels were not shown.
  • Image export parameters "colorScheme" and "valenceErrorVisible" did not work in Molconvert and from API.
  • Only positive numbers are accepted as input values of Multipage margins (File > Multipage Settings > Margins).

New in Marvin Suite 20.1.0 (Jan 14, 2020)

  • Drawing:
  • Bond snapping to useful angles has been introduced. When rotating a bond, placing a new bond by dragging, or moving an atom attached to a bond, the bond in question snaps by 7.5 °. If the user presses SHIFT while rotating, the rotation will be continuous.
  • Bugfixes:
  • The starting value of the index range of the "Relative stereo AND index " and "Relative stereo OR index " panels were changed from "0" to "1".

New in Marvin Suite 19.26.0 (Dec 14, 2019)

  • Improvements:
  • Installer:
  • Both macOS Marvin installers are signed to let Gatekeeper (from macOS Catalina) know it is safe to install (notarized).

New in Marvin Suite 19.25.0 (Dec 4, 2019)

  • Improvements:
  • Applet:
  • Deprecated Marvin Applet codes are now removed.
  • Known issues:
  • 32-bit installer is not available for this release.

New in Marvin Suite 19.24.0 (Nov 15, 2019)

  • No changes.

New in Marvin Suite 19.23.0 (Nov 11, 2019)

  • Checkers:
  • Wedge error checker is replaced by Incorrect Tetrahedral Stereo, Non-standard Wedge Scheme, and Non-stereo Wedge Bond checkers in the default Checker configuration list (Preferences > Checkers).
  • Bugfixes:
  • Image generation:
  • Under specific conditions SVG export placed atom numbers in wrong position.

New in Marvin Suite 19.21.0 (Oct 10, 2019)

  • Bugfixes:
  • View:
  • MarvinSketch froze when multiple group was drawn and the R/S calculation was enabled

New in Marvin Suite 19.20.0 (Sep 18, 2019)

  • Bugfixes:
  • View
  • Pseudoasymmetric centers were not displayed when View>Stereo>R/S labels>All option was enabled.
  • Improvement:
  • Abbreviated Groups
  • NHBr and NBr groups were added to the list of the built-in, default abbreviated groups.
  • User interface:
  • From the File>Find Structure online> submenu ChemSpider option was removed.

New in Marvin Suite 19.16.0 (Jul 4, 2019)

  • No changes.

New in Marvin Suite 19.15.0 (Jun 28, 2019)

  • When CXN Extended SMILES was pasted, it was interpeted as Daylight SMILES.
  • "Reset to Default" option didn't work for the atomlabels in the Format dialog.

New in Marvin Suite 19.13.0 (Jun 28, 2019)

  • Known issues:
  • When pasting CXN extended SMILES, MDL SMILES is displayed.
  • In some cases the position of atomlabel is misplaced.
  • Bugfix:
  • When a MDL Mol file containing a name in the first row was opened the structure corresponding to name was imported, not the structure in the Connection Table (CTAB).

New in Marvin Suite 19.12.0 (Jun 3, 2019)

  • No changes.

New in Marvin Suite 19.11.0 (May 21, 2019)

  • Bugfixes:
  • Printing:
  • In certain cases cis-trans stereoisomers were not assigned.
  • The update of the Analysis box was not consistent.
  • Upon opening certain files no structure was visible on the canvas.
  • Alias/pseudo atoms and abbreviated groups without left name were not aligned properly.
  • IO:
  • Manually added + sign(s) in reaction were lost when exported into image (graphical file).
  • Improvement:
  • Stereocalculation:
  • New method for calculation of optical isomerism has been introduced.

New in Marvin Suite 19.10.0 (May 7, 2019)

  • Bugfixes:
  • Editing:
  • Dot disconnected formula with charges did not work in Analysis box.
  • MarvinSketch had performance problem in case of large structures with enabled M/P labels calculation.
  • When symbol characters were inserted, the textbox did not resized automatically.
  • Text from Naming window could not be pasted into a MarvinSketch's textbox.
  • Background, outline, alignment settings are lost when a textbox was copied.
  • GUI:
  • No feedback was displayed for the selected tool on Mac OS.
  • In some cases the selected Save>Folder changed when the user modified the file format.
  • Context menu item was missing when contracting more expanded groups at the same time.
  • IO:
  • TROPOS mol2 file was not saved correctly from GUI.
  • In some cases a part of the grey background of position variation bond was cut from images.
  • Improvements:
  • GUI:
  • MDL Mol V3000 format has been added to the Copy As... options
  • Stereocalculation
  • New method for calculation of Cis–trans isomerism has been introduced.

New in Marvin Suite 19.8.0 (Mar 18, 2019)

  • No changes.

New in Marvin Suite 19.7.0 (Mar 11, 2019)

  • Improvement:
  • Analysis Box:
  • Formula in Analysis Box is displayed without charged molecular species.
  • GUI:
  • ChemDraw, ISIS like, Marvin 1-5, Marvin5 presets are not available anymore.
  • Bugfixes:
  • Editing:
  • Simple text could not be pasted into a textbox.

New in Marvin Suite 19.3.0 (Feb 14, 2019)

  • Bugfixes:
  • Editing:
  • Label of data S-group was misplaced.

New in Marvin Suite 19.3.0 (Feb 14, 2019)

  • Bugfixes:
  • Editing:
  • Label of data S-group was misplaced.

New in Marvin Suite 19.2.0 (Jan 23, 2019)

  • The retention/inversion flags were not displayed correctly.
  • Colored lone pairs were painted using monochrome view.

New in Marvin Suite 19.1.0 (Jan 17, 2019)

  • Bugfix:
  • There was a significant slowdown in the import of SMILES of some molecules with huge ring system.

New in Marvin Suite 18.30.0 (Dec 17, 2018)

  • Improvement:
  • Documents larger than A4 are exported as poster in .CDX file format.
  • Bugfixes:
  • Editing
  • signs in reactions were not positioned correctly.
  • API:
  • In certain cases the coordinates of textbox were miscalculated.
  • I/O:
  • There was a significant slowdown in the import of SMILES of some molecules with huge ring system.
  • Wrong bond spacing values were exported in .CDX file format.

New in Marvin Suite 18.29.0 (Dec 7, 2018)

  • GUI:
  • Structure to Name and About dialog has been revisited.

New in Marvin Suite 18.28.0 (Nov 28, 2018)

  • Bugfix:
  • Molprinter:
  • Concurrency issues could be invoked.

New in Marvin Suite 18.27.0 (Nov 15, 2018)

  • GUI:
  • Structure to Name and About dialogs have been revisited.

New in Marvin Suite 18.26.0 (Nov 12, 2018)

  • Improvements:
  • Editing:
  • The label of the attachment points in abbreviated group was not scaled.

New in Marvin Suite 18.25.0 (Oct 31, 2018)

  • Improvements:
  • IO:
  • Bond length, bond thickness, bold bond width, bond spacing hash spacing and margin are imported from .CDX and .CDXML formats.
  • Text font size are corrected in .MRV files created before version 18.22.0.
  • GUI:
  • Structure to Name and About dialogs have been revisited.
  • MolPrinter:
  • The performance of MolPrinter has been improved.
  • Bugfixes:
  • Editing:
  • Analysis box was not displayed when a selected structure contained abbreviated group.
  • The reactants and products were copied with the reaction arrow.
  • Removal of selected atoms/bonds switched to erase mode.

New in Marvin Suite 18.23.0 (Sep 26, 2018)

  • Improvements:
  • Copy from Analysis box has been introduced.
  • Textbox handling has been revisited.
  • Bugfixes:
  • Analysis box was not erased when the molecule was deleted.
  • Empty analysis box was added when a product/reactant was deleted next to a merged product/reactant.

New in Marvin Suite 18.22.0 (Sep 7, 2018)

  • Bugfixes:
  • Editing:
  • Chain drawing didn't mirror the mouse movement.
  • The fontsize in textboxes wasn't independent of bondlength.
  • Analysis box:
  • The analysis box wasn't centered, it shifted to the left.
  • Clipboard:
  • Plain text was not added to the clipboard when textbox was copied.

New in Marvin Suite 18.21.0 (Aug 30, 2018)

  • Improvements:
  • Editing:
  • The drawing speed has been improved.
  • Help:
  • No off-line documentation is added anymore.
  • Bugfixes:
  • Editing:
  • The viewport changed when 'Esc' was pressed or was clicked into a textbox.

New in Marvin Suite 18.18.0 (Aug 3, 2018)

  • Bugfixes:
  • Editing:
  • Brackets in multiple S-groups were not selected by double-clicking.
  • Analysis box:
  • Values for multiple groups were miscalculated.
  • Clipboard:
  • The plus signs were not placed to the clipboard when a reaction was copied.
  • Image generation:
  • The label of simple salt sometimes was cut.

New in Marvin Suite 18.17.0 (Jul 25, 2018)

  • No changes

New in Marvin Suite 18.16.0 (Jul 9, 2018)

  • Improvements:
  • Naming:
  • CAS number is available from Structure>Generate name submenu.

New in Marvin Suite 18.14.0 (Jun 22, 2018)

  • Bugfixes:
  • Printing:
  • Atom numbers were not shown on printed picture.
  • MarvinView:
  • If marvin.properties file contained deprecated property "wireknobs", MarvinView did not start.
  • "Save?" dialog did not appear when MarvinView was closed after modifying a file.

New in Marvin Suite 18.13.0 (Jun 12, 2018)

  • Improvements:
  • Editing:
  • Basic template bar has been changed.
  • Bugfixes:
  • Editing:
  • First and second merge points weren't indicated with same size patches.

New in Marvin Suite 18.11.0 (May 23, 2018)

  • Bugfixes:
  • Editing:
  • "All" zoom option didn't handle atom labels correctly when Journal Style is applied.
  • Preferences menu didn't not open under JAVA 10.
  • Scale/Zoom factor were omitted upon copy.
  • MarvinView:
  • Marvin View didn't open structures via double click on files on Mac OS.
  • Image generation
  • The label of abbreviated groups sometimes was cut.

New in Marvin Suite 18.10.0 (Apr 16, 2018)

  • Improvements:
  • Editing:
  • Ctrl+D shortcut and new Edit menu item have been added for Copy as OLE.
  • Bugfixes:
  • Editing:
  • NPE was thrown on the console when atom formatting was done.
  • Text notes were lost when a new bond was attached to a homology atom.
  • Molconvert:
  • *.mol was not found.

New in Marvin Suite 18.8.0 (Mar 14, 2018)

  • Improvements:
  • MarvinSketch:
  • Default minimum heap size has been changed to 512MB.
  • Option for selecting MDL Molfile v2000 and v3000 has been introduced into Save as and Source dialogs.
  • OLE format has been removed from the transferable list of Ctrl+c.
  • API:
  • 'strict' option has been introduced for MDL Molfile conversions . When it is applied, the output strictly follows the CTFile format specification i.e. names longer than 80 characters are omitted.

New in Marvin Suite 18.5.0 (Mar 1, 2018)

  • Improvements
  • I/O:
  • The order has became flexible in the in AttachmentPointArray block of .MRV files.
  • Data S group import from .CDX and .CDXML files has been improved.
  • Editing:
  • 'Discard existing formats' option has been introduced form atom sets to the Document Style Settings dialog.
  • Bugfixes
  • MarvinView:
  • Structures were not centralized correctly when the window was resized.
  • Printing:
  • Printing didn't work using JAVA 9 in Windows.

New in Marvin Suite 18.4.0 (Feb 14, 2018)

  • Bugfixes:
  • I/O:
  • MRV import of abbreviated group failed if the file did not contain AttachmentPointArray
  • OLE:
  • Dimensions of EMF image was recalculated during generation in MarvinOLEPanel.

New in Marvin Suite 18.3.0 (Jan 31, 2018)

  • Bugfixes:
  • Stereocalculation:
  • In some cases higher order stereo detection incorrectly returned WIGGLY result instead of UNKNOWN.
  • I/O:
  • NPE was thrown during the import of some tetrahedral stereo molecules containing explicit Hydrogens on the stereo centers.
  • Installer:
  • MarvinSketch could not be launched by clicking its icon on MAC OSX.

New in Marvin Suite 18.2.0 (Jan 18, 2018)

  • Bug fixes:
  • MarvinView:
  • Upon import unnecessary cleaning was performed
  • I/O:
  • NPE was thrown during the import of some tetrahedral stereo molecules containing explicit Hydrogens on the stereo centers

New in Marvin Suite 17.29.0 (Dec 22, 2017)

  • Improvements:
  • Editing:
  • Shortcuts Alt+? and Alt+? for super- and subscript has been introduced for textbox.
  • Shortcuts Alt+? and Alt+? for super- and subscript has been introduced for Atom Label Editor.
  • Bugfixes:
  • Editing:
  • Structure cannot be seen in Marvin Services result window.
  • Zoom scale changed when a R group attachment point was added
  • Upon rich text pasting sub/superscript formatting was lost.
  • Escaping did not work for DataSGroup.
  • Copy as .MRV didn't work when Save/Load GUI Settings option was disabled.
  • IO:
  • The plus signs of the reaction imported from SMILES was painted in wrong position in MarvinView.

New in Marvin Suite 17.25.0 (Oct 19, 2017)

  • Bugfixes:
  • Editing:
  • Clean and arrange duplicated the arrow in reactions when the automatic plus sign calculation was disabled.
  • Pasting to a newly opened window didn't work.

New in Marvin Suite 17.23.0 (Sep 22, 2017)

  • Bugfixes:
  • Editing - 'Copy as png' option didn't work.

New in Marvin Suite 17.22.0 (Sep 1, 2017)

  • Bugfixes:
  • Editing:
  • In some cases the selection wasn't disabled by 'Esc'.
  • The definition of Markush structures was lost when a reaction arrow was drawn.
  • IO:
  • Atom numbers weren't considered during molecule bound calculation.

New in Marvin Suite 17.16.0 (Jul 22, 2017)

  • Bugfixes
  • Editing:
  • Copy/pasting structures having M/P label froze Marvin.
  • Atropisomerism for agents wasn't calculated.
  • In some cases aromatic rings were drawn incorrectly after canvas have been got increased
  • OS:
  • Copy/pasting as PDF to/from Sketch and Office didn't work properly.
  • Installer:
  • Marvinbeans.jar was missing from 'MarvinSketch Installer with OLE Support'.

New in Marvin Suite 16.9.5.0 (Sep 14, 2016)

  • Bugfixes:
  • Editing:
  • Plus sign was not added in reaction when creating two structures from one via bond deletion.
  • Problems with historization of reaction drawing were eliminated.
  • Auto + sign cold be be deleted using the Eraser tool.
  • Plus signs in a reaction remained after deleting the arrow in reactions.
  • " +" symbol were not drawn automatically when adding a diatomic molecule to a reaction.
  • I/O:
  • R-group attachment points were not imported properly from MDL Molfile.

New in Marvin Suite 16.8.29.0 (Sep 14, 2016)

  • Bugfixes:
  • Editing:
  • Duplicated graphical elements were drawn (rectangle, electronflow arrows) in reaction.
  • Plus signs did not appear between reactants (products) during SMILES import.
  • Plus sign were not deleted when two components got connected in reactions.

New in Marvin Suite 16.8.22.0 (Sep 14, 2016)

  • Improvements:
  • For exporting structures with position variation bond to MDL v2000 molfile a new API option has been introduced

New in Marvin Suite 16.8.8.0 (Aug 10, 2016)

  • IMPROVEMENTS:
  • Editing:
  • Reaction arrows snap every7.5 degree.
  • Dragging and Pressing 'Shift' enables the free rotation of reaction arrows.
  • BUG FIXES:
  • Editing:
  • No electron flow arrow could not be drawn from a lone pair.
  • In some cases analysis box could be called for a selected part of a molecule.
  • Feedback of attachment points were painted too close to the atom label.
  • In some case Analysis box was not updated properly when the molecule had been graphically formatted.

New in Marvin Suite 16.7.18.0 (Jul 19, 2016)

  • Improvements:
  • Editing:
  • Aromatic ring calculation in case of 3D rotated ring has been revised.
  • `Apply for Selection Only` option for coloring has been introduced enabling different coloring of the atom label and adherent bonds.
  • Bug fixes:
  • Editing:The Analysis box was not updated properly in case of alias or pseudo atoms.

New in Marvin Suite 16.6.20 (Jul 19, 2016)

  • BUG FIXES:
  • Editing:
  • The feedback of expanded abbreviated group showed the formatting.

New in Marvin Suite 16.6.6 (Jul 19, 2016)

  • IMPROVEMENTS:
  • GUI:
  • Ctrl+M shortcut has been introduced for Copy as MRV command.
  • 3D rotate (F6) mouse mode has been removed.
  • On atom format panel, atom label size can set instead of the former scale option.
  • BUG FIXES:
  • Editing:
  • In some cases placing a reaction arrow deleted the "No Stucture".
  • Name of the items was displayed on the canvas even it they had been set off on the Preferences dialog or the Analysis box editing dialog.
  • Editing analysis box: changing the order of the items did not work for name and traditional name.
  • The reaction arrow in single step reaction could not be copied using Ctrl+C, Ctrl+V.
  • IO:
  • CxSmiles string with extended part containing '(+)' string was not recognized as cxsmiles/cxsmarts format. CxSmiles string with extended part containing 'v5' string was not recognized as cxsmiles but as cxsmarts format.

New in Marvin Suite 15.6.22 (Jul 3, 2015)

  • StructureChecker
  • Bugfixes
  • Solvent Checker threw exception if input molecule couldn't be converted to SMILES format.

New in Marvin Suite 15.6.15 (Jul 3, 2015)

  • MarvinSketch
  • Bugfix
  • Editing
  • S-group containing S-groups imported from a molfile was lost on selecting or clicking on the canvas.
  • Bounding rectangle was too big around certain S-groups.
  • Import
  • Molfile containing copolymers were not imported properly.

New in Marvin Suite 15.6.8 (Jul 3, 2015)

  • MarvinSketch
  • Improvements:
  • Document styles
  • Documentum Style Settings window and functions have been revisited.
  • Charge painting
  • Charge painting has been improved. Charge font settings change together with the atom label settings from now on. Parameters ChargeSize and ChargeFont have been deprecated.
  • Bugfix
  • I/O
  • Molconvert would sometimes print "error: null". It now prints the name of the relevant Exception.
  • Exporting molecule with R-Group definition and scaffold gave a unscaled image.

New in Marvin Suite 15.5.11 (Jul 3, 2015)

  • MarvinSketch
  • Improvements
  • Journal styles
  • New journal styles are saved in the journal_styles folder.
  • Bugfix
  • Editing
  • Scrolling and zooming were disabled when Atom Label editor was opened.
  • MarvinView
  • Bugfixes
  • Printing
  • "Print All" function resulted in missing or misplaced atom labels when the document was printed into .pdf file.

New in Marvin Suite 15.4.27 (Jul 3, 2015)

  • MarvinSketch
  • Improvement
  • Document style handling has been improved and style properties files ha been changed.
  • Before updating MarvinSketch please delete Userhome/Chemaxon/Styles folder (if exists).

New in Marvin Suite 15.4.20 (Jul 3, 2015)

  • MarvinSketch
  • Improvement
  • Structure drawing has been revisited.

New in Marvin Suite 15.4.13 (Jul 3, 2015)

  • StructureChecker
  • New features
  • New checker: Brackets Checker.

New in Marvin Suite 15.4.6 (Jul 3, 2015)

  • MarvinSketch
  • Improvement
  • Painting performance has been improved due to revised caching.
  • Bug
  • Memory limits (128MB) on Mac OSX could cause serious slowdown.
  • Editing
  • Aromatic rings within R-groups were drawn with aromatic bond.
  • API
  • Setting a rectangle with x and y coordinates other then zero lead to loss the upper and left part of the created image, when MolPrinter.paint(Graphics2D, Rectangle) method call was used.

New in Marvin Suite 15.3.30 (Jul 3, 2015)

  • MarvinSketch
  • Bug
  • Editing
  • Non-selected brackets were copied as well.
  • Marvin
  • On Turkish locale since 15.2.9 MarvinSketch and MarvinView was unable to start due to a Java character conversion issue in Java.
  • When molecules were saved separetely and load them again bonds sets were lost.
  • I/O
  • Exported svg files could not be read.
  • Export of Sgroup with attached data into v3000 molfile failed in some cases.

New in Marvin Suite 15.3.23 (Jul 3, 2015)

  • MarvinSketch
  • Improvement
  • Marvin GUI
  • Drawing settings has been moved from the Preferences menu to File < Document Style < Settings panel.

New in Marvin Suite 6.3.1 (Jul 1, 2014)

  • New features and improvements:
  • Image I/O:
  • New image IO parameter "aminoAcidBondColoringEnabled" has been introduced for peptide bond coloring.
  • Import/Export:
  • SKC - If they are set to visible in ISIS, "Atom numbers" are imported as atom mapping from SKC.
  • Bugfixes:
  • Clipboard handling:
  • If a structure had been pasted onto an empty canvas and MSketch was closed without modifying the structure, the structure was not saved.
  • Files with "smiles" extension did not load by dragging them and dropping into MarvinSketch.
  • Clicking on the Transfer button (of MSketch) after editing a structure in MView caused NPE.
  • Editing:
  • If a template was merged to an atom of an abbreviated group which did not have any attachment point, the abbreviated group was not ungrouped.
  • Bond shortcuts did not work until the user pressed the "Bond" button on the "Tools" toolbar.
  • Image I/O:
  • Bond set coloring image export parameter was not effective, and in some cases it was able to modify the atom set coloring.
  • When saving a structure in pdf format, the image was cut too narrow.
  • Circled charge was not copied into PDF clipboard format on Mac. Currently it is represented without the circle.
  • Molecule Representation:
  • Valence Check - False valence error appeared on aromatic rings containing Nitrogen-like atoms in their aromatic form.
  • S-groups - The direction of S-group labels was changed at wrong angle.
  • Painting:
  • The " * " character was not supported in (among others) Arial, Times New Roman, and Lucida font family.
  • The leftname/rightname rendering of abbreviated groups have been incorrect in several cases such as "OMe".
  • Name to Structure (n2s):
  • Some substituents separated by a space from an acid parent were wrongly interpreted as esters.
  • The naming webservice was not working in the applet.

New in Marvin Suite 6.2.2 (Apr 8, 2014)

  • Bugfixes:
  • Clipboard handling - Compounds in a reaction could not be copied.

New in Marvin Suite 6.1.6 (Jan 17, 2014)

  • Applet:
  • Missing resources caused issues in applets with bridged structures. For instance, template based cleaning and pasting names did not work in these cases

New in Marvin Suite 6.1.4 (Dec 11, 2013)

  • Applet:
  • The mol property change event was not fired when an empty molecule was set initially for the MarvinSketch applet. This could cause misbehaviour in cases where the client JavaScript code relied on this marker to know when the applet was initialized.

New in Marvin Suite 6.1.3 (Nov 5, 2013)

  • Import/Export:
  • CXSMILES/CXSMARTS:
  • CXSMARTS containing valence property information was recognized and read as SMARTS.
  • SKC:
  • Some reaction was read as R-definition from SKC format.

New in Marvin Suite 6.1.2 (Oct 30, 2013)

  • New features and improvements:
  • MarvinSketch Dialog:
  • 'Zoom to scaffold' checkbox option has been added to the "Preferences>Save/Load" tab. Documentation
  • Structure Checker:
  • External structure checker configuration file URL can be set via Java System Property.
  • Bugfixes:
  • Editing:
  • Electron-flow arrow could not be drawn from the A-B bond to the incipient A-C bond of an A-B-C structure. Forum
  • Import/Export:
  • MolInputStream and MolImporter could have different format options.
  • MolImporter did not close its inputstream when an exception was thrown in the constructor.
  • MOL, SDF, RXN, RDF:
  • Molecule type property was allowed in SDF, CSSDF export.
  • The coordinates of the sequence residue imported from SCSR MOL files were wrong if the residue had three attachment point.
  • CDX/CDXML:
  • Color and text format of atom label is exported to CDX and imported from CDX and CDXML. Forum
  • Graphical brackets were not imported from CDX files.
  • Gaussian Z-matrix input format:
  • Command line, title line, and extra input properties were not exported to Gaussian Z-matrix input format. Forum
  • Clean 2D:
  • Cleaning of position variation bonds could create overlapping bonds.
  • Cleaning of bridged systems could result in overlapping atoms. Forum
  • Calculations:
  • Topology Analysis:
  • Missing method has been added: TopologyAnalyserPlugin.getFsp3(). API Documentation
  • logD:
  • New logD training documentation has been added. Documentation
  • Structure Checker:
  • Fixer options in MarvinSketch are updated with newly defined settings.
  • External checkers can be loaded from JAR file in case the JAR file contains a space.

New in Marvin Suite 6.1.0 (Sep 27, 2013)

  • New features and improvements:
  • MarvinSketch GUI
  • Peptide cycles and bridges can be drawn according to IUPAC recommendations. Documentation
  • IUPAC numbering can be displayed on the atoms of each molecule using the "View > Advanced > Atom Numbering > IUPAC Numbering" menu.
  • Lone Pair (LP button) was removed from the "Special nodes" group of the Periodic Table > Advanced tab, so it cannot be reached from the GUI anymore.
  • MarvinSketch Menu
  • The "Calculations > Predictor" menu option has been removed from the default Marvin menu.
  • Painting
  • Drawing of electron flow arrows has been changed. Single electron flow arrows can now start either from a radical or from an electron of a lone pair. Electron pair flow arrows can only start from lone pairs. Documentation
  • Atom property values belonging to the same atom are now separated with semicolons instead of commas.
  • When lone pairs were displayed on a structure, the charge symbol was nearly invisible.
  • Load/Save handling in UI
  • The same last-used folder is saved for the "File > Open" and the "File > Insert file" functions.
  • MarvinView GUI
  • IUPAC numbering can be displayed on the atoms of each molecule using the "View > Misc > Atom Numbers > IUPAC Numbering" menu.
  • Import/Export
  • MRV/CML
  • Namespace has been introduced to mrv format.
  • MOL, SDF, RXN, RDF
  • New export option, cc, is introduced to V2000 export in order to write absolute chiral flag if there are only ABS enhanced stereo labels in the molecule. Documentation
  • New import option, z, is introduced to MDL import that converts Carbon atoms with "Z" label to R-group attachment points. Documentation
  • SMILES/SMARTS
  • [Z] is imported as R-group attachment point from SMILES. Documentation
  • CXSMILES/CXSMARTS
  • New export option, b, has been introduced to CXSMILES/CXSMARTS in order to turn off the export of bicyclostereo-information. Documentation
  • Name to Structure (n2s)
  • Name and corporate ID resolution webservice now supports NTLM authentification.
  • Names with a missing dash before the suffix locants are now recognized.
  • Non-standard IUPAC specification of stereochemistry inside suffix locants is supported.
  • Names with superscript locants of a bridged ring system numbering are denoted by spaces are now supported.
  • As a result of numerous improvements to the systematic name conversion algorithm, more names are converted by n2s and detected by d2s. The accuracy of structure generation has also increased. (For instance, 5% more names were detected and converted in a large, diverse set of patents.)
  • An example custom dictionary has been added to the documentation. Documentation
  • Document to Structure (d2s)
  • Chinese names are now detected in text documents using an approach which recognizes names in Chinese sentences without the spaces that separate words in English.
  • In addition to OSRA, the CLiDE and Imago Optical Structure Recognition tools (Chemical OCR) can be used to convert images to structures. These tools need to be installed separately from Marvin. Documentation
  • When processing USPTO patents in XML format, the section in which a name is found is recorded as metadata (title, abstract, citation, description, or claim number). Additionally, document metadata is extracted (patent title and ID, inventors and assignees, IPCR categories).
  • When processing a USPTO patent XML document, referenced CDX files are imported automatically if they are in the same directory as the XML file.
  • Processing of USPTO XML patents has become faster: an average 20% speed-up, more than ten times faster process for some patents.
  • PDF document pages with images in the JBIG2 format are now supported.
  • PDF documents generated by Adobe Acrobat Paper Capture Plug-In and ExperVision are now handled specially, since they contain both an original scanned image of text and the text resulting from OCR of the image. This allows much faster processing of such documents, and avoids double hits for the same text.
  • PDF documents with many small high-resolution images are now processed much faster, even when Optical Structure Recognition is used.
  • The document creation date property is stored as a java.util.Date object instead of string.
  • Structures returned by image recognition tools (OSRA, CLiDE, Imago) are better filtered to avoid false positives.
  • OCR processing for scanned texts can be disabled using the -ocr format option. Documentation
  • Processing of PDF documents with scanned black and white images (e.g., most non-searchable patent documents) has become approximately two times faster.
  • Structure to Name (s2n)
  • When converting a structure to CAS registry number, the InChiKey of the structure is used to search for the structure. This allows more structures to get a CAS registry number in such cases where several different SMILES with chemically irrelevant differences are associated with the structure.
  • Molecule Representation
  • New method, SelectionMolecule.addAtom(MolAtom, boolean), is introduced. Forum
  • New methods, MolAtom.getBondArray() and Sgroup.getBondArray() are introduced. Forum
  • Calculations
  • NMR (CNMR, HNMR Prediction...)
  • Various phosphorus-proton spin-spin coupling parameters have been added to the predictor database.
  • Geometry (Topology Analysis, Geometrical Descriptors, PSA, MSA)
  • "Fsp3" option has been introduced in the Topology Analysis plugin for calculation of sp3 carbon atom fraction. Documentation
  • Elemental Analyzer
  • Charge is taken into account in atomic mass calculation.
  • Chemical Terms
  • Chemical Terms's (CT) Structure Checker functions accept XML configuration as string parameter, thus Structure Checker XML configurations can be used in JChem Cartridge via CT.
  • New checkErrorCount Chemical Terms function returns the number of errors/issues found by the checker(s) in the configuration. Documentation
  • Structure Checker
  • Checker "substructure checker" has become available in Marvin Beans, so installing Marvin Beans will install the fully functional Structure Checker application.
  • Set Structure Checker configuration can be copied to the clipboard as action string from Structure Checker GUI and Structure Checker Editor. Documentation
  • The "excluded" list of Structure Checker's Abbreviated Group Checker accepts quotation marks in command-line. Possible definitions can be the following: "abbrevgroup:excluded=Ph,Ala,Gly", "abbrevgroup:excluded='Ph,Ala,Gly'" or "abbrevgroup:excluded="Ph,Ala,Gly"".
  • The checkers and fixers can be localized or customized according to individual requirements. Documentation
  • Build/Installation
  • Mac OS X installer images were not digitally signed, and GateKeeper in newer OS X versions (10.7.5+) reported our installers as damaged and refused to install them.
  • Bugfixes:
  • MarvinSketch GUI
  • Aliphatic/Aromatic atom query property had three options ("a", "A", and "A,a") instead of the necessary two ("a" and "A").
  • MarvinSketch Dialog
  • In case of long names, only a part of the whole name appeared on the naming panel.
  • Editing
  • Deleting an atom having an R-group attachment did not delete the attachment.
  • The end of an arrow did not stick to the midpoint of an existing arrow.
  • Load/Save handling in UI
  • In MarvinView, "File > Save All... > Advanced > Into SEPARATE FILES" did not save the last structure.
  • History functions
  • When the "Stereo" atom property had been changed, Undo/Redo did not work properly and the IUPAC name was not updated.
  • Graphical object handling
  • Labels written in text box were shifted when they were pasted either as an OLE object or as a PNG image.
  • MarvinView GUI
  • When a structure which contained an R-group definition was opened from MarvinView for editing in MarvinSketch, the structure appeared with 0% zoom factor.
  • Text elements (atom labels, atom indices, text box contents, IUPAC name) were not resized in MarvinView while zooming the structure using the "View > Transform > Zoom" function. Forum
  • Printing in MarvinView
  • When choosing "Print > All Visible", the structures overlapped in the preview, and "Print > All Visible > Print to PDF" resulted in an empty file.
  • MarvinSpace
  • A bug occuring at PDB import has been fixed.
  • The "Edit > Cut" menu option has been fixed in the MarvinSpace menubar.
  • Import/Export
  • Aliphatic and aromatic query property, when they are used together, is not imported and exported any more. The "no property", no aromatic or aliphatic query property, has the same meaning.
  • Only lower case file extensions were recognized.
  • MRV/CML
  • MRV files that contained circular R-group references without attachment point information could not be imported.
  • MOL, SDF, RXN, RDF
  • Export of structures containing multicenter S-groups to format MOL V2000 resulted in a non-standard file.
  • Newline characters in molecule name were not escaped.
  • MDL MOL import did not use MDL valence model for non-charged metals.
  • Atom list embedded to atom list in MDL file formats resulted in invalid atom list elements after import.
  • CDX/CDXML
  • Reactions containing anonymous alternative groups were not imported from CDX format. Forum
  • XML files with complex header could have been recognized as CDXML.
  • SMILES/SMARTS
  • Query Hydrogen atom with parity definition confused SMARTS import.
  • SMILES export did not throw exception when the molecule contained not supported reaction stereo information.
  • Newline characters in molecule name were not escaped.
  • SMILES import read Meitnerium atom (Mt) as any atom (*).
  • Strings containing valence property were recognized and imported as SMILES instead of SMARTS.
  • CXSMILES/CXSMARTS
  • Import of CXSMILES/CXSMARTS strings that describes the coordinates of atoms with option c added 'CIS OR TRANS' stereo information to double bonds in small rings.
  • Single or aromatic bonds could be lost during CXSMARTS export and import.
  • InChi/InChiKey
  • InChI was not recognized in MolConverter as one line molecular format that can be given as the argument of -s option without specifying the format.
  • PDF
  • Reactions could not be exported to PDF.
  • Name to structure (n2s)
  • Names with a cis- or trans-imine bond were failing to be converted to structures
  • Ions, such as "bismuth(3+)", were imported with valence property set to 0.
  • Ortho substitution on acetophenone generated wrong structures.
  • Some E/Z and R/S stereochemistry was missing in structures imported from names when the locant of the atom or bond with stereochemistry was not specified explicitly.
  • The "H-" ion was missing from names containing "hydride", e.g., sodium hydride, they only had e.g., "Na+ instead of the correct NaH.
  • Names containing atoms with both a non-standard valence (λ) and a positive charge were converted to structures with an extra implicit hydrogen on that atom.
  • Primary and secondary amine oxides were represented as N-OH instead of [N+]-[O-].
  • The "Name" format was not automatically recognized for names with XML/HTML character references, such as "β" or "α".
  • In some cases, amino acids with α, β, and γ prefixes were not converted.
  • Using n2s in the applet required the downloading of an unnecessary component. This, in turn, made the first applet usage much slower.
  • Document to structure (d2s)
  • Some common words such as "DUST" or "crank", were recognized as names because, e.g., DUST is a rare acronym for a chemical structure. These words are now ignored.
  • The insideTag format option was not working for XML and XHTML documents.
  • Some uppercase words were mistakenly recognized as SMILES strings, such as "CISCO" or "ON-OFF".
  • Some embedded images were returned with 'PNG' type instead of 'OSR', and the usual OSRA options and properties (e.g., timeout, confidence filtering) were missing as well.
  • When d2s was interrupted (for instance, by a timeout), an OCR or OSR process could be left running in the background until it was completed. In similar cases such processes are now stopped immediately.
  • Extracted names sometimes contained some irrelevant characters at the end, such as "4-(trifluoromethyl)-2-((1H-1,2,4-triazol-1-yl)phenyl)-methanamine 2e" instead of "4-(trifluoromethyl)-2-((1H-1,2,4-triazol-1-yl)phenyl)-methanamine".
  • In some cases, single names separated by space were imported as if they were one compound, for instance, "2-hexanoyloxyethyl 1-formyloxypropyl".
  • Embedded structures in Office documents were always imported with the absolute chiral flag set.
  • Structure to name (s2n)
  • When generating names in parallel in multiple threads, some E/Z stereo bond modifiers were missing from the output.
  • Wrong names were generated for structures with multiple attachment points. These cases are now detected and no name is generated for them. Generating a name in this case will be implemented in the future.
  • Molecule Representation
  • Valence Check
  • Valence check changed standalone Bi to BiH3.
  • Valence error was not shown on a Carbon atom having a triple and an aromatic bond.
  • Valence Check accepted Stannane with any number of implicit hydrogens.
  • Implicit/Explicit Hydrogen Conversion
  • Stereoinformation was lost during explicit Hydrogen removal from stereocenter when all ligands of the stereocenter were also stereogenic.
  • Conversion of explicit Hydrogen to implicit one thrown exception when there is only a Hydrogen atom in an R-group definition or in a definition member.
  • Image I/O
  • Text box contents, atom labels and atom attributes (e.g., atom indices, stereo labels), and IUPAC names were not exported to PDF as text. When the "Save/Load GUI settings" checkbox was checked in the Preferences dialog, text attributes (e.g., font type, size) were not exported either.
  • Clean 2D
  • Clean removed stereo centers around the contracted superatom S-groups.
  • Clean2D got stuck and error message was thrown for some more complex molecules imported from SMILES.
  • Stereochemistry
  • Cis-Trans stereoisomerizm was recognized on flexible Nitrogen atoms.
  • Stereo information could lost in symmetric bridged systems with explicit Hydrogen atoms.
  • Calculations
  • Elemental Analysis
  • ElementalAnalyser.setMolecule(String) threw exception if the formula contained () brackets (e.g. C6H11N3.2(HCl)). API documentation, Forum topic
  • Protonation (pKa, Major Microspecies, Isoelectric Point)
  • Minor bug has been fixed on the distribution chart.
  • Isomers (Tautomers, Stereoisomers)
  • Stereoisomers plugin failed to generate all stereoisomers for tricyclic compounds. Forum topic
  • Generic tautomer generation threw exception on some molecules.
  • Some invalid 3D structures were not filtered out during stereoisomer generation although 3D-filter option was turned on. Forum topic
  • Some cycloolefine stereoisomers were mistakenly filtered out as duplicates, so they were missing from the generated list of stereoisomers. Forum topic
  • Structure Checker
  • In Structure Checker GUI, the scroll bar was missing in the report tab if the report contained four to six structures.
  • When the Structure Checker configuration contained multiple substructure checkers, their order would change during structure checking process.

New in Marvin Suite 6.0.0 (May 24, 2013)

  • New features and improvements
  • MarvinSketch GUI
  • The default tool in MarvinSketch is Rectangle Selection instead of Single Bond.
  • MarvinSketch GUI has been refreshed: Icon set has been changed in MarvinSketch. Menu items have been rearranged. Several dialogs, tooltips, menus has been renamed.
  • A new Marvin configuration has been added to MarvinSketch. Already existing Marvin configurations have been renamed. Documentation
  • MarvinSketch now starts with the native "Look & Feel" on Windows and on Mac OS X.
  • MarvinSketch Dialog
  • At the first launch of MarvinSketch after installation, a dialog asks the user to select the desired skin for the GUI configuration. Documentation
  • The Open dialog has been modified. Selecting molecules to load from a multistructure file happens now directly on the Open dialog.
  • New dialog, called "Insert file", has been introduced into MarvinSketch for adding structures from new files to the canvas contents. Documentation
  • The Save dialog has been extended with an Advanced panel to set saving options.
  • Painting
  • Drawing quality has been improved: join of single bonds has been refined.
  • Superatom S-group attachment points are denoted by numbers instead of asterisks.
  • Editing
  • MarvinSketch GUI can handle unlimited number of attachment points on Superatom S-groups. There are new menu options for adding and removing attachment points in the Atom menu and in the contextual menu. Documentation
  • Bond length can be scaled. Bond length and size of other objects can be set by dragging the displayed corners of the bounding rectangle. Scaling is also available on the Document Style dialog. Scaling does not work when the structure has been rotated in 3D mode (with F7). Documentation
  • Load/Save handling in UI
  • New loading mechanism has been introduced in MarvinSketch. New menu option, Insert file, has been added to the File menu; it appends the contents of the chosen file to the structure on the canvas. Documentation
  • New saving mechanism has been introduced in MarvinSketch. Documentation
  • New save mechanism has been introduced for MarvinView. Documentation
  • Reactions and structures containing R-group definitions cannot be saved either in separate files or separately in the same file. Documentation
  • Clipboard handling
  • Images of chemical structures can be imported from the clipboard via the configured image import service or locally installed OSRA.
  • Template Library
  • New template set, Organometallics, has been added to the Template Library.
  • New amino acid templates have been added (e.g., pyrrolysine, selenocysteine, "any/unknown/undetermined aminoacid").
  • The following amino acid templates have three attachment points: arginine, cysteine, histidine, lysine, selenocysteine, serine, threonine, tryptophan, tyrosine.
  • Integration
  • The new Automapper has been introduced in MarvinSketch.
  • MarvinSpace
  • Copy and Paste functions have been added to MarvinSpace.
  • 3D editor: Molecules can be edited in 2D in MarvinSketch, and aligned to the original 3D molecule.
  • Import/Export
  • MRV/CML
  • Import and export of more than two Superatom S-group attachment points are supported.
  • MRV schema
  • New element, AttachmentPointArray, is introduced in format MRV to describe the new Superatom S-group attachment point representation. MRV Schema, Documentation
  • MOL, SDF, RXN, RDF
  • The import of template based MDL MOL files is introduced.
  • Import and export of more than two Superatom S-group attachment points are supported from MDL MOL based formats.
  • SKC
  • Import and export of more than two Superatom S-group attachment points are supported. Superatom S-groups having at least one crossing bond are exported in their expanded form.
  • CDX/CDXML
  • Import and export of more than two Superatom S-group attachments point are supported.
  • Curved lines can be imported from CDX files.
  • CXSMILES/CXSMARTS
  • Generic, Polymer, and Mixture type S-groups are stored in CXSMILES/CXSMARTS format. Documentation
  • SMILES/SMARTS
  • In SMILES import, radicals are not added anymore to atoms with atomic number above chlorine, except for bromine and iodine. If implicit hydrogen can not be added to or removed from the atom (as it is in brackets in the SMILES definition), then a valence property is set to correct its valence if necessary. Documentation
  • Peptide
  • Amino acids: Cysteine, Aspartic acid, Glutamic acid, Histidine, Lysine, Asparagine, Glutamine, Arginine, Serine, Threonine, Selenocysteine, Tryptophane, and Tyrosine are imported with three attachment points from peptide format.
  • New 1-Letter and 3-letter amino acid codes were added: U and Sec for selenocysteine; O and Pyl for pyrrolysine; X and Xaa for "any/unknown/undetermined amino acid"; B and Asx for "Aspartic acid or Asparagine"; Z and Glx for "Glutamic acid or Glutamine"; J and Xle for "Leucine or Isoleucine".
  • FASTA
  • Peptide, DNA, and RNA import from FASTA format has been introduced. Documentation
  • Name to Structure (n2s)
  • Custom name-to-structure webservices can now be configured to receive the name in the middle of the URL, not just at the end, by using the [NAME] marker in the configuration URL.
  • More forms of ranged generic names are supported, such as "-C1-6alkyl". These are found extensively as part of markush structures in patents.
  • Document to Structure (d2s)
  • Text document processing has become faster (around 20% speedup for typical texts with a small proportion of chemical names).
  • The context (surrounding text) in which names appear in the document is now available as a property of the returned structures.
  • The osraTimeout option has been added to configure the maximum time to wait for OSRA to convert an image to structure (the default is 20 seconds).
  • Structure to Name(s2n)
  • The new format option "cas#" allows converting structures to their CAS Registry Number using a public webservice.
  • Molecule Representation
  • S-groups
  • Any number of attachment points can be added to Superatom S-groups.
  • S-group attachment point information can be set only to atoms being part of a Superatom S-group.
  • Valence Check
  • Valence check does not deal with free attachment points.
  • New valence check option is introduced to allow/deny traditional forms of pentavalent Nitrogen.
  • Calculation
  • Protonation (pKa, Major Microspecies, Isoelectric Point)
  • log[%] vs. pH distribution chart is introduced in case of pKa calculation. Documentation
  • Major miscrospecies calculation is supported for molecules with coordinate bonds. Forum topic
  • NMR (HNMR, CNMR Prediction, ...)
  • NMR predictor considers novel coupling types.
  • Updated trainingset has improved the NMR shift prediction accuracy in both 1H and 13C NMR predictors.
  • 1H NMR calculation has become faster as no 3D conformer generation is applied.
  • Geometry (Topology Analysis, Geometry, PSA, MSA)
  • Setting any ChemAxon supported aromatization method (general, basic, loose) is available in TopologyAnalyserPlugin which affects the result of many topology analyser calculations (e.g., aromatic atom/bond/ring count).
  • Chemical Terms
  • New sortableFormula() function is introduced. The generated sortable formula can be used to sort formulas in alphabetical order. Documentation
  • cxcalc
  • pKa training library can be used without relying on user home. Use option --correctionlibrarypath to read custom training file.
  • New sortableFormula option is introduced. The generated sortable formula can be used to sort formulas in alphabetical order.
  • cxtrain
  • New option, -p, has been introduced to save the training result to custom path.
  • Automapper
  • New Automapper tool is introduced. It maps reactions more accurately. Documentation
  • Automapper tool requires Standardizer license.
  • API documentation: com.chemaxon.mapper.Automapper
  • Structure Checker
  • "Traditional nitrogen representation allowed" option is available in Valence Error Checker. Documentation
  • External structure checker and fixer manager is integrated into Structure Checker GUI application. It is accessible from the preferences menu as "Checker/Fixer Manager". Documentation
  • Known issue:
  • MarvinSketch Applet
  • External checker classes do not load if browser uses Java SE 6. Please, use Java SE 7 for successful checker class loading.
  • Bugfixes:
  • MarvinSketch Menu
  • The "Recent Files" list was not updated with the new file name when the file contained multiple structures and more records were selected.
  • Painting
  • There was a gap between the lines of the double bond and the single bonds when two single bonds connected to the same (non-visible) carbon atom on one end of a double bond.
  • Electron flow arrows partially hid lone pairs in some cases.
  • Clipboard handling
  • When copying and pasting between Marvin applications in Linux, an exception was thrown which froze the application where the copy operation had been performed. The exception originated from the applied freehep library, which has been updated.
  • MarvinSpace
  • 3D alignment: MCS mode is fixed to align molecules in 3D.
  • Image I/O
  • Image export did not remember the last folder used for saving.
  • Molecule source was not saved in jpg, png, and svg files when "Save As Image" was selected. Forum topic
  • Import/Export
  • MOL, SDF, RXN, RDF
  • Structures that contained two S-groups with exactly the same atoms imported from MDL MOL format could cause java.lang.RuntimeException. Forum topic
  • Property name was imported as its value from SDF file when the property name contained square brackets.
  • Exporting a peptide sequence containing bridge between two ungrouped amino acids to MOL format (V2000 or V3000), then importing it back, changed the coordinates of the contracted groups.
  • CDX/CDXML
  • CDX files created by ChemDraw 9.0.1 containing abbreviated groups with no attachment points was not imported.
  • ChemDraw CDX files containing textboxes with Chinese characters were not imported.
  • Chemical formula-like subscript of a Superatom S-group was read in reverse order from CDX when the group was to the left of the fragment.
  • Superatom S-groups not having crossing bonds were read as textbox from CDX files.
  • CDX files exported from ChemDraw 5.0 and containing contracted Superatom S-group was not imported.
  • CDX import read half headed arrows as full headed.
  • CXSMILES/CXSMARTS
  • CXSMARTS export did not keep CIS/TRANS information for symmetrical structures.
  • Extended part of CXSMARTS was not written correctly for any halogen query atoms.
  • SMILES/SMARTS
  • Unique SMILES string generation for a fragment could have differed depending on the fragment count of the molecule
  • Peptide
  • User defined custom amino acid dictionary caused wrong custom amino acid structure or java.lang.ArrayIndexOutOfBoundsException during peptide import.
  • Name to Structure (n2s)
  • When calling a custom name-to-structure webservice, names with special characters (including space) were not URL encoded, possibly resulting in failed conversions for such names.
  • Name containing fused rings and converted to all uppercase letters were not recognized.
  • Name to Structure could get stuck in a deadlock during the first usage when that occurred concurrently in several threads.
  • When using the "name converters" API, converters were not properly removed after using thread-local converters.
  • Document to Structure (d2s)
  • When interrupted while doing OCR or OSR, document to structure logged an exception about the interrupt. This caused in particular a warning dialog to appear in Instant JChem during a document import.
  • Names were not recognized when they contained a complex bracketed bond locant followed by a comma, such as "2(7)" in tricyclo[6.3.1.02,7]dodeca-2(7),3,5-triene.
  • Scrolling back in MarvinView could have caused failures for very large documents (more than 1000 structures) and names with non-ASCII characters.
  • Structure to Name(s2n)
  • name:source returned an empty name for empty structures instead of the actual stored name.
  • The name "perimidine" was not attributed to the right structure.
  • Molecule Representation
  • Implicit/Explicit Hydrogen Conversion
  • Removing explicit hydrogens on some larger PubChem compounds caused infinite loop.
  • Clean 2D
  • Partial clean misplaced the molecule when only one atom was fixed.
  • Clean 2D failed to preserve cis/trans stereo information in some cases.
  • Calculation
  • NMR (HNMR, CNMR Prediction, ...)
  • PDF export of NMR spectra was failed when the generated new page contained a blank line only.
  • When displaying NMR spectra of selected tautomers, the background of the tautomer preview window was black in Linux OS.
  • Deprecation:
  • Deprecated methods
  • Molecule Representation
  • Valence Check: MoleculeGraph.VALENCE_CHECK_AMBIGUOUS, MoleculeGraph.ValenceCheckState, MoleculeGraph.setValenceCheckState(ValenceCheckState), MoleculeGraph.getValenceCheckState() MoleculeGraph.getPossibleAttachmentPoints(MolAtom)
  • S-groups: SuperatomSgroup.getAttachAtoms(), SuperatomSgroup.getLegalAttachAtoms(), SuperatomSgroup.getFreeLegalAttachAtoms(), SuperatomSgroup.isFreeLegalAttachAtom(MolAtom), SuperatomSgroup.isLegalAttachment(MolAtom), SuperatomSgroup.sortXBonds(), MolAtom.getAttach(), MolAtom.setAttach(int), MolAtom.setAttach(int, Sgroup)
  • Elemental Analysis: ElementalAnalyser.setMolecule(SMolecule)
  • Other deprecated methods Molecule.exportToFormat(String), Molecule.exportToBinFormat(String), Molecule exportToObject(String) throws java.lang.IOException.
  • Structure to Name (s2n)
  • The method chemaxon.marvin.io.formats.name.nameexport.IUPACNamer.generateName(Molecule) , though not documented, was public for internal reasons, and used a non-thread-safe way to receive options. It is now deprecated in favor of chemaxon.formats.MolExporter(Molecule, String format) , where format can be for instance "name" for IUPAC name, "name:t" for traditional name. See https://www.chemaxon.com/marvin/help/formats/name-doc.html#export for all possible options.
  • Automapper
  • chemaxon.marvin.modules.AutoMapper
  • Removed methods
  • Molecule Representation
  • MolAtom.setMassnoIfKnown(String), MolAtom.isNobleGas(), MolAtom.isArrowEnd(), MolAtom.valenceCheck(), MolAtom.getEdgeCount(), MolAtom.getEdge(int), MolAtom.getEdgeTo(MolAtom), MolAtom.haveSimilarEdges(MolAtom),
  • MolBond.ARROW(), MolBond.isCoordinative(), MolBond.isArrow(), MolBond.getNode1(), MolBond.getNode2(), MolBond.getOtherNode(MolAtom), MolBond.cloneEdge(MolAtom a1, MolAtom a2)
  • MoleculeGraph.AROM_CHEMAXON, MoleculeGraph.AROM_DAYLIGHT(), MoleculeGraph.setSetSeqs(int id), MoleculeGraph.getAromrings(), MoleculeGraph.getNonAromrings(), MoleculeGraph.getAromrings(int), MoleculeGraph.getNonAromrings(int), MoleculeGraph.mergeFrags(), MoleculeGraph.getFragIds(), MoleculeGraph.getfindFragById(int fragId, MoleculeGraph frag), MoleculeGraph.getNode(int), MoleculeGraph.setNode(int, MolAtom), MoleculeGraph.insertNode(int, MolAtom), MoleculeGraph.removeNode(MolAtom), MoleculeGraph.removeNode(MolAtom, int), MoleculeGraph.removeNodeVector(), MoleculeGraph.getEdgeCount(), MoleculeGraph.getEdge(int), MoleculeGraph.setEdge(int, MolBond), MoleculeGraph.insertEdge(int, MolBond), MoleculeGraph.insertEdgeInOrder(MolBond, MolBond[]), MoleculeGraph.replaceEdge(MolBond, MolBond), MoleculeGraph.removeEdge(MolBond), MoleculeGraph.getEdgeArray(), MoleculeGraph.getEdgeVector(), MoleculeGraph.getAllEdges(), MoleculeGraph.regenEdges(), MoleculeGraph.sortEdgesAccordingTo(MolBond[]), MoleculeGraph.mergeNodes(MolAtom that, MolAtom), MoleculeGraph.mergeFrags(int, int)
  • Molecule.mergeFrags()
  • RgMolecule.setAbsStereo(boolean, int, int), RgMolecule.createMol(String), RgMolecule.getBtab()
  • RxnMolecule.getBtab(), RxnMolecule.getStructureCount(int), RxnMolecule.getStructure(int, int), RxnMolecule.addStructure(Molecule, int), RxnMolecule.removeStructure(int, int)
  • CEdge, CNode, CGraph
  • MDocument.setGUIProperyContainer(MPropertyContainer)

New in Marvin Suite 5.12.4 (May 24, 2013)

  • Bugfixes:
  • Import/Export
  • MOL, SDF, RXN, RDF
  • Valid MOL file header was not recognized and therefore the file was not imported.

New in Marvin Suite 5.12.3 (May 24, 2013)

  • Bugfixes:
  • Import/Export
  • Name to Structure (n2s)
  • Names with ylium and uide suffixes are now supported.
  • Calculation
  • NMR (HNMR, CNMR Prediction, ...)
  • Coupling of a nucleus with a group of magnetically equivalent nuclei was not handled properly.
  • NMR Predictor did not consider negative coupling constant values.

New in Marvin Suite 5.12.2 (May 24, 2013)

  • Bugfixes:
  • Molecule Representation
  • Conversion from explicit hydrogen to implicit one removed stereo centers not having explicit hydrogen ligand. Forum topic
  • Import/Export
  • SMILES/SMARTS
  • Non ring bond information were imported as query strings from SMARTS.
  • After SMARTS import, those atoms that had no explicit aromatic property but had aromatic bond got query aromaticity property.

New in Marvin Suite 5.12.1 (May 24, 2013)

  • New features and improvements:
  • Import/Export
  • CDX/CDXML
  • S orbitals and oval shaped s or p orbitals are imported from CDX/CDXML. Forum topic
  • Bugfixes:
  • Painting
  • Charge symbol on carbon atoms was missing when the atom numbers were visible and the display of carbon atom labels was turned off.
  • When two atoms had more than one electron flow arrows between them, the electron flow arrows overlapped each other.
  • The second electron flow arrow started from a wrong position when a single electron and an electron pair flow arrow started from an atom which had a lone pair and a radical as well.
  • Editing
  • Atom Lists and NOT Lists could not be created by typing atomic symbols separated with commas (e.g., "f,br,cl" or "!f,br,cl").
  • Import/Export
  • MRV/CML
  • MRV and CML export wrote out characters incorrectly which are not supported by the character set.
  • MOL, SDF, RXN, RDF
  • SDF files having invalid header could not been imported.
  • Deuterium and tritium isotopes were converted to simple hydrogen atom if a molecule was exported to ChemAxon compressed MOL format (CSMOL).
  • SMILES/SMARTS
  • MolExporter.exportToObject() added an extra newline to SMILES.
  • Nitrogens connecting two aromatic rings had radical after import if nitrogen was bracketed in the SMILES representation. Forum topic
  • InChi/InChiKey
  • Absolute stereo flag was missing during InChi export/import and InChiKey export. Forum topic
  • Molecule Representation
  • Valence check
  • Number of added implicit Hydrogen atoms were incorrect in some cases for positively charged sulfur atom.
  • Calculation
  • Isomers (Tautomers, Stereoisomers)
  • After canonical tautomer generation, the information of "double cis or trans" bond type might have been lost in certain cases. Forum topic