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Marvin Changelog

What's new in Marvin 19.6.0

Mar 1, 2019
  • Bugfixes:
  • Editing:
  • The label of atoms with implicit hydrogens displayed on the top of the atom was misplaced
  • The arrow tool did not snip the target atom while mapping reactions.
  • Molprinter:
  • In some case MolPrinter did not render reaction signs.

New in Marvin 19.3.0 (Feb 7, 2019)

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

New in Marvin 19.2.0 (Feb 7, 2019)

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

New in Marvin 19.1.0 (Feb 7, 2019)

  • Bugfixes:
  • I/O:
  • There was a significant slowdown in the import of SMILES of some molecules with huge ring system.

New in Marvin 18.30.0 (Feb 7, 2019)

  • Improvement:
  • I/O:
  • D ocuments 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 18.29.0 (Feb 7, 2019)

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

New in Marvin 18.28.0 (Feb 7, 2019)

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

New in Marvin 18.27.0 (Feb 7, 2019)

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

New in Marvin 18.26.0 (Feb 7, 2019)

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

New in Marvin 18.25.0 (Feb 7, 2019)

  • 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 18.24.0 (Feb 7, 2019)

  • Bugfixes:
  • Editing:
  • Expanding abbreviated groups gave distorted structure.
  • View port changed for a different Journal were applied.
  • The feedback of Lasso selection tool didn't work for single-step reactions.

New in Marvin 18.23.0 (Sep 27, 2018)

  • Improvements:
  • Editing:
  • Copy from Analysis box has been introduced.
  • Textbox handling has been revisited.
  • Bugfixes:
  • Editing:
  • 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 18.21.0 (Aug 30, 2018)

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

New in Marvin 18.18.0 (Aug 3, 2018)

  • BUG FIXES:
  • 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 18.17.0 (Jul 30, 2018)

  • IMPROVEMENTS AND BUGS FIXED:
  • Copy to MS Office option (IJC-10257):
  • Structure is stored in clipboard in smiles format for simple copy (CTRL+C) command
  • Structure is stored in clipboard in mrv format for "Copy to MS Office" command (You need to have JC4O installed)

New in Marvin 18.15.0 (Jul 10, 2018)

  • IMPROVEMENTS:
  • Naming:
  • CAS number is available from Structure>Generate name submenu.
  • Mac OS:
  • Copy as .PDF option has been removed.

New in Marvin 18.14.0 (Jun 23, 2018)

  • Bug fixes:
  • 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 18.13.0 (Jun 13, 2018)

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

New in Marvin 18.11.0 (May 25, 2018)

  • BUG FIXES:
  • 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 18.10.0 (Apr 16, 2018)

  • IMPROVEMENTS:
  • Editing:
  • Ctrl+D shortcut and new Edit menu item have been added for Copy as OLE.
  • BUG FIXES:
  • 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 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.
  • From this version on OLE format can be copied using the Copy as... (Ctrl+K) option.
  • 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 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.
  • BUG FIXES:
  • MarvinView:
  • Structures were not centralized correctly when the window was resized.

New in Marvin 18.4.0 (Feb 14, 2018)

  • BUG FIXES:
  • 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 18.3.0 (Feb 1, 2018)

  • IMPROVEMENTS:
  • Editing:
  • The size of the default UNDO stack has been changed to 25 steps.
  • BUG FIXES:
  • 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.
  • When CDX/CDXML file was imported, the font size of text was smaller than the original one.
  • Installer:
  • MarvinSketch could not be launched by clicking its icon on MAC OSX.

New in Marvin 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 17.25.0 (Oct 19, 2017)

  • BUG FIXES:
  • 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 17.24.0 (Sep 22, 2017)

  • IMPROVEMENTS:
  • Editing:
  • Aryl Heteroaryl Heteroalicyclyl Fusedheteroaryl, Fusedheteroalicyclyl is added to the Homology groups.
  • Analysis box handles pseudo formulas.
  • The size of textbox follows the changing in font type/size.
  • Stereo calculations:
  • Assignment of quaternary stereocenters aligns with the IUPAC recommendations.
  • BUG FIXES:
  • Editing:
  • Charges were missing from the chemical formula in Analysis Box.
  • Copy of a reactant of a reaction threw null pointer exception in some cases.
  • Opening new MarvinSketch window deleted the clipboard.
  • In some cases the bounding box of text box was active even in unselected state.
  • Image IO:
  • Image export options for (de)aromatization were not considered.
  • IO:
  • Extra plus signs were added when exporting reactions to SKC format.
  • SKC export transforms the coordinates in a way that the molecules will be rendered in the middle of the canvas.
  • Names longer than 80 characters were saved in MOL v2000 files.

New in Marvin 17.22.0 (Sep 14, 2017)

  • IMPROVEMENTS:
  • Speed of editing (dragging/rotating) big molecules decreased.
  • Abbreviations NBoc and OBoc have been introduced.
  • Aromatic ring templates have been added to the template library.
  • BUGFIXES:
  • Editing:
  • When rotating structure containing aromatic ring in 3D, the aromatic ring was painted in a wrong position in few cases.
  • The blue feedback of a selected molecule changed its position when the user moved the mouse.
  • `Send to back` context menu of graphical objects did not work.
  • When trying to create an R-group definition in a reaction, the drawing pane stopped refreshing, and the response time increased.
  • MarvinSketch mirrored the rectangle object which was created by MarvinJS.
  • Text box:
  • Exception was thrown when pressing space key in one character long text box.
  • When a user copied a text which was a name of a chemical compound into an empty text box, the structure was displayed.
  • Print:
  • The molecule was not centralised on printouts, resulted that some part of the structure was cut.
  • In Macintosh computers, structure printouts did not include coloured bonds.
  • Image IO:
  • Quality of generated EMF was low when .Net libraries were not installed on the user`s computer.

New in Marvin 17.21.0 (Aug 28, 2017)

  • Bug fixes:
  • IO: There was a space between the version number and the timestamp in the header of .MOL files.

New in Marvin 17.16.0 (Jul 22, 2017)

  • BUG FIXES:
  • 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'.
  • MARVINVIEW:
  • Print to pdf using 'All option' gave warning..
  • High usage of CPU was observed upon scrolling.

New in Marvin 17.15.0 (Jul 15, 2017)

  • BUG FIXES:
  • GUI:
  • Computers with a non-English local setting used their local language on MarvinSketch's GUI.

New in Marvin 17.14.0 (Jul 7, 2017)

  • BUG FIXES:
  • Editing:
  • When changing Journal style the structure disappeared.
  • Atom font could not be set when "Apply for selection only" was selected.
  • Marvin crashed when MP stereo visibility option was on and a single arrow was placed on the canvas.
  • In some cases the removal of explicit hydrogen atoms resulted in an error.
  • IO:
  • Bond coloring did not work in SVG export.
  • 2D Clean:
  • In some cases upon 2D cleaning of structures with atom properties an error message was thrown.

New in Marvin 17.12.0 (Jun 15, 2017)

  • 2D clean:
  • In some cases the double bond stereo information changed during 2D coordinate generation.

New in Marvin 17.10.0 (Jun 5, 2017)

  • IMPROVEMENTS:
  • Editing:
  • `Wireframe with knobs` display option has been eliminated.
  • IO:
  • 'Wireknobs' export option has been eliminated.
  • GroupId property has been introduced to CDX import/export
  • BUG FIXES:
  • Editing:
  • In some cases the display didn't get centered when the size of the window was changed.

New in Marvin 17.7.0 (May 5, 2017)

  • BUG FIXES:
  • Editing:
  • Curved arrows imported from MRV file that was created by Marvin before version 16.5.2. are malformed.
  • In some cases merging of two fragments transformed isolated bonds into aromatic bonds.

New in Marvin 17.5.0 (Apr 21, 2017)

  • BUG FIXES:
  • Editing:
  • Coordinates of the feedback of abbrev groups were positioned imperfectly.
  • Only the atoms were highligted when colored bonds were selected.
  • Merge feedback was indicated when bond tool was in hand.
  • Installing:
  • When MarvinSketch was installed to computers with single CPU exception was thrown.

New in Marvin 17.3.27.0 (Mar 30, 2017)

  • IMPROVEMENTS:
  • Editing:
  • The head of coordinate bond resizes with the length.
  • New R-group hit detection feedback has been introduced.
  • Stereo labels are not included in the selected structure.
  • BUG FIXES:
  • Editing:
  • The values of "Bond thickness" on "Document styles settings" and "Format" panels were different.
  • When there was a selected molecule on the canvas and the user pressed Ctrl+C, the molecule slightly shifted.

New in Marvin 17.2.13.0 (Feb 17, 2017)

  • IMPROVEMENTS:
  • Editing:
  • UIDs are not displayed
  • BUG FIXES:
  • Editing:
  • Insert character by typing it to the unicode table didn't work.
  • R-group attachment points were not painted in selected structures
  • Molconvert:
  • Molconvert did not take into account the colored atoms/bond.
  • Image generation:
  • An invalid XML character was inserted into thr generated SVG.

New in Marvin 17.2.6.0 (Feb 10, 2017)

  • IMPROVEMENTS:
  • Editing:
  • New icons have been added to Mirror and Flip functions.
  • I/O:
  • CDX/CDXML fragment object attributes are imported as molecule properties in MRV.
  • CDX/CDXML fragment IDs are imported as molecule properties in MRV.
  • Molecule properties are exported as CDX fragment object attributes.
  • BUG FIXES:
  • Editing:
  • Link to Chemicalize was broken.
  • Display:
  • If imported MRV file contained atom and bond uniqe IDs, they were visible on the canvas.
  • I/O:
  • Forced SMILES export for molecule fragments with attachment point fixed.
  • Scale factor was not saved when the user saved the content of the canvas to the clipboard in MRV format.

New in Marvin 17.1.30.0 (Feb 1, 2017)

  • IMPROVEMENTS:
  • Editing:
  • Atom number position has been revisited in case of structures having implicit hydrogens.
  • TM/P notation for atropisomers has been revisited.
  • BUG FIXES:
  • Editing:
  • Overwriting an atom with the keyboard did not refreshed the analysis box.
  • Naming - Name to Structure:
  • CAS number resolution using the remote webservice didn't work in Java versions lower than 8.

New in Marvin 17.1.9.0 (Jan 11, 2017)

  • BUG FIXES:
  • Editing:
  • Merging two molecules on the canvas by dragging failed, however feedback indicated the merge.
  • Merge did not work after rotation.
  • Merge feedback indicated, but merge does not happen in case of chain tool.
  • Single bond turned into triple bond on a single click if previously a double bond has been drawn with the single bond tool.
  • Shift button did not expand the abbreviated group.

New in Marvin 16.12.19.0 (Dec 21, 2016)

  • BUG FIXES:
  • Editing:
  • Marvin froze when one tried to aromatize a three-membered ring or imported this kind of structure.
  • Direct copy of EMF image in other applications resulted in poor quality picture.

New in Marvin 16.11.28.0 (Dec 3, 2016)

  • BUG FIXES:
  • Editing:
  • Double bond could not be changed to to Double Cis or Trans
  • Second arrow appeared when there is a reaction on the canvas, and the user deleted something then reverted the deleted item with UNDO.

New in Marvin 16.11.21.0 (Nov 29, 2016)

  • Editing:
  • "Place analysis box" option did not work if the whole canvas whole cleared before during the editing.
  • Copy/Paste:
  • Only MRV and MDLSK formats were available on the clipboard after copying two fragments with two attachment points from Marvin Sketch.
  • OLE:
  • During OLE editing, if one places a single arrow to the canvas, the arrow changed its position.
  • I/O:
  • When a picture of a reaction was exported via API from SMILES string, the plus signs were missing.

New in Marvin 16.11.14.0 (Nov 15, 2016)

  • Bug fixes:
  • Search Engine: The tautomer duplicate and full structure search could have been very slow in case of large, highly symmetrical, and stereo configured molecules.

New in Marvin 16.11.7.0 (Nov 15, 2016)

  • Improvements and bugs fixed:
  • Users with the ROLE_EXPORT_DATA can now export data from Instant JChem directly into Plexus Analysis. The documentation on this feature can be found here. (PS-148)
  • Molecule auto-scale in Marvin sketch switched off (IJC-10122)
  • Fixed bug in Marvin Sketch - changing bond type using right click menu was causing an exception (IJC-10054)
  • Selection and query results updated on charts after resume (IJC-9803)

New in Marvin 16.10.31.0 (Nov 2, 2016)

  • IMPROVEMENTS:
  • Editing:
  • MolPrinter option for S-group attachment visibility has been implemented.
  • Atom map and atom number positioning has been revisited.
  • The highlight of valance error has been changed to a red patch.
  • BUG FIXES:
  • Editing:
  • Map numbers visibility was bad in exported png images for middle sized structures..
  • R/S label position did not take into account bold bond thickness.
  • Atom mapping numbers were positioned badly in some cases.
  • Aromatic rings could not be seen in selected structures.
  • I/O:
  • Scale factor wass not saved when the user saved the content of the canvas to the clipboard in MRV format.

New in Marvin 16.10.17.0 (Oct 20, 2016)

  • IMPROVEMENTS:
  • Editing:
  • Arrow type can be changed.
  • Analysis box can be used for selected merged products/reactants.
  • BUG FIXES:
  • Editing:
  • Distribute and/or Align messes up position of polymer brackets.
  • When a picture of a reaction is exported via Marvin API, the plus signs were missing.
  • Deleting an arrow from empty canvas threw a NPE.
  • Unmerge reactant/product deleting another component.
  • Text from Firefox, Google Chrome and some text editing application could not be pasted to text box in MarvinSketch.

New in Marvin 16.10.3.0 (Oct 13, 2016)

  • Improvements and bugs fixed:
  • The pivoting functionality was introduced to Instant JChem. More details about the new entity type and its use can be found in the documentation. (IJC-1066)
  • Only a valid recent URL is now offered in the database connection wizard. (IJC-6622)
  • Axis labels in radar chart widget display japanese characters properly. (IJC-9655)
  • Fixed editing of decimal number values in widgets. In some cases the decimal part was lost. (IJC-9943)
  • Data are sorted correctly when exporting with results filter. (IJC-9980)
  • Fixed AdminTool's operation for managing security configurations. It is now possible to copy a security config from one schema to another. The operation performs much faster by touching only the source and target IJC schemas.(IJC-9985)
  • Fixed the deadlock (freeze) on IJC close. This issue can appear in versions 16.9.5.0 and 16.9.12.0. (IJC-9993)

New in Marvin 16.9.26.0 (Sep 29, 2016)

  • IMPROVEMENTS:
  • Editing:
  • Selection has been revisited.
  • BUG FIXES:
  • Editing:
  • Clicking on the canvas with the Atom assigning tool during directed merge painted a reaction

New in Marvin 16.9.5.0 (Sep 7, 2016)

  • BUG FIXES:
  • 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 16.8.29.0 (Sep 1, 2016)

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

New in Marvin 16.8.22.0 (Aug 24, 2016)

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

New in Marvin 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 16.8.1.0 (Aug 3, 2016)

  • IMPROVEMENTS:
  • Marvin GUI:
  • Off-line documentation has been improved.
  • BUG FIXES:
  • Editing:
  • Merging agents in reaction threw a NPE.
  • Analysis box was not updated properly if it had been replaced before the modification.
  • OSRA:
  • OSRA import did not work for CopyPaste and DragN'Drop.
  • Import/export:
  • Greek characters were not exported in svg format.

New in Marvin 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 16.6.20.0 (Jun 29, 2016)

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

New in Marvin 16.6.6.0 (Jun 7, 2016)

  • IMPROVEMENTS:
  • GUI
  • Ctrl+M shortcut has been introduced for Copy as MRV command.
  • 3D rotate (F6) mouse mode has been removed.
  • `Scale` has been switched to `Size`on atom format panel.
  • 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.
  • Arrow drawing deleted the No Structure.
  • 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 16.5.23.0 (May 25, 2016)

  • IMPROVEMENTS:
  • Editing:
  • Invert selection (Ctrl+Shift+I ) has been added.
  • GUI:
  • Help has been revisited.
  • BUG FIXES:
  • Editing:
  • Directed merge involving more than 2 atoms did not work properly.
  • Aromatic circles were not visible (they were painted in black) when the background was set black.

New in Marvin 16.5.2.0 (May 9, 2016)

  • Improvements and bugs fixed:
  • Fixed issue in M:N data retrieval for certain circumstances. (IJC-9551)
  • Improvements in loading large amount of data from Oracle. (IJC-9492)
  • Use java.lang.Double for floating-point numbers by default. (IJC-9494)

New in Marvin 16.4.18.0 (Apr 24, 2016)

  • Marvin/Jchem 16.4.18.0 are used. JChem tables will not be regenerated from 16.2.22.0. IJC metadata will not be regenerated from previous version.

New in Marvin 16.4.11.0 (Apr 19, 2016)

  • IMPROVEMENTS:
  • Editing:
  • Grid and guidedlines are added to the canvas to make easier the drawing.
  • BUG FIXES:
  • Editig:
  • Sometimes the formatting of IUPAC names was wrong.
  • When the adamantane molecule was placed into the canvas from a template, the bond which was the back should have been in the front.

New in Marvin 16.4.4.0 (Apr 12, 2016)

  • Improvements and bugs fixed:
  • A small improvement in Admin Tool notification messages. (IJC-8936)

New in Marvin 15.12.7.0 (Dec 8, 2015)

  • IMPROVEMENTS:
  • OLE:
  • Keyboard shortcuts can be used in OLE editor.
  • BUGFIX:
  • I/O:
  • The import of Mol files containing sequences with ungrouped structures generated wrong molecules.
  • Editing:
  • Charges of polymers were displayed both on the atom label and the bracket.
  • The atom list label was sometimes cut upon selection.
  • Changing bond type using the Bond< Type menu generated different structure than the Bond tool.
  • Image export:
  • Circled charges were cut from images when no margin was set.

New in Marvin 15.11.30.0 (Dec 2, 2015)

  • Bug fix:
  • Marvin was unable to start with Synth look and feel due to an initialization issue.

New in Marvin 15.11.23.0 (Nov 24, 2015)

  • IMPROVEMENTS:
  • No structure:
  • "No structure" label has been introduced. It is available from the Structure and the contextual menu. This new feature involves changes in the .mrv format as well (For detailed information click here.)
  • Bug fix:
  • Copy/Paste on OS X:
  • E/Z label display options are missing when copying to pdf.

New in Marvin 15.10.26 (Oct 29, 2015)

  • IMPROVEMENTS:
  • Editing:
  • The result of Elemental Analysis can be copied to into a text editor or in a textbox.
  • BUG FIX:
  • Textbox:
  • Textboxes could not be formatted at the same time.

New in Marvin 15.10.19.0 (Oct 22, 2015)

  • Bug fix:
  • .NET:
  • It was not possible to copy using Ctrl+K in binary file formats (ie: .skc, .cdx) from Marvin .NET.
  • Binary formats could not be pasted into Marvin .NET.

New in Marvin 15.10.5 (Oct 13, 2015)

  • Bug fix:
  • 2DClean: In certain cases2Dclean switched the stereochemistry of double bonds.

New in Marvin 15.9.28.0 (Sep 30, 2015)

  • Improvements:
  • Templates:
  • 'Conformers' template has been added to the default library.
  • 'Organometallics' have been revised.
  • The former 'Amino acids' template has been renamed to 'Peptide building blocks' and 'Amino acids' containing the 22 proteinogenic amino acid has been added.

New in Marvin 15.9.14.0 (Sep 16, 2015)

  • Improvements:
  • Abbreviated groups - New abbreviated groups have been added to the default abbreviated group dictionary.

New in Marvin 15.8.31.0 (Sep 3, 2015)

  • IMPROVEMENTS:
  • Customization:
  • No possibility to set default selection tool
  • Editing:
  • After deleting an alias or pseudo atoms the original atom (i.e, R,A ) are kept.
  • BUG FIX:
  • 2D Cleaning:
  • The Ctrl+2 cleaning did not centralize the molecule.
  • Customization:
  • When a system level setting was overridden by a non default value, then the default value could not be reapplied.
  • MarvinGUI:
  • Pop -up dialogues did not work on Mac.
  • Typing in the Insert Abbreviated Group window's textbox froze the application.

New in Marvin 15.7.20.0 (Jul 22, 2015)

  • Improvements:
  • Journal sytles - New journal styles have been added.
  • Bug fix:
  • 2D Cleaning - In some cases wedged bonds were lost when structures were partially cleaned in reaction schemes.

New in Marvin 15.6.22.0 (Jun 26, 2015)

  • BUG FIX:
  • Import:
  • In certain cases molfiles having embedded S-groups with the same content were imported incorrectly.

New in Marvin 15.6.15.0 (Jun 16, 2015)

  • BUG FIX:
  • 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 15.6.8.0 (Jun 10, 2015)

  • 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.
  • BUG FIX:
  • 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 15.5.11.0 (May 14, 2015)

  • IMPROVEMENTS:
  • Journal styles:
  • New journal styles are saved in the journal_styles folder.
  • BUG FIX:
  • Editing:
  • Scrolling and zooming were disabled when Atom Label editor was in action.

New in Marvin 15.4.27.0 (Apr 30, 2015)

  • Improvement:
  • Document style handling has been improved and style properties files ha been changed.

New in Marvin 15.4.20.0 (Apr 22, 2015)

  • Improvement:
  • Structure drawing has been revisited.

New in Marvin 15.4.6.0 (Apr 10, 2015)

  • IMPROVEMENT:
  • MarvinSketch:
  • Painting performance has been improved due to revised caching.
  • BUG:
  • MarvinSketch:
  • Memory limits (128MB) on Mac OS X could cause serious slowdown.

New in Marvin 15.3.30.0 (Apr 7, 2015)

  • 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 15.3.23.0 (Mar 26, 2015)

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

New in Marvin 15.3.16.0 (Mar 20, 2015)

  • IMPROVEMENT:
  • Editing:
  • Position variation bond drawing from aromatic rings has been improved.
  • Naming:
  • Display specific conversion error message.
  • Marvin GUI:
  • Measurement unit : % of bond length has been added to the "Document style" dialog.
  • The end of a wedge bold has been changed to 1.5 times the bold bond width.
  • BUG FIXES:
  • Editing:
  • 2D clean of peptides in some cases resulted in temporary loss of bridges.
  • Peptide drawing: delete and re-draw a non-side connection in an amino acid having side-connection caused switch of the attachment points.
  • Graphical objects were lost during Paste when there was no chemical structure on the canvas.
  • Atom label and properties were rendered incorrectly.

New in Marvin 15.3.2.0 (Mar 5, 2015)

  • IMPROVEMENT:
  • Editing:
  • The alignment of isotopes and implicit H on the same atom has been improved.
  • I\O:
  • Margins size parameter has been introduced.
  • Header of MDL Molfiles has been changed and now contains the version of the software generated it. The format is YYmDD where YY is the last two digits of the current year, m is the month in hexadecimal format (from 1 to c) and YY is the day of the month the software was released.
  • Marvin GUI:
  • GUI options are saved in MRV file by default. (This can be switched off on the Load/Save Tab of the Preference dialog.)
  • BUG FIXES:
  • Editing:
  • The reason of name generation failures was displayed on the canvas.
  • I/O:
  • Circled changes were displayed twice during .cdx import.

New in Marvin 15.2.23.0 (Feb 26, 2015)

  • IMPROVEMENT:
  • Editing:
  • Circle painting inside aromatic rings has been improved.
  • Marvin GUI:
  • Bold width parameter has been introduced.
  • Format dialog has been revised.
  • Wire thickness parameter on Preferences panel is displayed with 2 digit precision.
  • BUG FIXES:
  • Editing:
  • 2D clean of large molecules failed.
  • Selected Reacting Center properties became unrecognizable.
  • I/O:
  • Valence property set on Sn, Tl and Te were lost in Molfile import-export.
  • Images with reaction arrow were exported incorrectly.
  • OLE:
  • Font size of charge was not kept.

New in Marvin 15.2.16.0 (Feb 23, 2015)

  • IMPROVEMENT:
  • Editing:
  • Alignment of the double bonds can be changed. See documentation.
  • Customizable hash bond spacing has been introduced.
  • Stereo search desciptors are always displayed in black.
  • Marvin GUI:
  • Bond spacing parameter is applied for triple bods as well.The "Double bond spacing" option in Preferences

New in Marvin 15.2.9.0 (Feb 11, 2015)

  • IMPROVEMENT:
  • MarvinGUI:
  • "Open Marvin Space" menu item was removed from the Edit menu.
  • BUG FIX:
  • MarvinGUI:
  • Zooming did not work properly on MacPro.
  • Editing:
  • Atom Labels having "^" characters at the last position threw exception.
  • Numbers in attached data were displayed as subscript.
  • I/O: .mrv - Some cases Marvin saved null bytes (/empty bytes) to the end of the structure files.

New in Marvin 15.2.2.0 (Feb 3, 2015)

  • BUG FIXES:
  • Editing:
  • Abbreviated groups did not get ungrouped when an extra bond was drawn from one of their attachment points.
  • Image export:
  • Absolute label was cut from the exported image

New in Marvin 15.1.19.0 (Jan 21, 2015)

  • IMPROVEMENTS:
  • MarvinSketch GUI:
  • Measurement unit for Thickness,With and Skip is pt in the Graphics Object Properties dialog.
  • BUG FIXES:
  • Naming:
  • The name of the molecule did not change when extended stereo information (OR) had been added to a structure.

New in Marvin 15.1.12.0 (Jan 14, 2015)

  • IMPROVEMENTS:
  • MarvinSketch GUI:
  • Structure

New in Marvin 15.1.5.0 (Jan 10, 2015)

  • BUG FIXES:
  • Molecule representation:
  • S-groups: S-groups without attachment point number 1 - but having other attachment point(s) - could not be contracted.
  • Painting:
  • It was not possible to draw Double C/T or Unspec" bonds when View>Stereo>E/Z was enabled.

New in Marvin 14.12.15.0 (Dec 29, 2014)

  • IMPROVEMENTS:
  • MarvinSketch GUI:
  • When eraser tool is active, its icon is displayed on mouse tip and the selection color is changed to red.
  • Abbreviated groups with valence error are underlined by red.
  • "Clean and arrange in 2D" option has been introduced (Short cut: SHIFT+CTRL+2).
  • MarvinBeans:
  • It is possible to set the bond length in pt in MolPrinter.
  • Applet:
  • The background can be set dynamically.
  • BUG FIXES:
  • Painting:
  • Atom and bond coloring in Markush enumeration were not consistent.
  • Editing:
  • When one typed map numbering as a short cut then dragged on the canvas a molecule was created without atoms. For example "Map:9-Map:9" molecule was created, with a bond between the "Map:9" numbers.

New in Marvin 14.12.1.0 (Dec 8, 2014)

  • IMPROVEMENTS:
  • MarvinSketch GUI:
  • Pt has been introduced as measure unit for bond length and atom size.
  • Bond length can be set on Preferences dialog and in marvin.properties file. This property is kept during image export. Applet parameter: bondLength and image export parameter bondl are also introduced.
  • Valence check has been improved for negatively charged polyhalogen ions.
  • BUG FIXES:
  • Editing:
  • Delete/backspace did not work in textbox on Mac.

New in Marvin 14.11.24.0 (Nov 26, 2014)

  • IMPROVEMENTS:
  • MarvinSketch GUI:
  • New view option has been introduced to display undefined chiral centers.
  • BUG FIXES:
  • Editing:
  • It was not possible to draw a bond from an amino acid which is connected to a side chain of an other amino acid.
  • Export:
  • Labels with larger than the default font size were cut during image export in some cases.

New in Marvin 14.11.17.0 (Nov 26, 2014)

  • IMPROVEMENTS:
  • MarvinSketch GUI:
  • New GUI properties has been introduced and some old ones eliminated from mrv file schema. Documentation.
  • Import/Export
  • .cdx import has been improved: special characters in textbox, empty S-groups can be imported
  • .skc import has been improved: reactions (agents/arrows/mapping) can be imported
  • Bug fixes:
  • Editing:
  • The centre of the multi-center bond was not the geometric center of the atoms.
  • Numbers in visual feedback of data fields were displayed as subscript.
  • More icons of the General Toolbar could be enabled at the same time.
  • Export:
  • Bondstyle for any and coordinate bonds was not considered during pdf export.

New in Marvin 14.11.3.0 (Nov 10, 2014)

  • Improvements:
  • Structure representation: 2D clean of certain cyclic structures and peptides has been improved.

New in Marvin 14.9.29.0 (Oct 1, 2014)

  • NEW FEATURES AND IMPROVEMENTS:
  • Structure Representation:
  • Atom numbers and atom query properties are rendered outside ring in cyclic structures.
  • MarvinSketch GUI:
  • Edit < Preferences < OLE Server was removed.
  • BUG FIX:
  • Image I/O:
  • The size of circled charge labels was not considered during image export.
  • Radical was displayed as electronpair after emf export.

New in Marvin 14.9.22.0 (Sep 24, 2014)

  • NEW FEATURES AND IMPROVEMENTS:
  • Structure Representation:
  • Aromatic "wedge down" bond can be drawn.
  • BUG FIXES:
  • Image I/O:
  • Absolute label was partly missing from exported images.
  • Transparent png images were rendered with some artifact on java 7.
  • Applet:
  • Image generation in applet did not work.
  • MarvinSketch GUI:
  • Copy as dialog always opened on the centre of the primary screen in a multi-display environment.
  • Editing:
  • Joining points of graphical objects were considered even though one of them had been removed.

New in Marvin 14.9.15.0 (Sep 17, 2014)

  • BUG FIXES:
  • Structure Representation:
  • Special query atoms M, MH, X, XH were given too much space during clean 2D.

New in Marvin 14.9.8.0 (Sep 12, 2014)

  • NEW FEATURE:
  • Structure Representation:
  • Abbreviation groups have been revisited and formatted according to the IUPAC recommendation.
  • BUG FIXES:
  • Import/Export:
  • H_hetero option in the Pdf export did not work.
  • Structure Representation:
  • The atom numbers in rings were displayed relatively far.

New in Marvin 14.9.1.0 (Sep 4, 2014)

  • Bug fixes:
  • Import/Export:
  • Formatted text import was improved from SKC format.
  • Molecule properties with quotation marks and whitespaces were lost during export to Smiles/Smarts
  • Structure Representation:
  • Chorene dioxide had false valence error.

New in Marvin 14.8.25.0 (Sep 2, 2014)

  • New Features and Improvements:
  • API: Class chemaxon.struc.Sgroup.MulticenterSgroup is now public.
  • Bug fixes:
  • Applet: Applet parameter "extraBonds" disabled the chain tool if the "Any bond" parameter was not set.

New in Marvin 14.8.11.0 (Aug 12, 2014)

  • NEW FEATURES AND IMPROVEMENTS:
  • MSketch:
  • The default Msketch window size has been increased.
  • BUG FIXES:
  • Image I/O:
  • Exported .png files could not be imported because the source was not attached to the png metadata.
  • Editor:
  • Absolut label disappeared when Data was attached.
  • Mview:
  • Mview printed an "a" on the console when it had been launched.

New in Marvin 14.7.28.0 (Jul 31, 2014)

  • IMPROVEMENTS:
  • Structure Representation:
  • Atomic masses and isotopic weights are updated to the 2013 standards and the isotope file format have changed. Documentation
  • Multiple S-group cannot be expanded if it contains one or more child S-group.
  • Pseudo labels are displayed centered.
  • MarvinSketch:
  • "Copy Special" dialog in the Edit menu is renamed to "Copy as".
  • Image I/O:
  • Images are exported with "fog effect" set by the user. Image export parameter "fogFactor" has been intoduced.
  • BUG FIXES:
  • Import/Export:
  • Parity was inverted during import of 0 dimensional CML files. Forum

New in Marvin 14.7.21.0 (Jul 22, 2014)

  • BUG FIXES:
  • Editing:
  • R-group editing (such as connecting atoms in R-group definitions) froze MSketch.
  • Image I/O:
  • Implicit H atoms and R/S stereo labels overlapped bonds on exported EMF images.

New in Marvin 6.3.1 (Jul 8, 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.
  • BUG FIXES:
  • 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 6.3.0 (May 16, 2014)

  • NEW FEATURES AND IMPROVEMENTS:
  • Painting:
  • Bond properties are displayed on the canvas.
  • Clipboard handling:
  • When the clipboard format is not recognized as a chemical object, the format chooser dialog is not displayed and Marvin does not import anything. Forum
  • MarvinSketch Menu:
  • The "Switch Transformation" menu item is removed from the "Edit > Transform" menu.
  • The "Graph Invariants" menu option is removed from the "View > Advanced" menu.
  • MarvinSketch Dialogs:
  • Look&Feel option has been eliminated from the "Preferences" dialog.
  • Import/Export:
  • CXSMILES, CXSMARTS:
  • R-logic is supported by the CXSMILES and CXSMARTS formats.
  • Atom properties of homology groups are supported by the CXSMILES/CXSMARTS formats.
  • CDX, CDXML:
  • 3-letter abbreviated amino acid labels can be imported from CDX. Forum
  • Name to Structure (n2s):
  • Japanese Name to Structure is supported. It requires a separate license.
  • The custom dictionary can be encoded in UTF-16 (both UTF-16BE and UTF-16LE variants) even if the system default encoding is different. The file needs to start with a byte order mark (BOM) character.
  • Document to Structure (d2s):
  • OSRA 2.0 is supported.
  • A format option has been introduced allowing the user to select an optical structure recognition tool: CLiDE, OSRA or Imago when more than one is installed on the computer. For instance, d2s:osra will request OSRA to be used.
  • Structure to Name (s2n):
  • Locants with a number and an atom type are written, for instance, as N6 instead of 6-N following the latest IUPAC recommendations.
  • Molecule Representation:
  • Method chemaxon.struc.MolBond.equals() compares the bonds by reference and not by the end points.
  • Clean 2D:
  • Clean 2D of structures containing explicit hydrogen atoms is improved. Forum
  • Applet:
  • When the Marvin Applet does not work because the Java version is outdated, a proper warning message is displayed.
  • Licensing:
  • Reading of licenses has changed: now licenses in the ChemAxon home directory are read even if the CHEMAXON_LICENSE_URL environment variable or the chemaxon.license.url java system property is set.
  • Structure Checker:
  • "Double Bond Stereo Error Checker" has been introduced, which searches for invalid either double bonds. Its corresponding fixer converts the invalid either double bonds to plain double bonds. Documentation
  • "Stereo Inversion Retention Mark Checker" has been introduced, which identifies stereo inversion/retention marks on single molecules and in reactions. Its associated fixer removes the stereo inversion/retention marks from the structures. Documentation
  • "Valence Error Checker" detects all valence errors in Markush structures, even if the valence error is inside R-group definitions. Its fixer corrects all fixable valence errors in Markush structures.
  • Calculations:
  • Solubility:
  • Aqueous Solubility Predictor has been added to Calculator Plugins. Documentation
  • Stereo Analysis:
  • Available via cxcalc and Chemical Terms. Documentation
  • Conformations:
  • Advanced conformational search. Documentation
  • BUG FIXES:
  • Editing:
  • Trying to merge an S-group on a multicenter atom threw a NullPointerException.
  • Hovering over a rounded rectangle with the mouse cursor caused a NullPointerException.
  • Replacing a selected single atom with a hydrogen using the toolbar button resulted in a "HH" atom.
  • Bonds could not be drawn from hydrogen atoms to other atoms.
  • The "Absolute" chiral flag disappeared from the canvas when the reaction arrow was deleted.
  • The brackets of an S-group disappeared when the group became part of a reaction.
  • Replacing an amino acid in a sequence merged the new amino acid in the wrong direction.
  • When single atoms in a chain were replaced by amino acids, attachment orders were incorrect.
  • Rotation of molecules in 3D did not work properly.
  • If a query property was set for an atom and - in a later step- a bond was drawn from this atom, the value of the atomic query property changed to zero regardless from its original setting.
  • Load/Save handling in UI:
  • Changing the background color when a 3D structure was converted to 2D, then saving in PNG format saved the structure with the earlier, 3D background color.
  • Clipboard handling:
  • Structure display options were not preserved when structures were copy-pasted as Marvin OLE objects.
  • Pasting a file in a one-line molecule format (e.g., SMILES) on the canvas merged the lines of the file content. Currently, only the first line of the file is pasted.
  • MarvinView GUI:
  • The "Save Selection..." menu option could not be used for selecting structures for saving from a multimolecule file.
  • Import/Export:
  • MRV, CML:
  • CML and MRV import threw java.lang.ArrayIndexOutOfBoundsException when reading parallel bonds atoms. Now chemaxon.formats.MolFormatException is thrown instead.
  • SMILES, SMARTS:
  • SMARTS string starting with parentheses was recognized as SMILES.
  • CXSMILES, CXSMARTS:
  • Chiral flag (or molecular absolute stereo) was not exported to CXSMILES if enhanced stereo existed in the molecule.
  • InChi, InChiKey:
  • Coordinate bond was exported as single bond to InChi. From now, we do not export these bonds according to the IUPAC recommendation. Forum
  • Name to Structure (n2s):
  • The multiplying prefix "eicosa", a non-IUPAC variant of "icosa" was not supported.
  • The Chinese names of some alkanoic acids, such as 十一烷酸, were not supported.
  • Some common names containing "chloride" were imported without a chlorine atom.
  • Some chiral heterocenters were reversed in anhydrides.
  • Some names with cis and trans stereodescriptors for rings were imported without stereochemistry.
  • Entries in the custom dictionary that consist of an empty structure failed to be imported.
  • The stereochemistry of some sugars, for example, 1-(2-Deoxy-2,2-difluoro-β-L-erythro-pentofuranos-1-yl)uracil, was wrong.
  • Stereochemistry was missing on some chiral centers of steroid derivatives.
  • Document to Structure (d2s):
  • The encoding of HTML files was not always detected from the META tag.
  • When the extraction of OLE embedded structures from Office documents was disabled using the d2s:-ole format option, the optical structure recognition of images was disabled as well.
  • The character position field of structures was sometimes higher by a few characters when extracted from HTML documents with CRLF (\r\n) line endings.
  • The CLiDE optical structure recognition tool was not automatically detected on 64 bit versions of Windows.
  • When using OSRA, some structures with implicit hydrogens were wrongly filtered out.
  • After processing only a part of an HTML document, the processing of the next HTML document could give some incorrect results.
  • Structure to Name (s2n):
  • IUPAC numbering was not displayed for some classes of structures, for instance, secondary amines.
  • The common names generated for some structures with a chloride counter-ion did not include the ending "chloride".
  • In a few cases, generated traditional names were imperfect, for instance, "nitrobenzeen" instead of "nitrobenzene".
  • Molecule Representation:
  • Clean 2D:
  • Clean failed on atoms having two chain ligands with the same length.
  • Implicit/Explicit Hydrogen Conversion:
  • Hydrogen atoms were added with invalid coordinates to carbon atoms having triple bond in 3D. Forum
  • Image I/O:
  • R/S stereo labels on chiral atoms were partly covered by bonds during EMF export. Forum
  • Structure Checker:
  • "Bond Angle Error Checker" reported incorrectly for molecules containing S-groups.
  • The first letter of a typed word did not appear in the search box of the "Configure Checkers" panel.
  • Calculations:
  • Remove Predictor from Marvin GUI, Chem Term, cxcalc and cxtrain.
  • Conformers:
  • Lowest energy conformer calculation has been fixed.
  • Marvin - Conformers Plugin options has been improved along with corresponding documentation.

New in Marvin 6.1.4 (Dec 12, 2013)

  • Bug fixes:
  • 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 6.1.3 (Nov 9, 2013)

  • BUG FIXES:
  • MarvinSketch GUI:
  • MSketchPane setPiece(Molecule) method did not work, it set the molecule on the canvas instead of putting it on the cursor.
  • 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 6.1.0 (Oct 7, 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.
  • Bug fixes:
  • 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 6.0.1 (Jun 22, 2013)

  • NEW FEATURES AND IMPROVEMENTS:
  • Image I/O:
  • The following file extensions were removed from the "Files of Type" list on the Import Image dialog: *.ps, *.pdf, and "All Files". PDF files can be imported through the "File > Open" menu.
  • Calculation:
  • Services:
  • SOAP webservices:
  • SOAP version 1.2 webservices are supported.
  • BUG FIXES:
  • Painting:
  • R/S stereo labels were not displayed when there was an R-group on the canvas.
  • S-groups, created from structures containing a position variation bond, retained the grey patch of the position variation bond when the group was contracted.
  • Editing:
  • An atom of an expanded S-group could not be replaced with an S-group correctly
  • Clipboard handling:
  • On Mac OS X, copy-paste (from MarvinSketch to, e.g., TextEdit) did not transfer the atom colors.
  • Graphical object handling:
  • Formatting the head of a graphical arrow to a half-left arrow using the Document Style dialog crashed the display of the arrow.
  • Import/Export:
  • MRV/CML:
  • MRV and CML export failed with the woodstock xml processor.
  • InChi/InChiKey:
  • InChi export did not return standard InChi when the absolute stereo was not set in a non-chiral molecule.
  • Document to Structure:
  • Documents with many consecutive names would lead to extremely long processing time (appeared as hanging, unless reaching the timeout).
  • Molecule Representation:
  • Implicit/Explicit Hydrogen Conversion
  • Adding explicit hydrogen to an atom being part of a Multicenter S-group added the hydrogen to the S-group as well.
  • Clean 2D:
  • Stereo clean created non-IUPAC standard depiction of certain tetrahedral configurations.
  • Data Transfer:
  • OLE:
  • Redirecting ChemDraw OLE objects did not work.
  • Applet:
  • Applet parameter extraBonds did not work therefore the bond type menu appearance could not be changed.
  • Image I/O:
  • The xml header information was always included in the generated SVG content during image export. SVG export now has an option "headless" to exclude this information.
  • Calculation:
  • Protonation (pKa, Major Microspecies, Isoelectric Point):
  • "Keep explicit hydrogen" option caused exception during pKa calculation.
  • NMR (HNMR, CNMR Prediction, …):
  • When the mouse cursor was moved over an NMR peak on the chart, the relevant atom was not highlighted on NMR predictor molecule preview panel.
  • Services:
  • SOAP webservices:
  • Parameters did not load from WSDL properly in SOAP version 1.1 webservices.

New in Marvin 6.0.0 (May 24, 2013)

  • 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.
  • 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.
  • 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.
  • 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.
  • 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).
  • 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.
  • New saving mechanism has been introduced in MarvinSketch.
  • New save mechanism has been introduced for MarvinView.
  • Reactions and structures containing R-group definitions cannot be saved either in separate files or separately in the same file.
  • 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,
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Automapper tool requires Standardizer license.
  • API : com.chemaxon.mapper.Automapper
  • Structure Checker:
  • "Traditional nitrogen representation allowed" option is available in Valence Error Checker.
  • External structure checker and fixer manager is integrated into Structure Checker GUI application. It is accessible from the preferences menu as "Checker/Fixer Manager".
  • 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.

New in Marvin 5.12.4 (May 7, 2013)

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

New in Marvin 5.12.3 (Apr 12, 2013)

  • BUG FIXES:
  • 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 5.12.2 (Mar 29, 2013)

  • Bug fixes:
  • 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 5.12.1 (Mar 21, 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
  • BUG FIXES:
  • 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.
  • 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.

New in Marvin 5.12.0 (Mar 5, 2013)

  • New features and improvements:
  • MarvinSketch GUI:
  • Typing abbreviated group names is now case sensitive. Documentation
  • MarvinSketch Dialog:
  • "Cancel" button has been added to the "Customize" dialog.
  • Painting:
  • The font size and type of circled charge symbols can be modified on the "Display" tab of the "Preferences" dialog. Documentation
  • Position variation bond has been recolored for better visibility in a projected presentation.
  • Clipboard handling:
  • When pasting unrecognized format onto the canvas, "Import as" dialog appears, and the user can choose the correct format.
  • Structures can be copied as "Daylight SMARTS" and "ChemAxon SMARTS (CXSMARTS)" formats. Documentation
  • MarvinView GUI:
  • Double-clicking on a molecule in MarvinView to open it in a separate window does not result in the disappearance of the original molecule from MarvinView while the separate window is open.
  • The original molecule does not disappear from MarvinView while it is edited in MarvinSketch.
  • Applet:
  • New applet parameter for specifying the URL of a name recognition and import service: namingWebServiceURL
  • Import/Export:
  • SKC:
  • SKC import has been improved.
  • CDX/CDXML:
  • Mapping of reaction agents can be imported.
  • Name to Structure (n2s):
  • Initial support for Chinese IUPAC and common names has been added, e.g., 2-氨基-4-硝基苯酚.
  • Names with extra closing brackets can be converted when OCR error correction mode is enabled.
  • Name to structure now also works when bridge and spiro numberings are represented by using unicode superscript numbers, such as: tetracyclo[12.4.0.02,6.07,12]octadecane.
  • Custom webservice to extend name to structure conversion - for instance using corporate IDs (e.g., ABC0001234) or common name dictionaries in addition to the default one - is supported. Documentation
  • Automatically fix and import spiro names where the superscript formatting has been lost, for instance, after copy-pasting. As an example, trispiro[2.2.2.29.26.23]pentadecane will be imported as if from the correct form, trispiro[2.2.2.29.26.23]pentadecane.
  • Name to structure now works on names of bridged ring compounds where the superscript formatting of ring numbering is not present.
  • The custom dictionary can be encoded in UTF-8 - even if the system default encoding is not UTF-8 - providing a byte order mark (BOM) for the file. This can be used, for instance, to support dictionary in multiple languages on Windows OS.
  • Document to Structure (d2s):
  • Invalid hexadecimal character entities (e.g., " lah") are now ignored instead of making the document processing fail.
  • Image to structure conversion using OSRA is working on Mac OS X.
  • Text OCR for scanned documents is now supported on Mac OS X.
  • Documents compressed in xml.bz2 and xml.xz formats can be processed directly.
  • The memory usage has been reduced when processing documents with several thousand hits. This improvement is in addition to the memory improvements already present in version 5.11.
  • Option "+/-groups" has been added to enable (+) or disable (-) the conversion of groups and fragments, such as "ethyl", "nitro", "phenoxy", etc.
  • OCR of scanned PDF documents has been improved on Windows OS thus reaching the same performance level as that of OCR on Mac OS X and Linux OSs.
  • Structure to Name(s2n):
  • The speed of batch conversion using a timeout (which is enabled by default) has been increased by about 15%; the earlier instability in case of timeout relying on the deprecated Thread.stop method has been avoided.
  • Molecule Representation:
  • The size of the Molecule object has been decreased.
  • Data Transfer:
  • OLE:
  • New settings are available for both administrators and end-users (from the "Edit > Preferences > MarvinOLE" menu) to preset the displayed OLE document in a maximized child window.
  • MRV files are read and validated by DOM (document object model) in Marvin OLE.
  • Clean 3D:
  • MMFF94 forcefield has been added to Generate3D. Use option "[mmff94]" to switch it on; use "molconvert -H3D" for detailed help.
  • Calculation:
  • Isomers (Tautomers, Stereoisomers):
  • Performance improvement: Tautomerization will not apply "Clean2D" if the output result has no 2D coordinates. Forum topic
  • Resonance structure is taken into account in dominant tautomer generation.
  • Conformation (Conformers, Molecular Dynamics, …):
  • New MMFF94 forcefield implementation has been introduced in Conformer Plugin and Molecular Dynamics Plugin.
  • Services:
  • Result structure of Marvin Services result panel can be copied to clipboard.
  • Structure Checker:
  • New checkers have been introduced:
  • Absolute Stereo Configuration
  • Chiral Flag
  • E/Z Double Bond
  • Multiple Stereocenter
  • Relative Stereo
  • Wiggly Bond
  • Fixer of checker "Query Atom": "Convert to Carbon" has been added.
  • Fixer of checker "Query Bond": "Convert to Single Bond" has been added.
  • Excluded list of abbreviated groups can be specified in "Abbreviated group" checker, i.e., checker will not find (and fix) abbreviated groups that are indicated in this list. Documentation
  • Structure Checker configuration can be accessed via URL from MarvinSketch, Structure Checker application, and via Structure Checker API call. Documentation
  • Integration of external structure checkers and fixers into ChemAxon products has become easier via MarvinSketch GUI. Documentation
  • In case of more than one fixer, a logical order of priority has been preset. The priority list of fixers can be found on page List of available checkers.
  • API:
  • New property change event to indicate when an editable MarvinView component is opened in MarvinSketch: sketchInView.
  • New property change event to indicate when a new MarvinSketch or MarvinView window is opened from the viewer: windowOpened.
  • New property change event to indicate when a MarvinSketch or MarvinView window, opened from the viewer, is being closed: windowClosed.
  • Java Web Start
  • Name to Structure and Document to Structure are now available in the Java WebStart distribution of Marvin.
  • Bug fixes:
  • MarvinSketch did not deal with java property initialization bug.
  • MarvinSketch GUI:
  • When a group abbreviation differed from an atomic symbol only in upper and lower case letters (e.g., NO and No), the abbreviated group could not be reached by typing.
  • MarvinSketch Dialog:
  • Focus did not appear on the "Source" and "Import Name" dialogs with Java 7.
  • Painting:
  • The charge was not displayed in circle on the bracket of an S-group when the "Show charge in circle" was set on the "Preferences" panel.
  • Charge label masked the adjacent bond in several cases.
  • Editing:
  • Deleting "extra" explicit hydrogens from an atom with valence error resulted in the appearance of erroneous implicit hydrogens on this atom.
  • When there were several disconnected structures on the canvas, partial clean was very slow.
  • It was possible to create a molecule with R-group definition containing a single attachment point (and no other atoms or bonds).
  • Sprouting did not work for Alias atoms.
  • The two ways of deleting implicit hydrogens (with eraser directly or selecting them first then deleting) behaved differently.
  • Load/Save handling in UI:
  • "File > Open" dialog froze when an mrv file contained a dashed arrow and the preview pane was checked.
  • When opening a multi molecule file and selecting a range that is open ended, a false error message appeared, which stated that there were too many molecules selected to open.
  • IUPAC name with alpha or beta signs could not be imported.
  • MarvinView did not open when importing a file from command line failed.
  • It was not possible to append a name to an existing .name file in MarvinSketch.
  • Clipboard handling:
  • It was not possible to drag a structure from MarvinView in "Translate or Drag" mode.
  • Ctrl + V shortcut for pasting structures did not work in MarvinView in case of "Spreadsheet" view.
  • Graphical object handling:
  • MBracket object "BRACES" did not render correctly when the orientation was set as "SINGLE".
  • Applet:
  • After reloading an applet from the lifecycle cache, the propertyChange method was called in the javascript side regardless of the listenPropertyChange parameter.
  • Image I/O:
  • The source was not saved from MarvinView in png, jpg, and svg formats.
  • Import/Export:
  • Option -g of molconvert ignored only MolFormatException.
  • MRV, CML:
  • MRV import could not handle contracted Superatom S-groups having less atoms than crossing bonds.
  • MRV export used operating system specific line ending, '\n'.
  • CML import failed on files that contained non-ASCII characters.
  • MOL, SDF, RXN, RDF:
  • Superatom S-group brackets were imported from MDL files.
  • CXSMILES/CXSMARTS:
  • CXSMARTS I/O lost the charge from generic metal atom.
  • CDX/CDXML:
  • Reaction agent not having reactant and product (e.g., >CC1=CC=CC=C1>) was read as reactant from CDXML files.
  • Name to Structure (n2s):
  • RS - as the marker of racemates - was not converted properly, for instance in (2RS)-1-(Adamantan-1-ylamino)-3-phenoxypropan-2-ol.
  • Lower CamelCase chemical names (such as 2-cyclopropylPiperazine) were not converted to chemical structures.
  • Common names, which are also non-chemical names, were recognized as chemical names during automatic format recognition, e.g., "Royal Blue".
  • E/Z bonds were sometimes set to the opposite value (in cases of non-trivial CIP rules).
  • For some rare inputs, which are not valid names, n2s created invalid structures that could be exported to mol format but could not be opened.
  • Both "phenylene" and "phen-1,3-ylene" were wrongly converted to benzene. Now all forms convert to the correct structure with two attachment points, including "m-phenylene", "1,3-phenylene", and "phen-1,3-ylene" (similarly for the o-, p-, 1,2-, and 1,4- forms).
  • Document to Structure (d2s):
  • Processing of multiple XML documents in concurrent threads was slow and sometimes skipped some hits.
  • Names separated by the "non-breaking space" character were not recognized.
  • Some names split by extra spaces were not found.
  • English names were not recognized in Japanese documents when the ideographic comma character followed them.
  • SMILES with aromatic atom after non-aromatic ones ("Cc1...") and with triple(#) or explicit single(-) bonds were not recognized.
  • Text OCR failed when the images in PDF were encoded in a certain variant of the CMYK color space.
  • Structure to Name(s2n):
  • Some characteristic group names were missing when expressed as a prefix of a sulfonyl group, for instance, in "propanamidosulfonyl".
  • Names could not be generated for structures containing "-[N+]≡" substituent. They are now named using the "azaniumylidyne" IUPAC name component.
  • Peptide:
  • During automatic format recognition, non-latin characters were recognized as peptide sequences.
  • Molecule Representation:
  • S-groups:
  • Multiple S-group expanded incorrectly when it had an embedded S-group.
  • S-groups/R-groups:
  • S-group creation was not possible for a structure within an R-group definition of a reaction; a warning message was given.
  • Clean 2D:
  • Wedge clean moved non-ring wedge bond between two rings into a ring. Forum
  • Calculations:
  • Protonation (pKa, Major Microspecies, Isoelectric Point):
  • Microspecies calculation of furan returned incorrect molecular formula at low pH.
  • Charge (Charge, Polarizability, …):
  • Resonant charge calculation generated exception when the major form of the molecule is invoked with explicit hydrogen atoms.
  • NMR (HNMR, CNMR Prediction, …):
  • Outdated HOSE database caused NullPointerException when predicting 1H NMR spectrum for some rare diastereotpic molecules.
  • Isomers (Tautomers, Stereoisomers):
  • D, T count in region labels of multifragment generic tautomers was computed incorrectly.
  • TautomerizationPlugin API did not clean the explicit hydrogens in the result molecule after tautomer generation which might have resulted in wrong stereo (R,S) specifiaction on chiral centers. Forum topic
  • Geometry (Topology Analysis, Geometry, ...)
  • The result of topological polar surface area (TPSA) plugin depended on the call order of setMolecule() and setpH() methods.
  • cxcalc:
  • Calculation "ringcountofatom" returned only the ring count of atom number zero. Forum topic
  • cxcalc returned irrelevant error message for calculations containing "ANY" bonds. Forum topic
  • Thole polarizablility (tpol) calculation didn't interrupt when clean3D failed.
  • Backend / Core:
  • Removing explicit hydrogens on some large PubChem compounds caused infinite loop. Forum topic
  • Structure Checker:
  • "Remove Stereo Care Box" was offered as fixer for results returned by "Query Bond Checker".
  • Fixer "Expand group" not only expanded but also ungrouped the abbreviated groups when using it via structurechecker command-line.
  • API:
  • The default value of parameters chargeWithCircle and lonePairsAsLine has been changed. The current default value of these parameters is "false". On the "Preferences" dialog, the "Restore default" button sets both parameters to "false", too.
  • Deprecation:
  • Structure Checker:
  • Deprecated checker action strings: aromaticity, chiralflag, circularrgroup, missingrgroup, rare, reactionmap, unusedrgroup, valence, wedge.
  • Deprecated fixer action strings: clearabsstereo, aliastocarbon, crossedtowiggly, converttosingle.
  • Deprecated fixer class names: AbsentChiralFlagFixer, AbsoluteStereoFixer, CrossedDoubleBondFixer, CovalentCounterionFixer, ExplicitHydrogenFixer, IsotopeFixer, RgroupReferenceFixer, WigglyDoubleBondFixer.

New in Marvin 5.11.5 (Jan 14, 2013)

  • Bug fixes:
  • Datatransfer: Structures copied from ChemDraw or Accelrys Draw could not be pasted onto MarvinSketch.

New in Marvin 5.11.4 (Dec 18, 2012)

  • New features and improvements:
  • Datatransfer
  • The imageImportServiceURL setting also affects the behavior of clipboard operations (drag and drop, paste).
  • Bug fixes:
  • Painting
  • Rounding error occurred in case of nearly 180 degree bond angle and it caused overflow error when resizing the structure.
  • Import/Export
  • New export option, BOM, is introduced for non-binary chemical file formats in order to write out Byte Order Mark (BOM) if UTF-8 encoding is used.
  • Structure to Name (s2n):
  • Since 5.11.0, names generated for bridged cyclic structures with explicit bridge head hydrogen contained a spurious "hydrogenio" prefix.
  • Clean 2D
  • Clean 2D got stuck in an infinite loop when fullerene-like molecules were cleaned.
  • Calculations
  • Atom index issue might have occurred when molecule contained explicit hydrogen.
  • Protonation (pKa, Major Microspecies, Isoelectric Point):
  • "averagemicrospeciescharge" calculation in cxcalc and "Isoelectric Point" calculation in MarvinSketch threw "ArrayIndexOutOfBoundsException" in the reported cases.
  • NMR (HNMR, CNMR Prediction, …):
  • The calculated chemical shifts of equivalent atoms were not consistent in case of compounds with symmetric ring systems. Forum topic

New in Marvin 5.1.4 (Jan 23, 2009)

  • New features and improvements:
  • MarvinSketch
  • Arrows group is restructured in the toolbar and in the menubar (forum topic).
  • The Insert > Groups menu is replaced by a more convenient dialog.
  • Import/Export
  • Unique SMILES should implicitize plain Hydrogens (forum topic).
  • Calculator Plugins
  • Unique Markush code can be generated for each enumerated structure.
  • logP and logD calculations are significantly faster.
  • API
  • New methods in chemaxon.beans.MViewPane: isViewWindowOpened(int), isSketchWindowOpened(int) and closeSketcher(int).
  • PDBReader and related classes were moved from chemaxon.modules to chemaxon.marvin.io.formats.pdb.
  • MacroMolecule and related classes were moved from chemaxon.modules to chemaxon.struc.
  • Bugfixes:
  • MarvinSketch
  • The layout of the Copy As... dialog is polished.
  • Periodic System button remained pressed on the toolbar even after the dialog was closed.
  • The Atom > Stereo > Enhanced, Atom > Charge, Atom > Map, Atom > R-group menus are replaced by more convenient dialogs. (forum topic)
  • Ctrl+Del in MarvinSketch did not delete properties.
  • Licenses
  • The command license -l produced bad output, not listing properly installed licenses.
  • Calculator Plugins
  • When using Calculator Plugins, the result window of a previous calculation sometimes reappeared (forum topic).
  • Huckel Analysis Plugin threw exception if the input molecule contained explicit hydrogens.

New in Marvin 5.0.04 (Jun 11, 2008)

  • New features and Improvements
  • MarvinSketch GUI:
  • In the default configuration, the Explicit Hydrogens option has been removed from the View/Misc menu. (From now on the explicit Hydrogens are always visible, but they can be added or removed using the corresponding options of the Structure/Add and in Structure/Remove menus.)
  • API:
  • New methods to control R-groups visibility in chemaxon.marvin.beans.MarvinPane: setRgroupsVisible(boolean), isRgroupsVisible()
  • Bugfixes
  • Molecule representation:
  • Ungrouping of embedded S-groups threw IndexOutOfBoundsException.
  • Import/Export:
  • There was a slowdown in MView when loading molecules during scrolling.
  • CalculatorPlugin:
  • Calculator Plugins threw exception for molecules with pseudo atoms.