All changes in reversed chronological order

January 12th 2016: Marvin 16.1.11.

          2D Cleaning

• • The stereogenic centers at ring fusion atoms are drawn with only one wedge bond.

January 6th 2015: Marvin 16.1.4.

      No changes.

December 15th 2015: Marvin 15.12.14.

Improvements:

Editing

• • Pseudo and Alias labels can be positioned.

December 8th 2015: Marvin 15.12.7.

Improvements:

OLE

• • Keyboard shortcuts can be used in OLE editor.

Bugfixes:

          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 .

December 2nd 2015: Marvin 15.11.30.

Bugfix:

Installation

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

November 24th 2015: Marvin 15.11.23.

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.

Bugfix:

Editing

• • Copy/Paste on OS X.
  • E/Z label display options are missing when copying to pdf.

October 28th 2015: Marvin 15.10.26.

Improvements:

Editing

• • The result of Elemental Analysis remains formatted when it is copied to into a MS Office or in a MarvinSketch textbox.

Bugfix:

Textbox

• • Textboxes could not be formatted at the same time.

October 20th 2015: Marvin 15.10.19.

Bugfix:

.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.

October 8th 2015: Marvin 15.10.5.

Bugfix:

2DClean

• In certain cases2Dclean switched the stereochemistry of double bonds.

September 30th 2015: Marvin 15.9.28.

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.

September 15th 2015: Marvin 15.9.14

Improvements:

Abbreviated groups

• • New abbreviated groups have been added to the default abbreviated group dictionary.

September 2nd 2015: Marvin 15.8.31.

Improvements:

Customization

• • Default selection tool can be set.

Editing

• • After deleting an alias or pseudo atoms the original atom (i.e, R,A ) are kept.

Bugfix:

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.

July 31th 2015: Marvin 15.7.27

Bugfix:

Editing

• • When atom font size was set from the Format panel, the size of the charge did not change.

July 22th 2015: Marvin 15.7.20.

Improvements:

Journal styles

• • New journal styles have been added.

Bugfix:

2D Cleaning

• • In some cases wedged bonds were lost when structures were partially cleaned in reaction schemes.

July 10th 2015: Marvin 15.7.6.

Improvements:

I/O

CXSMILES

• • R-atoms with alias strings are supported.

Charge painting

• • Charge painting has been revised.

Customization

• • New, general way to apply system level settings in MarvinSketch.

Bugfix

Painting

• • Red/blue pKa value painting did not work correctly.

Saving

• • Save/Load zoom factor in MRV format did not work

2D Cleaning

• • Wedged bonds were lost when reactions involving ionpairs were cleaned.

June 25th 2015: Marvin 15.6.22.

Bugfix

Import

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

June 16th 2015: Marvin 15.6.15.

Bugfixes

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.

June 8th 2015: Marvin 15.6.8.

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.

Bugfixes

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.

May 13th 2015: Marvin 15.5.11.

Improvements:

Journal styles

• • New journal styles are saved in the journal_styles folder.

Bugfix

Editing

• • Scrolling and zooming were disabled when Atom Label editor was in action.

May 5th 2015: Marvin 15.5.4.

No changes.

.

April 29th 2015: Marvin 15.4.27.0

Improvement

Editing

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

Improvement

• • Structure drawing has been revisited.

April 14th 2015: Marvin 15.4.13.0

No changes.

April 8th 2015: Marvin 15.4.6.0

Improvement

MarvinSketch

• • • Painting performance has been improved due to revised caching.

Bug

MarvinSketch

• • • Memory limits (128MB)  on Mac OSX  could cause serious slowdown.

Editing

• • Aromatic rings within R-groups were drawn with aromatic bond.

API

• • • Setting a rectangle with x and y coordinates other then zero lead to loss the upper and left part of the created image, when MolPrinter.paint(Graphics2D, Rectangle) method call was used.

March 31th 2015: Marvin 15.3.30.0

Bug

Editing

• • • Non-selected brackets were copied as well.

MarvinSketch

• • • 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.

March 25th 2015: Marvin 15.3.23.0

Improvement

Marvin GUI

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

March 17th 2015: Marvin 15.3.16.0

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.

Bugfixes

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.

March 11th 2015: Marvin 15.3.9.0

Improvement

Editing

• • The alignment of isotopes and implicit H on the same atom has been improved.
  • Position variation bond drawing in symmetrical structures has been improved.
  • Coordinate bond drawing has been improved.

I\O

• • Inner reference ids are unified in individual SVG files. This prevents id collision when multiple SVG files are embedded into one HTML page.

Marvin GUI

• • "Document style" dialog is added to the File menu.
  • Circle Charge font type dialogue offers only the applicable font types.

Naming

• • IUPAC name for structures in reaction has been improved.

Bugfixes

Editing

• • Abbreviated group did not get ungrouped when an atom was overwritten.
  • Abbreviated group did not get ungrouped when a chirality center was changed.

Applet

• •  Applet settings were overwritten by the user settings.

March 4th 2015: Marvin 15.3.2.0

Improvements

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.)

Bugfixes

Editing

• • The reason of name generation failures was displayed on the canvas.

I/O

• •  Circled changes were displayed twice during CDX import.

February 24th 2015: Marvin 15.2.23.0

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.

Bugfixes

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.

February 18th 2015: Marvin 15.2.16.0

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<Display has been renamed to "Bond spacing".
  • "Document Style" menu item has been renamed to "Format... " and moved to the Edit menu.
  • The measurement unit of bond thickness has been changed to pt.
  • "Circled charge label" has been renamed to "Charge label" and the setting is applied for all charge display options.

I/O

• • MOL file import:
  • Brackets of repeating unit are drawn even when the coordinates are not indicated in the MOL file.

Bugfixes

Editing

• • Abbreviated groups did not get expanded upon sprouting with Shift modifier key.
  • In several cases "value" overlapped with atom label.
  • Atom number, atom map, atom property, atom query property values are displayed in the same row separated by semicolon.

I/O

• • MOL file import:
  • 2D clean of large MOL files ( i.e large peptides) failed with error.

February 10th 2015: Marvin 15.2.9.0

Improvement

MarvinGUI

• • "Open Marvin Space" menu item was removed from the Edit menu.

Bugfix

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.

February 3rd 2015: Marvin 15.2.2.0

Bugfix

Stereo calculation

• • Unnecessary E/Z stereo was calculated in rings.

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

January 29th 2015: Marvin 15.1.26.0

Improvements

• MarvinSketch GUI
  • "Clean and Arrange in 2D" icon was added to the Structure<Clean 2D menu.
• Editing
  • Isotopes can be introduced/edited and formatted with the help of the Atom Label editor tool.

Bugfix

• Editing
  • Valence errors were not recalculated when charge(s) had been added by keyboard.

January 21th 2015: Marvin 15.1.19.0

Improvements

• MarvinSketch GUI
  • Measurement unit for Thickness,With and Skip is pt in the Graphics Object Properties dialog.

Bugfixes

• Naming
  • The name of the molecule did not change when extended stereo information (OR) had been added to a structure.

January 8th 2015: Marvin 15.1.5.0

Bugfixes

• 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.

December 17th 2014: Marvin 14.12.15.0

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.

Bugfixes

• 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.

December 9th, 2014: Marvin 14.12.8.0

Improvements

• Export/Import
  •  +  in textbox can be imported from SKC files.

December 3rd, 2014: Marvin 14.12.1.0

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.

Bugfixes

• Editing
  • Delete/backspace did not work in textbox on Mac.

November 26th, 2014: Marvin 14.11.24.0

Improvements

• MarvinSketch GUI
  
  •  New view option has been introduced to display undefined chiral centers.

Bugfixes

• • 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.
    • It was not possible to delete a structure with electron flow arrow using erase tool.
  • Export
    • Labels with larger than the default font size were cut during image export in some cases.

November 18th, 2014: Marvin 14.11.17.0

• MarvinSketch GUI
  
  •  New GUI properties has been introduced  and some old ones eliminated from MRV file schema.
• Import/Export
  • CDX import has been improved: special characters in textbox, empty S-groups, abbreviated group with left-name can be imported
  • .skc import has been improved: reactions (agents/arrows/mapping) can be imported

Bugfixes

• • 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.
  • 952
    • Bondstyle for any and coordinate bonds was not considered during pdf export.

November 11th, 2014: Marvin 14.11.10.0

Improvements

• MarvinSketch GUI
  
  •  New functionality has been introduced for changing and formatting abbreviated groups, atom lists/ not lists, R-groups, alias and pseudo atoms. Documentation.

• Structure representation
  •  When visibility option for R/S stereo labels is set, the undefined stereocenters are highlighted by (?).
• MarvinSketch Menu
  • Homology groups are sorted in alphabetical order in Advanced Tab of the Periodic Table.
• Molecule Representation
  • A warning is displayed when a user changes 2D canvas into 3D canvas, offering a clean method to preserve chirality.

Bugfixes

• Structure representation
  • Multiple groups were displayed as non-multiple in their expanded form.
  • It was possible to draw electron flow arrows in R group definitions.
• Editing
  • The square notation of `Stereo search` was wrongly positioned in case of double bonds.
  • Copy/Paste of formatted abbreviated group resulted in malformed label.
  • When using the Markush toolbar to add R-group attachement points to a structure, the order of attachment points was not assigned in R-group definitions.
  • MarvinSketch froze when an atom with its lone pairs displayed was overwritten by an abbreviated group.
  • Adding charge via toolbar or pop-up to a hetero atom in an aromatic ring gave different results in some cases.
• Image export
  • Font size of circled charge was not considered during image export.
  • When exporting a very small sized image, large atom labels were generated.
• Export/Import
  •  Molfile import: some input strings having brackets in its first line were recognized as smarts.

November 4th, 2014: Marvin 14.11.3.0

Improvements

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

December 17th 2014: Marvin 14.12.15.0

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.

Bugfixes

• 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.

October 28th, 2014: Marvin 14.10.27.0

Bugfix

• Editing

The index of repeating unit polymers was not properly formatted.

Empty atom label could be created.

Attachement point(s) got erased upon placing an abbreviated group in its expanded form on the canvas.

• Import

MDL Molfile generated by Marvin JS could not be pasted into MarvinSketch.

• Structure representation

2D clean of certain atropisomers resulted in chirality change.

October 21th, 2014: Marvin 14.10.20.0

New feature

• Structure representation
  M/P atropisomer stereodescriptors are assigned to biaryl compounds having at least 3 (2+1)  ortho substituents.

Bugfix

• Editing

Expanded amino acids got ungrouped when bond was drawn from one of their attachment point

October 14th, 2014: Marvin 14.10.13.0

Bugfix

• Export
  Hydrogen query properties of atoms within tetrahedral stereo configuration were not exported correctly to SMARTS.

October 8th, 2014: Marvin 14.10.6.0

New features and improvements

• Structure Representation

Alias, pseudo and abbreviated group labels are centered.

Bugfix

• Image I/O

The size of circled charge labels was not considered during image export.

September 30th, 2014: Marvin 14.9.29.0

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.

Bugfix

• Image import/export

Radical was displayed as electronpair after emf export.

 InChi native libraries were not initialized on OSX systems since 14.7.21.

September 23th, 2014: Marvin 14.9.22.0

New features and improvements

• Structure Representation

Aromatic "wedge down" bond can be drawn.

Bugfixes

• 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.

September 16th, 2014: Marvin 14.9.15.0

Bugfixes

• Structure Representation

Special query atoms M, MH, X, XH were given too much space during clean 2D.

September 11th, 2014: Marvin 14.9.8.0

New feature

• Structure Representation

Abbreviation groups have been revisited and formatted according to the IUPAC recommendation.

Bugfixes

• Import/Export

 H_hetero option in the Pdf export did not work.

• Structure Representation

Atom extra lables such as numbers, mapping, query properties etc. were displayed relatively far.

September 3rd, 2014: Marvin 14.9.1.0

Bugfixes

• 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.

August 5th, 2014: Marvin 14.8.4.0

No changes.

August 26th, 2014: Marvin 14.8.25.0

New Features and Improvements

• API

Class chemaxon.struc.Sgroup.MulticenterSgroup is now public.

 Bugfixes

• Applet

Applet parameter "extraBonds" disabled  the chain tool if the "Any bond" parameter was not set.

August 19th, 2014: Marvin 14.8.18.0

New features and improvements

• Structure Representation
  • Standalone ions are moved close to their counterion during Clean 2D.
  • Generated names (IUPAC/traditional) of compounds can be copied to a text editor using CTRL+C name box option

Bugfixes

• Structure Representation
  • End point of multicenter coordinated bond was moved out of the structure during 2 dimensional clean.

  • Decimal point was displayed at a wrong place and its relative place changed by zooming.

  • Dots representing electrons were displayed too far from the atom.

  • E/Z  labels overlapped bonds.

  • Bonds were rendered incorrectly in "Ball and Stick" mode.

• Image I/O

  • Position of atom labels was not correct in exported images.

• MarvinSketch GUI

  • New template files could not be added to the default template.

August 11th, 2014: Marvin 14.8.11.0

New features and improvements

• MarvinSketch
  • The default MSketch window size has been increased.

Bugfixes

• Structure Representation
  • Ortho-periodic acid was not accepted by valence check.
• Image I/O
  • Exported PNG files could not be imported because the source was not attached to the png metadata.
• Editor
  • "Absolute" label disappeared when Data was attached.
  • Numbers in abbreviated groups were not displayed as subscripts.
• MarvinView
  • MarvinView printed an "a" on the console when it had been launched.

July 29th, 2014: Marvin 14.7.28.0

Improvements

• Structure Representation
  • Atomic masses and isotopic weights are updated to the 2013 standards and the isotope file format have changed.
  • 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.

Bugfixes

• Import/Export
  • Parity was inverted during import of 0 dimensional CML files.

July 21th, 2014: Marvin 14.7.21.0

Improvements

• Editing
  • 'Alias' atoms cannot be sprouted.

Bugfixes

• Editing

  • Placing a graphical object (or a text box) on the canvas containing R-group definition, the position of the R group label changed as if the graphical object (or the text box) would be the part of the R-group definition.

• Import/Export
  • R-group members exported incorrectly SKC.
  • InChi I/O did not work on MacOS with Java 1.7 or higher. 
  • Stereo care flag was lost during compressed MOL import.
• Image I/O
  • Position of subscript numbers in labels changed when zooming in.
  • There were patches around atom labels when EMF image was exported with transparent background.
• Stereochemistry

  • Retrieving parity information could change the result of the CIP stereo recognition.

July 14th, 2014: Marvin 14.7.14.0

Bugfixes

• Editing

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

July 7th, 2014: Marvin 14.7.7.0

New features and improvements

• Molecule representation

  • New homology groups: "heteroSubstitutedAlkyl", "haloAlkyl" and "hydroxyalkyl" were introduced.
  • Invalid input is not accepted in the R-group logic definition field.
  • The terminal nucteotides are linked by bend bond in cleaned RNA/DNA sequences displayed in more than one row.
  • Text formatting options were introduced for abbreviated groups and alias atoms.
  • Validation was implemented for "Edit properties" dialog.

• Editing
  • Merging a contracted S-group while pressing shift button resulted in zero atom at the merging site.
  • S-group "Bracket style=Curved" was disabled.
  • In-hand contracted amino acid threw exception over an expanded amino acid.
  • vmn abbreviation groups are not supported.

• Clean 2D

  • Clean 2D was improved in order to keep the orientation of the molecule as much as possible.
  • Clean of sequences has been improved:
    
    • Sequences (even if they contain expanded residues) are aligned into a horizontal line and are broken into multiple lines after 20 residues. Each line is read from left to right.
    • Space is left for chemical parts connected to the third attachment of the residues, these attachments are aligned to the top of the residue. Attachments to expanded residues are also considered.
    • Chemical parts connected to the beginning and the end of the sequence are aligned to the left and to the right of the sequence.
    • Chains of sequences connected with chemical linkers are also handled: chemical linkers are aligned horizontally to the sequences to which they are connected and space is left for them between the lines of the sequences.
  • Default 2-dimensional clean of bicyclic molecules has been changed. The old behaviour can be switched back by selecting 'Bicyclics' on the Template Library GUI (Insert<Template) then ticking the 'Use molecules as template at 2D cleaning' option on the 'Properties' page.

• Import/Export

  • Picture format 'ppm' is not supported anymore.
  • New tag introduced in MRV file to store the atom properties of the abbreviation even if the Superatom S-group is expanded. Until now such properties were lost.
  • Default handling of bond lengths in the import of MDL formats has changed: bond lengths are rescaled to ChemAxon standard for 2D molecules not only for V2000 format input but also for V3000.
  • Character '.' which is the delimiter between atom property keys and values in CXMSMILES format is escaped, which allows the usage of '.' characters in property keys and values.
  • InChi improvement: import and export of axial chirality and not specified double bond stereo are now possible.
  • Atom properties set on the superatom of an abbreviation S-group can be exported to and imported from AbbrevGroup format (ChemAxon extension of smiles for abbreviated groups).

• MarvinSketch Menu

  • "Shapely" option was removed from View>Color menu.
  • "Quality" option was removed from View>Display menu.
  • "ChemAxon JChem Table format/JTF" was removed from the "Import As" dialog.
  • Edit<Copy as<IUPAC Name (ASCII) option was introduced.

• Calculator Plugins

  • Progress indication was introduced for Marvin Services.

• Applet

  • "Autocheckstructure" applet parameter is available.

• MolConverter
  
  • A new option "-f" was introduced in MolConvert in order to define import format and options even if the input files are defined with a wildcard. 

Bugfixes

• MarvinSketch

  • If MarvinSketch was started with edit structure from MarvinView by double click on a structure NPE was thrown.
  • MarvinOLEServer process was stopped when multiple MarvinSketch windows had been opened and one was closed.

• MarvinGUI

  • The font size in Marvin was smaller than other commercial drawing programs and text editors (such as Word).
  • Font size was different on different screen resolutions.

• Editing

  • Abbreviated groups
    • In generic, component, monomer and mer type abbreviated groups charge was shown both on the atom and on the bracket.
    • When wedge bond(single down, single up, single up and down) was drawn between two contracted S-groups an overlay of a single and a wedge bond was created.
    • The Sgroup was not positioned correctly at contracting/expanding the group.
    • Sgroup label was not displayed in expanded form.
    • The "On atoms"/"On brackets" options were not available on the Edit Group dialog when the structure was imported.
    • Edited  abbreviated group labels (except Sgroup labels) could not be saved.

• Import/Export

  • Import of MOL V3000 files containing aromatic wedge bonds threw MolFormatException.
  • MRV importer did not read molecule properties of R-group members.
  • SVG export threw exception.
  • When exporting graphical objects (e.g., brackets, arrows) into pdf and image formats part of the images was cut.
  • Extension ".properties" was not added atomatically to the 'File name' on the "Save style" dialog.
  • Bounding rectangle was calculated incorrectly for structures displayed in Ball&Stick view and this caused incorrect image export.
  • Attached data was lost upon export to png format.

• Elemental Analyzer
  • Molecule weight calculation could not read molecular formula with more than two dots.

• OLE
  • Opening OLE got into "Rotate in 3D" mode.
• Applet
  • Communication problem involving JavaScript was fixed.

Deprecated and Removed Methods

Deprecated or Removed Methods in version 14.7.7.0

September 16th, 2014: Marvin 6.3.4.

No changes.

August 5th, 2014: Marvin 6.3.3.

Bugfixes

• Import/Export
  • OLE objects created by Accelrys Draw 4.1 and further versions could not be redirected by MarvinOLE server.
  • OLE opened in 3D rotation mode (F7) mode.

July 7th, 2014: Marvin 6.3.2

Bugfixes

• Applet
  • Communication problem involving JavaScript was fixed.

June 4th, 2014: Marvin 6.3.1

New features and improvements

• Image I/O
  • New image IO parameter "aminoAcidBondColoringEnabled" has been introduced for peptide bond coloring.
• Import/Export
  • SKC
    • If they are set to visible in ISIS, "Atom numbers" are imported as atom mapping from SKC.

Bugfixes

• Clipboard handling
  • If a structure had been pasted onto an empty canvas and MarvinSketch 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 MarvinSketch) after editing a structure in MarvinView 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.

April 18th, 2014: Marvin 6.3.0

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.
• 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.
  • 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.
• 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.
  • "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. 
  • "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. 
  • Stereo Analysis
    • Available via cxcalc and Chemical Terms. 
  • Conformations
    • Advanced conformational search.

Bugfixes

• 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.
  • 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 ????, 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.
• Image I/O
  • R/S stereo labels on chiral atoms were partly covered by bonds during EMF export. 
• 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.

Deprecated and removed methods

• Deprecated and removed methods

Known issue

• Structure Checker
  • Online documentation help link does not work on Linux OS.

August 1st, 2014: Marvin 6.2.4.

Bugfixes

Import/Export

• • • OLE objects created by Accelrys Draw 4.1 and further versions could not be redirected by MarvinOLE server.
    • OLE opened in 3D rotation mode (F7) mode.

May 12th, 2014: Marvin 6.2.3

No changes.

April 4th, 2014: Marvin 6.2.2

Bugfixes

• Clipboard handling
  • Compounds in a reaction could not be copied.
• Import/Export
  • Structure to Name (s2n)
    • Name generation failed on some compounds with a radical, such as oxidanyls with a cyclic substituent. The error manifested itself as a StackOverflowError wrapped in an IOException.

February 28th, 2014: Marvin 6.2.1

New features and improvements

• Clipboard handling
  • When the clipboard content is not recognized as a chemical object, the format chooser dialog is not displayed. 
• MarvinView GUI
  • In MarvinView, the "Select" textbox was eliminated from the "Preview" tab of the "Open file" dialog.
• Import/Export
  • PDB
    • PDB import reads the following residue information of sequences: residue type, sequence number, atom ID in residue.
• Applet
  • Export of binary formats has become available from the applet API.

Bugfixes

• Editing
  • The toolbar buttons could not be used to add charge to single hydrogen atoms if there were other atoms on the canvas.
  • When drawing cycles and bridges in peptides, the blue feedback remained around the first bond.
  • When a repeating unit was created from one atom only and then the structure was selected, the content of the repeating unit changed.
  • Connecting a bond to an S-group which did not have any free attachment points changed the S-group to a carbon atom.
  • In some special cases, it was possible to overwirte an atom by just hovering the mouse over it with an active atom editing tool.
  • Rotating selected molecules in 3D changed the type of all bonds to single.
  • When a bond was connected to a multicenter, the whole molecule disappeared from the canvas.
• Molecule Representation
  • Valence Check
    • Tin atom with charge +2 had incorrect valence.
    • False valence error appeared on a sulfur atom having one negative charge and 5 or 6 bonds.
  • Clean 2D
    • Nucleic acid clean was not sensitive to arranging 5' to the left and 3' to the right end of the chain.
    • Two Dimensional Clean of Crown Ethers was ugly.
• Import/Export
  • MOL, SDF, RXN, RDF
    • Aromatic query property appeared after MDL MOL export and import on an aromatic atom having atom property.
  • SKC
    • Two single bonds of a cyclopropyl ring were read as coordinate bond. 
  • CDX/CDXML
    • Some CDX files that contain atom or bond label formatting were not read.
• Calculations
  • Stereo Analysis
    • CIP convention issue has been fixed.
    • Imine type structures were not recognized.
  • pKa
    • Calculation for boron compounds has been fixed.

Known issue

• MarvinSketch Applet
  • External checker classes do not load if browser uses Java SE 6. Please, use Java SE 7 for successful checker class loading.

January 30th, 2014: Marvin 6.2.0

New features and improvements

• MarvinSketch GUI
  • R* is displayed on the canvas if R-logic is unspecified for an R-group and the "View > Advanced > R-logic" visibility option is switched on.
  • R-logic is always displayed even if it is set to the default value when the relevant visibility option is switched on.
  • When R-group attachments are added to fragments not belonging to an R-group, the attachment order begins with "1" on each fragment.
  • "R/S" stereo label is displayed on atoms which are stereocenters and have a "Single Up or Down" bond if the relevant visibility option (in "View > Stereo > R/S Labels") is switched on.
  • Crosslinking peptide bridges are colored automatically if the "View > Colors > Peptide Bridges" visibility option is switched on. 
• MarvinSketch Dialog
  • Character encoding information has been added to the "About" dialog. 
  • In dialog "R-logic", "unspecified" is displayed in the "Occurrence range" field if it is not specified for an R-group.
• Editing
  • Molecules are no longer checked by MarvinSketch whether the "Absolute Stereo (CHIRAL)" flag can be added to them.
  • Drawing wedge bonds on a 3D canvas has been disabled. These bond types are active only when the canvas is in 2D mode.
• MarvinView GUI
  • "Save image" option has been added to the contextual menu of MarvinView
• MarvinSpace GUI
  • Hydrogen visualization toolbar button added.
  • Display/drawing settings saved on exit.
• Import/Export
  • SMILES/SMARTS
    • SMILES import handles CACTVS-type representation of coordinate bonds ('|' character). Please note that the export does not handle it.
  • Sequences, FASTA
    • Terminal H and OH are added to nucleic acids by nucleic acid import.
  • Name to Structure (n2s)
    • CAS Registry Numbers® can be converted to structures even when they contain coordinate bonds¹.
    • Conversion of nitrogen-substituted acetohydrazides is now supported.
    • Elements with isotopes, such as (14)C, are converted in name to structure by default, and, optionally, they can be converted with document to structure using the "d2s:elements" format option.
    • Some OCR errors have been fixed in carbon ranges for homology groups, for example, "Ci_10 alkyl".
    • Generic structure names (such as "alkyl" in English) are supported in Chinese as well, for instance, N-???-4-??? and C1-C4-??.
    • Polyspiro names with a polycyclic component, such as dispiro[cyclohexane-1,2'-indene-1',2"-imidazole], are supported.
  • Document to Structure (d2s)
    • For enzymes with a substrate in their name, such as "serine protease", the substrate (serine) is not converted by default. A new format option, "d2s:substrates", enables the recognition of the substrate in such cases.
    • New format option "d2s:specific" has been added to convert only specific structures. This option excludes structures with R-groups from the conversion.
    • More OCR error correction is performed.
    • In the case of processing XML fragments not starting with "<?xml version="..."?>", it has become possible to specify that the input text is in XML format by using the "d2s:content-type=application/xml" format option.
    • Metadata is also extracted from older (since 2001) USPTO patents in XML format: the section where a name is found is recorded as metadata (title, abstract, description, or claim number). Furthermore, document metadata is extracted as well: patent title and ID, inventors, IPC categories.
    • OCR error correction has been added for Chinese names.
  • Structure to Name (s2n)
    • In fused ring systems with an atom being in a non-standard valence state, the generated name conforms to the IUPAC rules by using the lambda notation only in front of the fused names and not inside the component name.
      See for instance: 1H,3H-2λ⁴-naphtho[2,3-c]thiophen-2-one.
    • Name generation has become faster by about 10%.
• Molecule Representation
  • R-logic
    • Default value of R-logic range has been changed: instead of ">0", now it is an empty string which means "as drawn". ">0" value is handled as non-default and is exported in file formats where ChemAxon supports R-logic information (MRV, SKC, MOL). From now on, if a file does not contain R-logic range information, then it is interpreted with the new default value: "as drawn". Documentation
  • Stereochemistry
    • Cahn-Ingold-Prelog (CIP) stereo recognition has been extended and it has been added to the public API.
  • Elemental Analyzer
    • Molecular mass calculation is more accurate.
• Image I/O
  • Structures can be exported in image formats "TIFF" and "EPS". 
  • S-group attachment point labels are not exported to image files (PNG, JPG, PPM, SVG, EPS, TIF, BMP). Exporting these labels to PDF files can be switched on/off using the "Edit > Preferences > Save/Load > Save/Load GUI Settings" checkbox.
  • During PDF export, text is also saved as image.
• Calculations
  • Stereo Analysis
    • New stereo analysis API.
  • 3D alignment
    • Hydrogens are taken into consideration during alignment process.
  • Conformers
    • New Generate3D documentation has been added.
• Structure Checker
  • "Overlapping Atoms Checker", "Overlapping Bonds Checker", and "Bond Length Checker" report correctly for molecules containing S-groups.
• API
  • IsotopesCompiler in isotopescomp.jar creates a UI in order to show error messages and information when it was not started from the console.
  • atomNumbersVisible parameter has been deprecated and has been replaced by the atomNumberingType parameter. 
• Third-party applications
  • The Java COM Bridge (Jacob) version was updated from v1.15-M3 to v1-17.

Bugfixes

• MarvinSketch GUI
  • MSketchPane setPiece(Molecule) method did not work; it set the molecule on the canvas instead of putting it on the cursor.
  • Starting points of electron flow arrows drawn from radicals and/or lone pairs were changed when lone pair visibility was switched off and then on again.
  • R-logic label was not taken into account by zoom action even if visibility option "R-logic" was switched on.
• Painting
  • Electron flow arrows starting from an atom, a negative charge, or an automatically calculated lone pair disappeared when lone pair visibility was turned off and then turned on again.
• Editing
  • Menu option "Link Node" was not disabled when an atom had less than two bonds.
  • A contracted tripeptide disappeared from view when it was expanded, but 2D Clean brought it back.
  • It was not possible to draw an electron flow arrow from an atom to an incipient bond between this atom and an abbreviated group.
  • Erasing a structure without an R-group attachment left "1" on the canvas, which behaved as an atom.
  • When an atom was selected and the "R-group attachment" button of the Markush toolbar was used, the selected atom was changed to an R-group attachment point; however, a new R-group attachment should have been added to the selected atom in this case.
  • Dragging with the R-group attachment tool, a bond was created connecting two R-group attachments.
  • Using the R-group attachment tool, R-group attachments could be added to an existing R-group attachment.
• Load/Save handling in UI
  • Lone pairs were lost at "Copy As... > PDF" at Mac OS X. 
  • PDF export did not use the color scheme setting.
• Clipboard handling
  • During PDF export, atom labels were turned upside down with some font types.
• MarvinView GUI
  • Pasting a SMILES string into MarvinView did not work.
• Import/Export
  • MRV/CML
    • After MRV export and reimport of a structure, its text box font color turned into the frame color of the text box and the font color turned to a not defined color (black).
  • Format recognition
    • '(S)-(-) Propanolol' was recognized as SMILES.
    • Chemical Registry Numbers® were recognized as MDL MOL format.
  • Name to Structure (n2s)
    • Automatic format recognition failed for names using unicode hyphens.
    • Names of some spiro compounds containing aromatic components were not converted. See, for instance, 6-(2, 5-dimethylphenyl)-5'-methylspiro[chroman-4,2'-imidazol]-4'-amine.
  • Document to Structure (d2s)
    • Some names containing a space character (for instance, "malonic acid") were not detected.
    • When using document to structure using the MRecordReader API, the MRecord.getMolString() method returned null.
    • The character position property of recognized names was sometimes wrong.
    • Spiro and fused ring system names were not recognized in HTML documents when the brackets were represented by HTML entities.
    • Processing an HTML document failed when the document was declared to be in XHTML format, but was not actually a valid XML (for instance, contained unclosed tags).
    • Processing a USPTO XML patent file in the current directory failed when it referred to CDX structures files.
    • Some structures embedded in Office documents were not extracted.
  • Structure to Name (s2n)
    • Names could not be generated for structures with lone pairs (MolAtom.LP).
    • The name generated for OH^- was "oxidanide" instead of the preferred form "hydroxide".
    • An extra locant was included in the name of cyclic structures with multiple hetero atoms with one of them having non-standard valence, for instance, 1λ⁶,4-thiomorpholine-1,1-dione instead of 1λ⁶-thiomorpholine-1,1-dione.
    • In cases where a cyclic substituent was connected indirectly to the parent through an ether, sometimes wrong names were generated.
    • Name generation failed for structures with a methanethione parent.
• Molecule Representation
  • S-groups
    • Flip property could be set on any polymer-type S-group resulting in structures with incorrect information. From now on, only ladder type polymer S-groups can have flip property, and it will disappear from invalid structures.
    • java.lang.ArrayIndexOutOfBoundsException was thrown when a multicenter atom being the only member of an S-group was removed.
  • Valence Check
    • Valence check did not accept chlorine and heavier halogens with 1 negative charge and with 2, 4 or 6 pieces of fluoride ligands.
  • Stereochemistry
    • Incorrect stereogenic center was found in some spiro compound.
  • Aromatization
    • General aromatization handled selenium differently than sulfur.
• Clean 2D
  • Cleaning of position variation bonds could make bonds overlap.
• Datatransfer
  • OLE
    • The buttons in the Periodic Table and on the Atoms toolbar were not rendered properly in Marvin OLE.
• Applet
  • Missing resources prevented successful name import of bridged structures in applets. For instance, template based cleaning and pasting names did not work in these cases.
• Image I/O
  • Lone pairs were painted only at the second call of painting.
  • R-logic label was not exported into images, although visibility option "R-logic" was switched on.
  • Circled charge font was not considered during image export.
  • During PDF export, stoichiometric numbers in subscript were placed wrongly. 

Deprecated and removed methods

August 1st, 2014: Marvin 6.1.9.

Bugfixes

• Import/Export
  • OLE objects from Accelrys Draw 4.1 and further versions could not be redirected by MarvinOLE server.
  • OLE opened in 3D rotation mode (F7) mode.

April 9th, 2014: Marvin 6.1.8

No changes.

January 23rd, 2014: Marvin 6.1.7

No changes.

January 16th, 2014: Marvin 6.1.6

Bugfixes

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

December 18th, 2013: Marvin 6.1.5

Bugfixes

• Java Webstart
  • Java Webstart did not run on Macintosh computers.

December 7th, 2013: Marvin 6.1.4

Bugfixes

• 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.

October 31st, 2013: Marvin 6.1.3

Bugfixes

• 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.

October 17th, 2013: Marvin 6.1.2

New features and improvements

• MarvinSketch Dialog
  • 'Zoom to scaffold' checkbox option has been added to the "Preferences > Save/Load" tab.
• Structure Checker
  • External structure checker configuration file URL can be set via Java System Property.

Bugfixes

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

October 11th, 2013: Marvin 6.1.1

No changes.

September 10th, 2013: Marvin 6.1.0

New features and improvements

• MarvinSketch GUI
  • Peptide cycles and bridges can be drawn according to IUPAC recommendations.
  • IUPAC numbering can be displayed on the atoms of each molecule using the "View > Advanced > Atom Numbering > IUPAC Numbering" menu item.
  • 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.
  • 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.
• Graphical object handling
  • Electron flow arrows can be started from or targeted to multicenter atoms.
• MarvinView GUI
  • IUPAC numbering can be displayed on the atoms of each molecule using the "View > Misc > Atom Numbers > IUPAC Numbering" menu item.
• 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.
    • New import option, z, is introduced to MDL import that converts carbon atoms with "Z" label to R-group attachment points. 
  • SMILES/SMARTS
    • [Z] is imported as R-group attachment point from SMILES.
  • CXSMILES/CXSMARTS
    • New export option, b, has been introduced to CXSMILES/CXSMARTS in order to turn off the export of bicyclostereo-information.
  • Name to Structure (n2s)
    • Name and corporate ID resolution webservice now supports NTLM authentication.
    • 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.
  • 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.
    • 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.
    • 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 retrieving a Chemical Registry Number® from , the InChiKey of the structure is used to search for the structure. This allows more structures to get a 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.
  • New methods, MolAtom.getBondArray() and Sgroup.getBondArray() are introduced.
• 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.
• 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.
• 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.
  • 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. 
• Build/Installation
  • Mac OS X installer images were not digitally signed, and GateKeeper in newer OS X versions (10.7.5+) reported our installers as damaged and refused to install them.

Bugfixes

• MarvinSketch GUI
  • Aliphatic/Aromatic atom query property had three options ("a", "A", and "A,a") instead of the necessary two ("a" and "A").
• MarvinSketch Dialog
  • In case of long names, only a part of the whole name appeared on the naming panel.
• Editing
  • Deleting an atom having an R-group attachment did not delete the attachment.
  • The end of an arrow did not stick to the midpoint of an existing arrow.
• Load/Save handling in UI
  • In MarvinView, "File > Save All... > Advanced > Into SEPARATE FILES" did not save the last structure.
• History functions
  • When the "Stereo" atom property had been changed, Undo/Redo did not work properly and the IUPAC name was not updated.
• Graphical object handling
  • Labels written in text box were shifted when they were pasted either as an OLE object or as a PNG image.
• MarvinView GUI
  • When a structure which contained an R-group definition was opened from MarvinView for editing in MarvinSketch, the structure appeared with 0% zoom factor.
  • Text elements (atom labels, atom indices, text box contents, IUPAC name) were not resized in MarvinView while zooming the structure using the "View > Transform > Zoom" function.
• 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. 
    • 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 "&#946;" or "&alpha;".
    • 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)). 
  • 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.
    • 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.
    • Some cycloolefine stereoisomers were mistakenly filtered out as duplicates, so they were missing from the generated list of stereoisomers.
• 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.

Deprecated and removed methods

• Deprecated and removed methods

November 25th, 2013: Marvin 6.0.6

Bugfixes

• 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.

August 27th, 2013: Marvin 6.0.5

Bugfixes

• MarvinView GUI
  • Opening a structure for editing in MarvinView was opened with 0% zoom factor in the MarvinSketch window, when the structure contained an R-group.

August 6th, 2013: Marvin 6.0.4

• MarvinSpace
  • Transferring 3D molecules from MarvinSpace to MarvinSketch resulted in 2D structures in the sketcher.

July 23th, 2013: Marvin 6.0.3

No changes.

June 25th, 2013: Marvin 6.0.2

No changes.

June 21st, 2013: Marvin 6.0.1

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.
• Calculations
  • Services
    • SOAP webservices:
      • SOAP version 1.2 webservices are supported.

Bugfixes

• 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.
• Calculations
  • 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.

May 17th, 2013: Marvin 6.0.0

New features and improvements

• MarvinSketch GUI
  • The default tool in MarvinSketch is Rectangle Selection instead of Single Bond.
  • MarvinSketch GUI has been refreshed: Icon set has been changed in MarvinSketch. Menu items have been rearranged. Several dialogs, tooltips, menus has been renamed.
  • A new Marvin configuration has been added to MarvinSketch. Already existing Marvin configurations have been renamed. 
  • 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.
  • 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 "-C_1-6alkyl". 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 the retrieval of  Chemical Registry Numbers® from publicly available sources hosted by the U.S. National Institutes of Health (“NIH”) and the Wikimedia Foundation..
• 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.
• Calculations
  • 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. 
  • 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.
• 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".

Known issue

• MarvinSketch Applet
  • External checker classes do not load if browser uses Java SE 6. Please, use Java SE 7 for successful checker class loading.

Bugfixes

• MarvinSketch Menu
  • The "Recent Files" list was not updated with the new file name when the file contained multiple structures and more records were selected.
• Painting
  • There was a gap between the lines of the double bond and the single bonds when two single bonds connected to the same (non-visible) carbon atom on one end of a double bond.
  • Electron flow arrows partially hid lone pairs in some cases.
• Clipboard handling
  • When copying and pasting between Marvin applications in Linux, an exception was thrown which froze the application where the copy operation had been performed. The exception originated from the applied freehep library, which has been updated.
• MarvinSpace
  • 3D alignment: MCS mode is fixed to align molecules in 3D.
• Image I/O
  • Image export did not remember the last folder used for saving.
  • Molecule source was not saved in jpg, png, and svg files when "Save As Image" was selected. 
• 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.
    • 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[6.3.1.0^2,7]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.
• Calculations
  • NMR (HNMR, CNMR Prediction, ...)
    • PDF export of NMR spectra was failed when the generated new page contained a blank line only.
    • When displaying NMR spectra of selected tautomers, the background of the tautomer preview window was black in Linux OS.

Deprecation

• Deprecated methods
  • Molecule Representation
    • Valence Check: MoleculeGraph.VALENCE_CHECK_AMBIGUOUS, MoleculeGraph.ValenceCheckState, MoleculeGraph.setValenceCheckState(ValenceCheckState), MoleculeGraph.getValenceCheckState() MoleculeGraph.getPossibleAttachmentPoints(MolAtom)
    • S-groups: SuperatomSgroup.getAttachAtoms(), SuperatomSgroup.getLegalAttachAtoms(), SuperatomSgroup.getFreeLegalAttachAtoms(), SuperatomSgroup.isFreeLegalAttachAtom(MolAtom), SuperatomSgroup.isLegalAttachment(MolAtom), SuperatomSgroup.sortXBonds(), MolAtom.getAttach(), MolAtom.setAttach(int), MolAtom.setAttach(int, Sgroup)
    • Elemental Analysis: ElementalAnalyser.setMolecule(SMolecule)
    • Other deprecated methods Molecule.exportToFormat(String), Molecule.exportToBinFormat(String), Molecule exportToObject(String) throws java.lang.IOException.
  • Structure to Name (s2n)
    • The method chemaxon.marvin.io.formats.name.nameexport.IUPACNamer.generateName(Molecule) , though not documented, was public for internal reasons, and used a non-thread-safe way to receive options. It is now deprecated in favor of chemaxon.formats.MolExporter(Molecule, String format) , where format can be for instance "name" for IUPAC name, "name:t" for traditional name.
  • Automapper
    • chemaxon.marvin.modules.AutoMapper
• Removed methods
  • Molecule Representation
    • MolAtom.setMassnoIfKnown(String), MolAtom.isNobleGas(), MolAtom.isArrowEnd(), MolAtom.valenceCheck(), MolAtom.getEdgeCount(), MolAtom.getEdge(int), MolAtom.getEdgeTo(MolAtom), MolAtom.haveSimilarEdges(MolAtom),
    • MolBond.ARROW(), MolBond.isCoordinative(), MolBond.isArrow(), MolBond.getNode1(), MolBond.getNode2(), MolBond.getOtherNode(MolAtom), MolBond.cloneEdge(MolAtom a1, MolAtom a2)
    • MoleculeGraph.AROM_CHEMAXON, MoleculeGraph.AROM_DAYLIGHT(), MoleculeGraph.setSetSeqs(int id), MoleculeGraph.getAromrings(), MoleculeGraph.getNonAromrings(), MoleculeGraph.getAromrings(int), MoleculeGraph.getNonAromrings(int), MoleculeGraph.mergeFrags(), MoleculeGraph.getFragIds(), MoleculeGraph.getfindFragById(int fragId, MoleculeGraph frag), MoleculeGraph.getNode(int), MoleculeGraph.setNode(int, MolAtom), MoleculeGraph.insertNode(int, MolAtom), MoleculeGraph.removeNode(MolAtom), MoleculeGraph.removeNode(MolAtom, int), MoleculeGraph.removeNodeVector(), MoleculeGraph.getEdgeCount(), MoleculeGraph.getEdge(int), MoleculeGraph.setEdge(int, MolBond), MoleculeGraph.insertEdge(int, MolBond), MoleculeGraph.insertEdgeInOrder(MolBond, MolBond[]), MoleculeGraph.replaceEdge(MolBond, MolBond), MoleculeGraph.removeEdge(MolBond), MoleculeGraph.getEdgeArray(), MoleculeGraph.getEdgeVector(), MoleculeGraph.getAllEdges(), MoleculeGraph.regenEdges(), MoleculeGraph.sortEdgesAccordingTo(MolBond[]), MoleculeGraph.mergeNodes(MolAtom that, MolAtom), MoleculeGraph.mergeFrags(int, int)
    • Molecule.mergeFrags()
    • RgMolecule.setAbsStereo(boolean, int, int), RgMolecule.createMol(String), RgMolecule.getBtab()
    • RxnMolecule.getBtab(), RxnMolecule.getStructureCount(int), RxnMolecule.getStructure(int, int), RxnMolecule.addStructure(Molecule, int), RxnMolecule.removeStructure(int, int)
    • CEdge, CNode, CGraph
    • MDocument.setGUIProperyContainer(MPropertyContainer)

October 31st, 2013: Marvin 5.12.6

No changes.

June 21st, 2013: Marvin 5.12.5

No changes.

May 6th, 2013: Marvin 5.12.4

Bugfixes

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

April 9th, 2013: Marvin 5.12.3

Bugfixes

• Import/Export
  • Name to Structure (n2s)
    • Names with ylium and uide suffixes are now supported.
• Calculations
  • 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.

March 28th, 2013: Marvin 5.12.2

Bugfixes

• Molecule Representation
  • Conversion from explicit hydrogen to implicit one removed stereo centers not having explicit hydrogen ligand.
• 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.

March 20th, 2013: Marvin 5.12.1

New features and improvements

• Import/Export
  • CDX/CDXML
    • S orbitals and oval shaped s or p orbitals are imported from CDX/CDXML.

Bugfixes

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

March 5th, 2013: Marvin 5.12.0

New features and improvements

• MarvinSketch GUI
  • Typing abbreviated group names is now case sensitive. 
• 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. 
  • 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.
• 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-??-4-????.
    • 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[12.4.0.0^2,6.0^7,12]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. 
    • 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., "&#xblah") 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.
• Calculations
  • Isomers (Tautomers, Stereoisomers)
    • Performance improvement: Tautomerization will not apply "Clean2D" if the output result has no 2D coordinates.
    • 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. 
  • Structure Checker configuration can be accessed via URL from MarvinSketch, Structure Checker application, and via Structure Checker API call.
  • Integration of external structure checkers and fixers into ChemAxon products has become easier via MarvinSketch GUI. 
  • In case of more than one fixer, a logical order of priority has been preset.
  
  
  • 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.

Bugfixes

• 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.
• 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.
  • 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.
  • cxcalc returned irrelevant error message for calculations containing "ANY" bonds.
  • Thole polarizablility (tpol) calculation didn't interrupt when clean3D failed.
• Backend / Core
  • Removing explicit hydrogens on some large PubChem compounds caused infinite loop. 
• 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.

January 14th 2013: Marvin 5.11.5

Bugfixes

• Datatransfer
  • Structures copied from ChemDraw, Accelrys Draw, or Symyx Draw could not be pasted onto MarvinSketch.

November 19th 2012: Marvin 5.11.4

New features and improvements

• Datatransfer
  • The imageImportServiceURL setting also affects the behavior of clipboard operations (drag and drop, paste).

Bugfixes

• 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.

October 20th 2012: Marvin 5.11.3

Bugfixes

• MView applet
  • Atom and Bond set coloring was not working properly when Marvin View Applet was called from JavaScript.
• Image I/O
  • When imageImportServiceURL startup option was not set for MarvinSketch, the same setting on the Preferences panel was lost. By default shortcuts and startup scripts do not specify this command line startup option.
• Java WebStart
  • chemaxon-core.jar, fontbox-1.7.1.jar and pdfbox1.7.1.jar were missing.
• Calculator Plugins
  • Tautomerization Plugin threw exception during generic tautomer generation if the input structure contained metal ions with valence error.

October 12th 2012: Marvin 5.11.2

New features and improvements

• Image I/O
  • Recently added rendering options are now available to be set from MolPrinter API (Absolute label visibility, Peptide display type, R-group visibility, Any bond style, Lone pair rendering style, Charge rendering style). 
• MarvinSketch GUI
  • A new "imageImportServiceURL=[URL]" program argument was added to the MarvinSketch application.
• MarvinSketch applet
  • A new "imageImportServiceURL" was added as an applet parameter.
• Graphical object handling
  • When an MMidPoint object was set as an end point for an MPolyLine, getting the MMidPoint location caused a StackOverFlowError.
• Import/Export
  • Document to Structure (d2s)
    • Names broken over two lines with a hyphen (-) are now recognized.
    • Names followed by a superscript text, for instance, a reference or footnote number (e.g., "aspirin¹¹") are now recognized.
  • Name to Structure (n2s)
    • In some cases, such as "4-methylthiophenylmethyl", there is an ambiguity whether "thiophenyl" refers to a compound derived from thiophene or thiophenol. Name to Structure now gives priority to the thiophenol related compound interpretation; though, "thiophenyl" by itself will still be supported as thiophene derivatives.

Bugfixes

• Painting
  • If R-group visibility was turned off and any of the bonds had label(s) to paint, an ArrayIndexOutOfBounds exception was thrown.
• Image I/O
  • Display parameters of charge, lone pair, peptide could not be set for molexporter. The default values were charge "in a circle", lone pair "as line", peptide "three letter format". Image copy also used these values.
• Import/Export
  • MOL, SDF, RXN, RDF
    • Aliphatic query properties of atoms with query string were not read from MDL formats.
    • After importing Extended MOL files that contain superatom S-groups the orientation of S-groups could be changed.
    • Atom containing both aliphatic and unsaturated query properties were exported incorrectly to MDL formats.
    • SDF import returned structure with incorrect S-group embedding.
  • SMILES/SMARTS
    • SMILES T* option did not export all SDF fields, but only those which appeared in the first molecule.
• Molecule Representation
  • S-groups
    • Two superatom S-groups being each others' parents caused infinite loop. In these cases, now java.lang.IllegalStateException is thrown.
  • Valence Check
    • Phosphorous atom in hexafluorophosphate was not accepted by Valence Check.
• Stereochemistry
  • Cloning of BicyclostereoDescriptor in RxnMolecules threw java.lang.ArrayIndexOutOfBoundException.
• Clean 2D
  • Terminal methyl-group in phosphate-ester was cleaned incorrectly.
  • Clean2D could not handle condensed adamantane derivatives.
• Calculations
  • Other (HBDA, Huckel Analysis, ...)
    • The --pH command line option did not work in hydrogen bond acceptor-donor calculation.
• Structure Checker
  • If fixer action was not defined, default fixer was not applied in structurechecker command line tool.

September 26th 2012: Marvin 5.11.1

New features and improvements

• Import/Export
  • Document to Structure (d2s)
    • Startup time of document to structure has been significantly reduced. This is especially important when processing very short text documents, such as a single sentence or paragraph. The speedup in such cases can be up to 10 times faster.

Bugfixes

• Calculations
  • NMR (HNMR, CNMR Prediction, ...)
    • NMR Prediction did not use the mixed prediction algorithm, so NMR shift predictions were less accurate.
• Chemical Terms
  • The -g (ignore error) option of evaluate did not work when -x (extract) option was used.
• Structure Checker
  • WedgeCleanFixer threw ArrayIndexOutOfBoundsException when the erroneous wedge bonds were located inside an S-group. 

September 20th 2012: Marvin 5.11.0

New features and improvements

• MarvinSketch GUI
  • Molecule properties like SDF fields can be added/edited/deleted in MarvinSketch GUI.
  • Bond properties can be added/edited/deleted in MarvinSketch GUI.
  • Lone pair can be displayed as a line. The option can be set from the "Preferences" panel.
  • Charge can be displayed in a circle. The option can be set from the "Preferences" panel.
  • An aromatic benzene template has been added to the Generic templates.
• Data transfer
  • Clipboard handling
    • Java wrapper for CXNSharedAddin library has been introduced to handle tabular data transfer from/to Microsoft Office applications.
• Import/Export
  • CDX/CDXML
    • Graphical arrows "retrosynthetic" and "equilibrium" are imported from CDX and CDXML files.
  • Name to Structure (n2s)
    • Names, such as "methyl ether", are used either to denote a group (CH3-O-*) or the dimethyl ether compound (CH3-O-CH3), as well. The default behavior still is to generate the complete compound, but a new name option "expectGroup" has been added to get the group instead.
    • A name converter can now prevent a name from being converted (even by other lower-priority converters). See the API of the chemaxon.naming.NameConverter class.
  • Document to Structure (d2s)
    • Peptide 3 letter abbreviations are now recognized in documents, for instance ValGlySerAla or Val-Gly-Ser-Ala.
    • A new option has been added to control the maximum time allowed for processing a document: format option "d2s:timeout=60" to allow a maximum of 60 seconds. Default is 0 meaning infinite timeout.
    • A new option has been added to disable the extraction of OLE embedded structures from Office documents (option name: "d2s:-ole").
    • Structures imported from the custom name dictionary now have the "Type" property set to "custom" instead of "common".
    • Memory usage has been significantly reduced when processing large PDF documents (for instance hundreds of scanned pages).
    • Structure image conversion by OSRA has become faster, resulting in more structures converted when previously a timeout was reached.
    • CAS Registry Numbers® (which typically include commas) are not converted by default by d2s anymore (they are still converted by n2s). The old behavior can be activated by using the "d2s:CASnames" format option.
    • The unwanted interpretation of some common words as chemical names, that are frequent especially in patents, has been avoided. For example, the 'amino' group when used in the phrase 'amino acid', or 'Ser' when it is not the abbreviation of Serine but 'Ser. No.' for 'serial number'.
  • Structure to Name(s2n)
    • Multiple name generation tasks can now be run in parallel at full speed to make use of multiple CPUs and cores.
    • Multiple name import tasks now run faster, as partial locking is no longer required and has been removed.
    • Generated names now use unicode characters when needed, for instance, 6λ⁴-thiadispiro[5.2.5⁹.2⁶]hexadecane instead of 6$l^{4}-thiadispiro[5.2.5^{9}.2^{6}]hexadecane. The pure ASCII output can be generated using the "name:ascii" format option.
  • Image I/O
    • New parameter imageImportServiceURL has been added to the image importer module. The URL can be set on the "Preferences" dialog or as an import option.
  • VMN import
    • VMNs of type "display" are now read.
    • VMN abbreviated group list has been extended: carbon chains up to 50 members have been added.
    • AV (abnormal valence) property is now stored in atom property and not set as atom valence. The VMN valence representation will be revised in a later version.
    • Deuterium and tritium count property is handled properly in VMN (added as D and T ligands for non-homology atoms). D and T are transposed during the import in comparison to the VMN, as this represents the correct information in the majority of the MMS database.
    • Correcting incorrect atom types in VMNs: C0 is transformed to CHK; C1 is transformed to C; homology groups in ring are transformed to XX
    • Attachment bond type is set to parent R-atom bond type if different.
    • VMN import option is available for switching off corrections:
• Molecule Representation
  • New option, MolAtom.BRIDGEATOM_H, is added to Hydrogenize.removeHAtoms(MoleculeGraph, int) method to remove hydrogens connected to bridgehead atoms.
  • Valence Check
    • Local valence check has been introduced, which calculates the valence by considering only the neighboring atoms. Although the new valence check is the default, the old one is also available. 
  • S-groups
    • ElementalAnalizerPlugin calculates Polymer Formula for molecules containing SRU or RepeatingUnit S-groups.
• Calculations
  • Charge (Charge, Polarizability, ...)
    • Dipole Moment Calculation plugin: calculates the net molecular polarity.
  • NMR (CNMR Prediction, HNMR Prediction)
    • New, mixed HOSE code/CXN model has been introduced, which results in more accurate NMR shift prediction.
    • C-F and H-F couplings are considered during NMR shift calculation.
    • Diastereotopic protons are supported in HNMR Prediction.
    • The tautomers of the predicted molecule are accessible via the Options > Select Tautomers... option of the NMR GUI. The spectra of the selected tautomers with defined percent composition are added to the predicted spectrum.
  • Chemical Terms
    • "molString" and "molFormat" Chemical Terms functions are accessible under the name "molConvert" as well.
• Structure Checker
  • New Structure Checker GUI has been introduced. Besides the redesigned GUI, new features are also available:
    • Profile management;
    • Filters in Report view.
  • Structure Checker is going to be moved to the MarvinBeans package. Until it is done, the new Structure Checker GUI is available in both JChem and MarvinBeans packages as Structure Checker JChem and Structure Checker, respectively.
  • Substructure Checker feature is accessible only in Structure Checker JChem until the complete relocation of Structure Checker.
  • Improved R-group Attachment Error Checker detects R-group definitions having incorrect R-group attachment orders. Fixer is not available for this feature yet.
  • New Explicit Hydrogen Checker options are ready for use.
  • Checkers that are not recognized as internal or external checker are called: "Invalid Checkers". Invalid Checkers cannot be used in valid Structure Checker configurations; they need to be removed to perform proper working behavior.
• Build/Installation
  • Marvin Beans and JChem installers - for Linux - bundled with Java 1.6.0_33 have been introduced.

Bugfixes

• MarvinSketch GUI
  • The bond related label backgrounds hid the bond partially if the bond was almost parallel with the horizontal axis.
  • Several mnemonics were duplicated or missing in the menu of MarvinSketch.
• Painting
  • Bond topology representation was not visible in R-groups.
• Dialogs
  • Periodic table view 'Blocks' showed Helium color coded as a part of 'p block' instead of the correct 's block'.
• Import/Export
  • Load/Save handling in UI
    • MarvinSketch did not overwrite the former PDF file when changes were made and it was saved as a PDF again with the same file name.
  • MRV, CML
    • The string value of a query property was imported as element.
  • MOL, SDF, RXN, RDF
    • Registry number of a molecule that is a property of an other molecule was not imported from RD file.
  • SMILES/SMARTS
    • Cis/Trans information was not exported for bonds being in two rings.
  • CXSMILES/CXSMARTS
    • Query pseudo atoms represented by CXSMARTS lost their valence property during import.
    • R-group definition of an Rg-molecule described in CXSMARTS was imported as CXSMILES.
  • CDX/CDXML
    • Reaction agent was not possible to read from CDXML file.
    • From CDXML file containing only a product of a reaction, the product was imported as reactant.
  • Name to Structure (n2s)
    • Names ending with "group", such as: "cyclohexyl group" were not imported.
    • Chirality specified without locant was sometimes not included in the generated structure, for instance in (R)-tert-butyl 3-aminopyrrolidine-1-carboxylate.
  • Document to Structure (d2s)
    • Several names separated by a comma were sometimes wrongly recognized as a single name.
    • Document to structure was leaking some memory in a way that was problematic for extremely large documents (tens of thousands of structures in a single document).
    • When using the d2s API, waiting threads could be left behind when large documents were converted but the structures were not read until the end. This is now fixed, provided the client calls MolImporter.close().
    • Document to structure was not processing text from PDFs with non-standard fonts, for instance English text encoded in Japanese fonts.
    • Certain images in PDFs were not processed correctly by OSRA during optional image-to-structure conversion.
    • Names found in documents may have included unwanted trailing characters when the next word started with an open bracket, for instance, "cholesterol [28]" instead of "cholesterol".
  • Structure to Name(s2n)
    • The group "[NH3+]-" was given traditional name "aminio", instead of the correct "ammonio".
    • Names were generated for structures with link nodes, as if the link nodes had been absent.
    • Incorrect names were generated for structures with one attachment point.
• Molecule Representation
  • Meitnerium appeared at a wrong position in the periodic table of MarvinSketch.
  • Explicit hydrogen that connects to an atom having more than one wedge bond was not converted to implicit one.
  • S-groups
    • When an expanded SuperAtom-Sgroup was inside an other S-group, its attachment points had invalid implicit hydrogen count.
  • Stereochemistry
    • Stereoinformation were not recognized on cyclohexane-1,3,5-triol.
• Clean 2D
  • Calling clean 2D on a 3D molecule resulted in short bond length between a Hydrogen and an other atom
  • Clean 2D inserted wiggly bond into a Kekule form of a 0 dimensional aromatic molecule.
• Aromatization/Dearomatization
  • Basic aromatization method aromatized rings containing sulfur atom that have four ligands.
  • Basic aromatization method aromatized rings with -S= substructure.
• Calculations
  • Isomers (Tautomer, Stereoisomers)
    • Cross bond was not handled correctly by canonical tautomer generator.
• Structure Checker
  • Abbreviated Group checker options did not work as expected: checker recognized both expanded and contracted groups regardless of the selected option.
• Build/Installation
  • Desktop icons were missing from the Marvin Beans for Linux installer.

October 31st, 2012: Marvin 5.10.5

New features and improvements

• Applet
  Class reorganization for more efficient applet loading.

September 7th, 2012: Marvin 5.10.4

New features and improvements

• Import/Export
  • MDocSource implements Iterable<Molecule>.
  • MOL, SDF, RXN, RDF
    • New option for MDL MOL format import, Fsg, has been introduced to ungroup superatom s-groups with more than two attachment points.

Bugfixes

• Import/Export
  • MRV
    • The string value of the query property was imported as element.

August 13th, 2012: Marvin 5.10.3

New features and improvements

• MarvinView Printing
  • Resolution of PDF printing has been increased.
• Datatransfer
  • Legacy MRV '\n\ header (5.7) format is supported in Marvin OLE.

July 27th, 2012: Marvin 5.10.2

New features and improvements

• Import/Export
  • MOL, SDF, RXN, RDF
    • Coordination bond is written and read from extended MOL file.
  • Name to Structure (n2S)
    • More extensive support for the retrieval of CAS Registry Numbers® from publicly available sources hosted by the U.S. National Institutes of Health (“NIH”) and the Wikimedia Foundation.
• Clean 2D
  • New clean option, Toff, is introduced to ignore template based cleaning.
  • Coordinate bond length has been increased for a better view of its arrow representation between atom labels.

Bugfixes

• MarvinView
  • MarvinView did not display the SD file property if no property values were attributed to the first entries.
• Painting
  • The bond related label backgrounds hid the bond partially if the bond was almost parallel with the horizontal axis.
• Editing
  • Transfer button did not appear on the "Sketch new substituent..." popup window when the 'Insert>New Substituent' menu item was selected.
• Import/Export
  • Byte Order Mark (BOM) was not written out during the export.
  • Default line separator was not unique in MolExporter.
  • CDX/CDXML
    • Empty CDX and CDXML files could not been imported.
• Molecule Representation
  • S-groups
    • Contracted Superatom S-groups drawn to MarvinSketch and having only one crossing bond had no attachment point information.
  • Stereochemistry
    • Absolute chiral flag calculation terminated with "java.lang.OutOfMemoryException" for large, symmetric molecules, e.g., fullerene derivatives. 
• Calculations
  • Protonation (pKa, Major Microspecies, Isoelectric Point)
    • Major microspecies calculation threw "ArrayIndexOutOfBoundsException" in the reported case.

July 6th, 2012: Marvin 5.10.1

New features and improvements

• Import/Export
  • MOL, SDF, RXN, RDF
    • The template based coding of amino acids in MOL V3000 files are read as pseudo atoms. However, the template based structure of peptides cannot be read.
    • Method MolFileHandler.collectFileInfo() returns molecule and reaction identifiers $MFMT $MIREG, $MFMT $MEREG, $RFMT $RIREG, $RFMT $REREG, $MIREG, $MEREG, $RIREG, $REREG as well.
• Clean 2D
  • An option is introduced to set explicit C-H bond length to 1.0 instead of 1.54 in case of two dimensional cleaning.
• Calculations
  • "Keep explicit hydrogens" option has been added to pKa plugin, Major Microspecies plugin, and Isoelectric Point plugin.
  • Protonation (pKa, Major Microspecies, Isoelectric Point)
    • The speed of major microspecies calculation has been improved when "Take major tautomeric form" option is used.
  • NMR
    • The accuracy of the NMR predictor has been improved.

Bugfixes

• Painting
  • "Absolute" label was not visible when only contracted Sgroups contained stereo information and the "Absolute" stereo flag was set on the Molecule.
  • Joining two product structures of a reaction erased both structures.
  • Joining aromatic rings drawn in Kekule form sometimes caused their aromatization.
• Editing
  • Atom labels could disappear when the structure was cleaned in 3D, rotated then cleaned in 2D.
• Import/Export
  • Byte Order Mark (BOM) was not written out during the export.
  • MRV/CML
    • Molconverter could not convert files containing multiple molecules to separate MRV/CML files.
    • Encoding could not been set during MRV and CML export.
  • MOL, SDF, RXN, RDF
    • Bond length of a molecule imported from MOL V3000 file was short, therefore the atoms overlapped.
    • RD file records written after an empty structure were not read correctly.
  • CDX
    • CDX files containing labels without chemical structures were not read. Now, these labels are read in text boxes.
  • SKC
    • SKC import put an R-group attachment point to Superatom S-groups.
    • Stereo information was lost at importing a peptide from an SKC file.
    • Wedge bond information of a contracted S-group was lost during the SKC import.
• Molecule Representation
  • Valence check
    • Valence check allowed any number of bonds on carbon atoms having implicit hydrogens.
  • R-groups
    • Method RgMolecule.fuse() resulted inconsistent molecule when it was invoked on RgMolecules having SuperAtom S-group in its definition.
  • Stereochemistry
    • Nitrogen being one of the fusion points of ring systems was detected as chiral when the carbon atom at the other fusion point had four explicit ligands.
• Aromatization/dearomatization
  • Dearomatization failed for porphyrin-like ring systems.
• Calculations
  • Charge (Charge, Polarizability, Orbital Electronegativity)
    • Charge calculation was not consistent on fragmented molecules.
  • Isomers (Tautomers, Stereoisomers)
    • Different rational canonical tautomers were generated for some molecules when they came from different sources (e.g., InChi and SMILES).
    • Tautomer distribution was not calculated for various porphyrin-like structures.
  • Geometry (Topology Analysis, Geometry, PSA, MSA)
    • Negative or zero Van der Waals and Solvent Accessible molecular surface area values were generated for molecules with inconsistent chemical structures.
• Structure Checker
  • Abbreviated group checker did not identify expanded and contracted groups correctly.
  • "substructre" action string did not work in command line.

June 08th, 2012: Marvin 5.10.0

New features and improvements

• MarvinSketch GUI
  • New graphical arrows: equilibrium arrow, curved arrow, dashed arrow, and crossed arrow has been introduced. 
  • The built-in abbreviated groups can be easily extended and overridden with custom abbreviated group definitions.
  • New display option has been introduced: peptide sequence can be visualized in 1-letter form besides the original 3-letter form.
  • Cleaning preset is added to template sets. It can be controlled on the Template library dialog.
  • When opening an item of the Recent File list fails, the entry is deleted.
  • All query atoms and query properties are available from menu and toolbar by customization.
  • Names of homology groups on "Advanced" tab of "Periodic System Dialog" and in "Template Library" have been updated.
  • The elements of the Advanced tab on the Periodic System dialog are now available from MarvinSketch by typing as shortcuts.
  • The picture of custom defined template appears at the mouse tooltip when the name of the structure is unknown.
  • The name of reaction arrow: "Resonance" and graphical arrow "Two-Headed Arrow" have been changed. 
• MarvinSketch Printing
  • The page format settings on the print dialog is now stored and do not need to be reset when starting a printing job from MarvinSketch or MarvinView.
• Import/Export
  • Load/Save handling in UI
    • Disconnected molecules can be saved separately in MarvinSketch.
    • When saving a document opened by d2s in MView, MRV is offered as default format.
  • Structure to Name (s2n)
    • Extended and updated structure to common name dictionary.
    • L-amino acid structures are all converted to L- traditional name.
  • Name to Structure (n2s)
    • Improved conversion of systematic names, notably names expressed as amides of acids, such as "pyridine-4-carboxylic acid (2-methoxy-ethyl)-methyl-amide".
    • Extended and updated common name to structure dictionary.
    • All peptide abbreviations are now consistently converted to the L- stereo form structure.
    • Possibility to set custom name converter plugins for n2s and d2s (e.g., converting internal company compound IDs) specific to a single conversion in a thread-safe way has been introduced (see API of the new method: chemaxon.naming.NameConverters.addThreadLocal).
    • Fragments names such as phenyl can be converted with attachment points *C1=CC=CC=C1 |$_AP1|, using the "name:+rgroups" format option.
  • Document to Structure (d2s)
    • Document to Structure can be instructed to process only a subset of pages in a document using the new startPage and endPage format options.
    • The custom dictionary format option (dict=...) is available in Document to Structure.
    • Possibility to set custom name converter plugins for n2s and d2s (e.g., converting internal company compound IDs) specific to a single conversion in a thread-safe way has been introduced (see API of the new method: chemaxon.naming.NameConverters.addThreadLocal).
    • Acronyms such as BBC are not converted anymore (as BromoBenzyl Cyanide) since they most often have a non-chemical meaning. Conversion of acronyms can be enabled if desired by using the "d2s:+acronyms" format option.
    • Fragments names such as phenyl are converted with attachment points, such as *C1=CC=CC=C1 |$_AP1|.
  • DNA/RNA
    • DNA nucleic acid sequence can be imported in four ways: ACGT, A-C-G-T, dAdCdGdT or dA-dC-dG-dT. RNA nucleic acid import accepts sequences like both ACGU and A-C-G-U.
• Molecule Representation
  • Molecule/atom/bond properties
    • Similarly to MolAtom, general properties are possible to be added to MolBond.
    • New, simple way is provided to replace isotopes.data and elements.zip used in PeriodicSystem.java.
  • S-groups
    • New method is introduced to set a data S-group to behave as relative after specifying its absolute position
  • R-groups
    • A new, fast method is available to delete one or more molecules from an R-group definition.
• Calculations
  • Isomers (tautomer., reson.)
    • Rational tautomer generation option has been introduced. Generation of All tautomers and Canonical tautomer can take this new option into consideration.
    • Improved generic tautomer generation in case of aromatic molecules.
  • NMR Predictor
    • NMR Predictor is available in MarvinSketch. It accurately predicts ¹³C and ¹H NMR spectra of standard organic molecules.
  • Services
    • LocalService allows to set URL based JAR path.
• Structure Checker
  • New checker: Absent Chiral Flag checker; when the molecule is chiral and all stereo centers are precisely marked, absolute chiral flag can be applied to the molecule.
  • R-group Reference Error Checker is deprecated and has been split into three separate checkers:
    • Circular R-group Reference Checker;
    • Missing R-group Checker;
    • Unused R-group Checker.
  • Partial clean fixer is available for certain structure checkers: it can fix the erroneous part of the molecule exclusively.
• Stereochemistry
  • A new method is available that finds atoms that can become (s) or (r) stereo centers after the stereo arrangement of the bonds around the atom is specified.
• API
  • New parameter to set accessibility of special nodes in Advanced tab of Periodic System dialog.

Bugfixes

• MarvinSketch
  • When MarvinSketch was launched from command line with -h or --help option, the application was not terminated after printing of help message.
  • When using MarvinSketchPane from an application, and pop it up as a modal dialog, its children could disappear behind the main application (e.g., DialogLauncher example).
• MarvinSketch GUI
  • Scaling bug occured on the button of the template toolbar if there was a contracted group displayed on the button.
  • "Calculations" menu did not appear in ISIS/Draw-like configuration.
• MarvinView GUI
  • The title of the MView application window was not updated on file open and save.
• MarvinSpace
  • MarvinSpace: JOGL 1.1 was replaced by the most recent version 2.0. This resolves various MSpace launch and initialization issues (in particular Applet problems on MacOSX).
• Applet
  • Although a valid URL was given in sketchHelp applet parameter, Marvin applet loaded the default help by selecting Help->Help Content instead of the given URL.
  • "My templates" became unavailable in applet after modifying it from template library.
• Painting
  • The rb* atomic query property was not displayed at the mouse tooltip when it was set through its keyboard shortcut: ".rb*".
• Chemical Structure Painting
  • Positioning of R-group labels was incorrect.
• Datatransfer
  • Clipboard handling
    • Copy as PDF used 100x100px as image metrics and not the appropriate size for the current scale in Mac OSX.
• Import/Export
  • MOL, SDF, RXN, RDF
    • The subscript information of the S-group generic bracket was not exported to MOL V3000 and V2000 formats.
    • Export of compressed MOL files allowed too large coordinate values, which caused distortion in the molecule after importing it.
    • After importing an RDfile that contains an empty S-group, its brackets didn't appear.
  • SDF
    • Data S-groups were lost after exporting it to SDF format.
  • SMILES, SMARTS
    • Export to abbreviated group format did not work since 5.8.
  • CXSMILES, CXSMARTS
    • CXSMILES import added radicals to atoms that have coordinate bond to a central, metal atom.
    • I/O of atom alias "," was not working in CXSMILES format.
  • CML, MRV
    • Format mrv had missing closing tags at the end of the generic S-group lines.
    • MolExporter exported to MRV format using operating system specific line ending, '\n'.
  • CDX
    • Standalone list atoms and labels were read as text boxes from CDX files.
    • Component grouping was not recognized during CDX import.
  • SKC
    • During the export to SKC format, chiral flags were lost and "AND enantiomer" flags were displayed.
  • CDX/SKC
    • When opening a ChemDraw CDX file or an ISIS/Draw .skc file containing structures with abbreviated groups, the attachment point of these groups was rendered incorrectly.
  • Structure to Name (s2n)
    • There were extraneous numbers in generated names for structures containing atom values.
    • Generation of IUPAC names for large structures might have stopped before the timeout.
  • Name to Structure (n2s)
    • The n2s import option to specify the location of the custom dictionary was not thread-safe, and was not accessible in d2s.
    • Name to structure failed to return a result on some very long names (several hundreds of characters).
  • Document to Structure (d2s)
    • Non-chemical data in embedded structures, for instance text labels, were not extracted from embedded documents.
    • Some embedded structures were not extracted from office documents.
    • Reactions embedded in documents were not extracted.
    • Some uppercase strings were wrongly interpreted as smiles, for instance "BOUCHON".
    • When OSRA was called by Document to Structure, it could run even after Marvin is stopped (on Windows only).
    • OSRA was not working on PDFs containing monochrome images.
  • Molconvert
    • A NullPointerException appeared in the console instead of an error message when using molconvert to convert an image with skiperror parameter set without OSRA installed.
• Molecule Representation
  • Valence Check
    • Aromatic carbon cations having three ligands were handled incorrectly by the Valence check.
    • False positive valence error was on aromatic rings which have sulfur ligand that is part of a ring.
    • Removing explicit hydrogen atoms from LiH, CaH₂, SH₄, PH₅, PbH₂, PbH₄ did not keep the original hydrogen count.
    • Aromatic carbon cations having three ligands were handled incorrectly by the Valence check.
  • S-groups
    • Bracket positioning did not take the implicit hydrogen atoms into account.
    • If data were added as "relative", the cleaning or arrange methods did not take them along with the fragment/component/molecule.
    • The chirality of expanded S-group's atom changed, when there wasn't enough space in the canvas for the expanded S-group.
    • After expanding S-groups, atoms of the molecule could overlap.
    • Removal of explicit hydrogen being the only atom of an S-group was unsuccessful. New flag, SGROUP_H, has been introduced, for remove such hydrogens.
    • Exception was occurred when an abbreviated group was copied then pasted.
    • Method MulticenterTransform.transformMulticenters(Molecule mol) and MulticenterTransform.restoreMulticenters(Molecule mol) changed the number of implicit hydrogens of atoms.
  • R-groups
    • Fragmantation of an Rg-molecule resulted inconsistent molecules.
• Clean 2D
  • In case of selection, stereoinformation of the molecule during two dimensional cleaning was lost.
• Aromatization/dearomatization
  • General aromatization worked incorrectly in case of molecules with a bond connecting 2 rings but not being part of any ring. Solving this problem, deprecated method int[] getSSSRBondSet(), was removed and, instead, BitSet getSSSRBondSet() was introduced.
• Calculations
  • Protonation (pKa, reson.)
    • The predicted pKa of certain CH acids were extremly low.
  • Isomers (tautomer., reson.)
    • Tautomer generation was very slow on proteins.
    • Some deuterium atoms were removed during tautomer generation.
    • The structure of the generated tautomer was not cleaned if the input molecule contained abbreviated group(s).
  • Conformation
    • Exception was thrown during conformer generation if Visualize H bonds option was selected.
• Structure Checker
  • Clean Wedge fixer of Wedge Error checker had no effect in case of wedge bond between two chiral centers.
  • Atoms and bonds inside S-groups were not handled correctly by certain checkers.
• Elemental Analyzer
  • Elemental analyzer calculated wrong molecular formula for molecules, that contains bond to a centroid.

May 4th, 2012: Marvin 5.9.4

Bugfixes

• Calculations
  • Marvin Services did not return string result in some cases.
• Backend / Core
  • Import/Export
    • MolImporter.importMol(String) returned null when no molecule was recognized from the input document.
• Structure Checker
  • Custom checker implementation related fixes.

April 20th, 2012: Marvin 5.9.3

Bugfixes

• Molecule representations
  • S-groups
    • The relative position of multiple data S-groups on an object during clean was not kept.
• Import/Export
  • MOL, SDF, RXN, RDF
    • File format "molV3000" was recognized only when it was imported from a file having "mol" extension.
  • Load/Save handling in UI
    • Image export did not use the color scheme setting.

April 6th, 2012: Marvin 5.9.2

Bugfixes

• Aromatization/dearomatization
  • Aromatic ring count returned zero in those cases, where the aromatic ring contained charged carbon with two aromatic and one single bond.

March 22nd, 2012: Marvin 5.9.1

New features and improvements

• Import/Export
  • CXSMILES import/export handles every special atom available in the Periodic System dialog window in MarvinSketch.
  • DNA/RNA sequences are imported in their acidic form (i.e., instead of negative charge, an implicit hydrogen is added to the phosphoric acid ester group).
• Calculations
  • Accuracy of pKa calculation for amides has been improved.
  • Tautomerization of molecules containing nitroso group results in chemically more feasible isomers.
  • Speed of standard tautomer generation has been improved significantly. (On average about one hundred times faster.)

Bugfixes

• MarvinSketch GUI
  • Painting
    • Displaying proteins was very slow in some cases.
• Import/Export
  • CDX/CDXML
    • Coordinates of graphical objects were incorrectly imported from CDX files. Currently, imported "Anonymous Alternative Groups" are placed next to the imported molecule; "Anonymous Alternative Groups" with no bonds are imported as textboxes.
    • MRV attributes that contain line breaks were not exported correctly: \n, \r, \r\n were not escaped.
  • SKC
    • Atom and bond colors, font types, and bond thickness in SKC import and export were incorrect.
    • SKC import was failing on some structures containing built-in abbreviations.
  • PDB
    • Element type in some non-standard PDB file was not recognized properly.
  • VMN
    • Charge and implicit hydrogen information was not read from VMN files.
  • Document to Structure (d2s)
    • Reactions embedded in documents were not extracted.
    • When OSRA was installed, a failure of OSRA prevented the rest of the document to be processed.
  • Peptide
    • DNA sequence import resulted in RNA sequence representation because of ambiguous one letter abbreviations. Currently, abbreviations dA, dC, dG, and dT are used to import DNA, while A, C, G, and U are used to import RNA sequences.
    • A peptide sequence containing custom amino acids was only imported when the custom amino acid was the last one in the sequence.
• Aromatization/dearomatization
  • Aromatic ring count returned zero in cases where the aromatic ring contained negatively charged carbon with two aromatic and one single bond.
• Calculations
  • Protonation (pKa, etc.)
    • CH acid type structures might have caused errors during pKa calculation.
  • Isomers (tautomer., reson.)
    • Wiggly bonds were changed to single bonds during standard canonical tautomer generation.
    • Resonance structure calculation of nitrogen containing molecules has been reconsidered: 10 valence electrons around a nitrogen are only allowed for nitro groups.
• Backend / Core
  • Import/Export
    • NullPointerException was thrown by MoleculeImporter if "d2s:+cas" or "d2s:-cas" format string was specified.
  • Character encoding
    • Some special characters were converted incorrectly from UTF.

March 2nd, 2012: Marvin 5.9.0

New features and improvements

• MarvinSketch GUI
  • Drawing electron flow arrow in a reaction has been enabled.
• MarvinView GUI
  • Document to Structure on PDF documents can display the first structures without waiting to process the whole document.
• Import/Export
  • CML, MRV
    • New option to MRV and CML export, :CN, is introduced, where 0 < N ≤ 9 and N is the length of the decimals of the exported coordinates. For example, mrv:C5
  • Name to Structure (n2s)
    • Conversion of systematic names has been increased by about 5%, and increased accuracy of the generated structures.
    • Prefix "nor" has been implemented (e.g., 17-Hydroxy-19-norpregn-4-ene).
    • Name with stereo-markers "r" or "s" where such stereoconfiguration cannot be present are now interpreted as "R" or "S". This allows names that have been completely lowercased to be converted correctly.
  • Document to Structure (d2s)
    • Document to Structure supports the following common office document formats: doc, docx, ppt, pptx, xls, xls, odt in addition to pdf, xml, html and txt.
    • Format options have been added to d2s, to specify what input formats should be converted (for CAS Registry Number®, SMILES and InChi). Format option "insideTag=<tag>" to restrict conversions to the content of a specific tag (for instance in HTML).
    • The type of source text used for the conversion is included in generated structures. Possibly values: systematic, generic, common (for names), smiles, InChI,  CAS Registry Numbers® (for text formats), cdx, mrv, symyx (for embedded structures in office documents).
    • Processing speed has been increased: doubled on typical documents including chemical names, and tripled on documents with few chemical names.
• Molecule Representation
  • Molecule/atom/bond properties
    • ArrayIndexOutOfBoundsException was thrown in the Parity.generateDigraph method in special circumstances.
  • Valence Check
    • A new option is provided which enables to turn off the valence check of nitrogen, phosphorus, or boron atoms in those cases when they are in aromatic compounds.
• Calculations
  • Isomers (tautomer., reson.)
    • Tautomerization can take into account the possibility of ring closure when "All tautomers" function is selected.
  • NMR Predictor Beta
    • "Copy to Clipboard" and "Export Prediction to PDF" actions have been implemented.
• cxcalc
  • Advanced logging in cxcalc: logging errors and execution times is available.
• Structure Checker
  • Chiral flag error checker options have been improved.
  • Custom fixers use annotations replacing property files. Backward compatibility is ensured for both custom checkers and fixers.
  • Pattern based report file generation is available as a new option in structurecheck commandline.
• MarvinSpace
  • Default aromatization method in MarvinSpace is the Basic aromatization (the same as in MarvinSketch).

Bugfixes

• MarvinSketch GUI
  • MarvinView 3D window could not be opened from the sketcher if MarvinView 2D window had been opened before.
• Applet
  • Applet settings could influence the client side desktop application settings.
• Painting
  • The query properties were wrongly painted in some cases and covered the atom labels.
  • 3D rotate action activated automatically when joining a structure in hand to a bond of a 2D structure on the canvas.
  • Double bond was not painted in centered position in case of terminal bonds when the label of the connected atom was displayed or both of the atom labels were displayed.
  • Single arrow type brackets were not painted.
  • The orientation of explicit hydrogens was incorrect when explicit hydrogens were added to the (selected) upper methylene C atom of a cyclohexane.
• Import/Export
  • MOL, SDF, RXN, RDF
    • Handling of special characters (-, ", space) in extended MDL MOL format IO was wrong.
    • RDF file exported by Instant JChem was not imported correctly to ISIS/Base.
  • SMILES, SMARTS
    • In some rare cases, the unique SMILES of a molecule depended on the numbering of the atoms.
  • CML, MRV
    • Parity value in CML format was stored the opposite way as the CML standard defines it. Now the correct value is stored which leads to backward inconsistency with CML files generated by ChemAxon applications in previous versions, but correct values are read from standard CML files. To avoid running into similar problems in the future, now a version information is stored both in CML and MRV formats. This information contains a version number of the file format and the application version by which the file was generated. The parity value is changed to opposite in MRV format as well to be consistent with the CML format but it does not lead to backward inconsistency in this case: parity values stored in not versioned MRV files are converted to their opposite while parity values from versioned MRV files are not.
  • PDF
    • View settings were not applied in exported pdf file.
  • VMN
    • VNM format sometimes was recognized wrongly as mol2.
  • Image I/O
    • The molecule source was generated in unnecessary cases.
    • javax.imageio left temp files open if the ImageOutputStream was not closed properly.
  • Structure to Name (s2n)
    • The generated names for bridged and spiro ring systems were missing E/Z stereodescriptors for double bonds in large rings.
    • Some unconventional names were generated with suffixes such as amido, sulfonyl, carbonyl, ... mentioned as prefixes. For instance 2-[(2-chlorophenyl)amido]benzoate for [O-]C(=O)C1=C(NC(=O)C2=C(Cl)C=CC=C2)C=CC=C1. The generated names is now 2-(2-chlorobenzamido)benzoate.
  • Name to Structure (n2s)
    • Stereochemistry was not indicated in the displayed structure when cis or trans is used to specify the configuration of the two substituents of a ring system.
    • Cycloalkane substituents of fused ring systems were aromatized.
    • The stereochemistry of chiral atoms in subsitutents was sometimes inverted.
    • Name to Structure was blocked on some very long names with unbalanced parentheses.
  • Document to Structure (d2s)
    • Some types of smiles strings were not recognized by Document to Structure, in particular those with stereochemistry or acyclic structures with two-letter heteroatoms.
  • Peptide
    • Numbers or sign "-" in the name of custom aminoacids were not accepted during the import of peptides (exception was thrown).
• Molecule Representation
  • Molecule/atom/bond properties
    • ArrayIndexOutOfBoundsException was thrown in the Parity.generateDigraph method in special circumstances.
    • Molecule.implicitizeHydrogens() threw "java.lang.IndexOutOfBoundsException" after fragmentation if the molecule contained information in MDocument field.
  • Valence Check
    • Valence Check gave false valence error for aromatic oxygen having +1 charge.
• Structure Checker
  • Aromaticity Error checker options could not be set.

Known issue

• Structure Checker
  • R-group Reference Error Checker cannot find circular and selfreferring R-atoms and R-groups.

February 20th, 2012: Marvin 5.8.3

Bugfixes

• Stereochemistry
  • Bicyclostereo information was calculated on symmetric ligands.
• Structure Checker
  • External fixers could not be applied properly in MarvinSketch.

February 8th, 2012: Marvin 5.8.2

New features and improvements

• MarvinSketch GUI
  • Standalone mode of OLE can be set on the preferences dialog if the application is launched in administrator mode.
• Import/Export
  • Molconvert has a new option, :D, which is important if the molecule has parity information and has 0 dimension. By default during the export, a clean method is invoked on the structure and the generated coordinates and wedge information are exported into MRV format but NOT the parity information. However, using this option coordinates and wedge information are not generated but parity information is exported.
  • Mrv files can be validated by using the XSD schema containing the description of the mrv format.
  • Export options of cml and mrv formats can be used in molconverter application.

Bugfixes

• MarvinSketch GUI
  • The tooltip of template groups was displayed incorrectly in some cases.
• Import/Export
  • Starting the OSRA utility failed on Unix and Macintosh platforms.

January 30th, 2012: Marvin 5.8.1

Bugfixes

• MarvinSketch GUI
  • Dialogs
    • Subscripts and superscripts (\s, \S, and \n) were not enabled in Group names in version 5.7.x and 5.8.0.
• Import/Export
  • MOL, SDF, RXN, RDF
    • The line break in the Sgroup Attachment Point information section of the Extended MOLFile (MOL V3000) format was wrongly inserted in case of longer peptide sequences containing Cysteine.
  • CML, MRV
    • From version 5.8.1, molecules having parity information are exported in 2D form instead of 0D form in order to avoid incorrect parity representation.
• Molecule Representation
  • Valence Check
    • The aromatic nitrogen handling in case of pyridine-oxide was incorrect.
    • In release 5.8, all amino acids of an amino acid chain were detected to have valence error if it was imported from the Edit > Source menu of MarvinSketch.
  • S-Groups
    • Hydrogens attaching to sgroups were not treated as special ones and from version 5.8.1, their removal is optional.
• Data Transfer
  • OLE
    • Symyx content conversion (by redirecting) crashed Marvin OLE.
• Calculations
  • The hydrogen count was incorrect in case of position variation and metallocene-like structures.
• Structure Checker
  • "neutralize" fixer did not work in structurcheck command line application; "null" output was generated.

January 11th, 2012: Marvin 5.8.0

New features and improvements

• MarvinSketch GUI
  • Group types on "group creation" dialog can be configured.
  • The icon of manual atom mapping has been changed.
  • A new radical electron setting and the corresponding toolbar icon group has been introduced, solely for educational purposes: Up to four radical electrons can be defined for an atom, and it is arranged evenly in the empty space around the atom label.
  • Recent file list length has been increased up to 50. (The default is 25.)
• MarvinView GUI
  • Atom mark and atom highlight display can be enabled/disabled.
• Import/Export
  • Structure to Name (s2n)
    • New name format option: "source" has been introduced to print the names present in the source molecule data. For instance, molconvert name:source input.sdf.
  • Name to Structure (n2s)
    • n2s handles stereochemistry of cyclic monosaccharides.
    • Extended support for common names: n2s can convert 123 thousand common names – including synonyms – corresponding to 34 thousand structures instead of the previous 63 and 28 thousand, respectively.
  • Document to Structure (d2s)
    • Automatic text OCR (optical character recognition) has been added to support document to structure conversion of scanned (non searchable) PDF documents.
  • MRV
    • The information on the selected atoms and bonds can be stored in MRV format.
    • MRV format has been changed: there is no indentation, there are line-breaks only after the header and after the documents. The original format (including line-breaks and indentation) can be achieved using the -P option; this previous format is displayed – for easier reading – in the Edit > Source window in Marvin graphical applications.
  • SMARTS
    • ChemAxon Extended SMARTS represents R-group (Markush) structures.
  • CML
    • CML bondStereo implementation has been completed with atom references.
    • CML format has been changed: there is no indentation, there are line-breaks only after the molecules and after the header. The original format (including line-breaks and indentation) can be achieved using the -P option; this previous format is displayed – for easier reading – in the Edit > Source window in Marvin graphical applications. 
• Calculator Plugins
  • New integrated component: NMR Predictor Beta has been implemented.
  • "Consider tautomerization" option has been renamed to "Consider tautomerization/resonance" in logP and logD calculator plugins.
  • "Tools" menu content has been moved to "Calculations" menu.
• Data transfer
  • Native PDF format as the default image pasteboard format is used on MAC systems. It allows the user to copy a structure (which was originally created by either Marvin or ChemDraw) from a Microsoft Office 2011 document and to paste it to Marvin.
  • More verbose logging from OLE .NET panel (catching managed bridge exceptions via COM) has been introduced.

Bugfixes

• MarvinView
  • Sometimes molecules were lost when switching from "Spreadsheet mode" (Table>Options>Table Type) to "Molecule matrix" mode.
  • When a zero length structure file was opened, the content of the previous file remained in the viewer until the first repainting.
  • Scrolling up and down increased the number of molecules and changed their orders.
• Painting
  • Until the first repaint, textbox was smaller than required, and the content was cropped to its size.
• Import/Export
  • Structure to Name (s2n)
    • Incorrect name was generated for chiral allenes, for instance: (2M)-1,3-dichloropropa-1,2-diene, the correct is 1M. (The locant was previously in the middle of the cumulated double bond system, but is now at the beginning of it, as prescribed by IUPAC.)
    • Fixed generation of names in the case where a radical marker "yl" was missing, for instance "...(4-methylbenzene)sulfonyl..." instead of the correct form "...(4-methylphenyl)sulfonyl..."
    • Name generation was sometimes failing on fused ring systems with a spiro connections or adjacent fusion bonds. Conversion rate of fused ring systems goes up from 99.83% to 99.95% on the NCI database set.
    • The numbering of fused ring systems was incorrect in about 1% of the cases both in s2n and n2s.
  • Name to Structure (n2s)
    • Automatic name format recognition failed for names containing unicode prime characters.
    • CAS Registrx Number® cache could get corrupted and created failures.
  • Document to Structure (d2s)
    • The total length (getEstimatedTotalCharacters) was not available to progress listeners during Document to Structure conversion of PDFs using the API.
  • SMILES
    • CXSMILES IO error due to non-escaped characters appeared.
    • The name imported from SMILES format was wrong in rare cases, when special characters (e.g., |) were in the fields part of the extended SMILES.
• Calculator Plugins
  • logP and pKa calculations threw error at heavy atom count 300.
  • Generic tautomer generation might have threw an error if the molecule contained Hydrogen isotopes.

January 25th, 2012: Marvin 5.7.2

No changes.

December 12th, 2011: Marvin 5.7.1

Bugfixes

• Molecule Painting
  • Valences higher than nine were wrongly displayed if the valence property visibility was turned off.
• Calculator Plugins
  • Some property calculations threw ArrayIndexOutOfBoundsException when the input molecule contained multiple fragments.
• Build/Installation
  • OLE defect occurred during side-by-side installations.

November 4th, 2011: Marvin 5.7.0

New features and improvements

• MarvinSketch GUI
  • New bond type: "Hashed bond" has been introduced.
  • "Coordinate" Bond Line Style – in the Edit>Preferences>Bonds menu – allows changing the type of coordinate bonds between the default ones (arrow for single atom and hashed for multicenter) and solid.
  • Selected structures can be aligned or distributed relative to each other horizontally or vertically. The Align&Distribute function aligns and distribute the objects at the same time.
  • New chain drawing tool: Curved chain tool. Instead of creating a straight chain it modifies the direction of the last bond of the chain based on the mouse movement. Curved chains or macrocycles can be created that way.
  • The chain drawing direction is mirrored based on the direction of the mouse movements.
  • Selection can be moved in greater units with SHIFT + arrow keys.
• Import/Export
  • Structure to Name
    • Traditional name for known class names (e.g., acylcholine) is generated.
  • Name to Structure
    • "Name to structure" converter supports more systematic names (6% to 50% measured on various sets of names extracted from patents). For instance, names representing esterification with locants (e.g., 1,4-di-tert-butyl piperazine-1,4-dicarboxylate).
    • Optional support for CAS Registry Numbers® in Document2Structure.
    • Faster loading of PDFs by Document to Structure (from 25% to 75% speedup in most cases). Names can be extracted from more types of PDFs.
  • CDX/CDXML
    • Hashed bond type has been implemented in Marvin. "Hashed to Down Wedge" conversion has been changed to "Hashed to Hashed" conversion.
• Clean 3D/optimization
  • Verbose mode has been added to Generate3D. Use option "[verbose]" to switch on; use "molconvert -H3D" for detailed help.
• Data transfer
  • Native pasteboard for Macintosh has been implemented. It solves general copy/paste issues, e.g., copy/paste between Marvin and other chemical sketcher programs (e.g., ChemDraw).
  • Marvin supports conversion of other Vendors (currently ISIS and Symys) embedded OLE objects to Marvin OLE.
• Structure Checker
  • New checkers are available:
    • R-atom Checker: detects R-atoms (all, disconnected, generic, linker, nested).
    • R-group Attachment Error Checker: detects attachment differences between R-atoms and R-group members. A new fixer corrects the attachment bond types and adds missing attachments in unambiguous cases.
    • R-group Reference Error Checker: detects missing R-atoms, missing R-groups, self or circular references of nested R-atoms.
  • Checker and fixer classes implemented by the user are loaded from given jar file.
• API
  • chemaxon.marvin.util.ColorGenerator class provides an easy way to generate the required number of different colors.
  • Several core functions are deprecated.
  • API support for running checkers and fixers multiple times automatically.

Bugfixes

• MarvinSketch
  • The Java beans and applet parameter for switching the valence property visibility OFF was missing.
• MarvinSketch GUI
  • Scrolling with mousewheel or arrow keys enlarged Marvin Sketch canvas.
  • Moving selection with arrow keys could not be undone.
  • Attachment points were not highlighted by green when they were selected.
  • Sugar templates: D-furanoses had S label on carbon 5.
  • Double click selection did not work when it pointed to an atom.
• MarvinView
  • MViewPane did not refresh when UserSettings changed.
• MarvinView printing
  • Several MarvinView display property was missing in MolPrinter
• Painting
  • Error highlight was partially visible and often disappeared on mouse move.
• Molecule Painting
  • Positive charge of hydrogen was not scaled properly in case of small magnification.
• Import/Export
  • Structure to Name
    • Incorrect names where generated when the parent structure has identical substituents orientated differently, for instance: 4-formamido-1H-pyrazole-3-carboxamide
  • Inchi Key
    • Inchi slowdown with inchikey call for 10000s of structures.
  • PDF
    • OSRA did not work in Marvin unless its library was set in the PATH.
  • SMILES/SMARTS
    • A molfile or sketch is carrying an 'rb*' flag on any atom(s) was translated incorrectly to SMARTS ('x' atomic primitive).
    • cxsmiles IO of Data sgroup was incorrect.
    • mol format from smarts which contained "[C,!N]" (representing "Carbon , not Nitrogen") was converted incorrectly.
• Molecule representation
  • Connecting an additional bond to an abbreviated group freezed Marvin Sketch.
• Stereochemistry
  • Allene parity lost by removing explicit hydrogens.
• Aromatization/dearomatization
  • Aromatization of an aromatized structure created new aromatic ring
• Elemental analysis
  • The Elemental Analyzer did not support Position-Variation bonds in formula calculation. Known issue: Dot-disconnected formula calculation is not working correctly in case of Position-Variation bonds.

December 13th, 2011: Marvin 5.6.0.5

No changes.

October 25th, 2011: Marvin 5.6.0.4

Bugfix

• Import/Export
  • Importing Molfile which starts with "BM" failed with OSRA related error message.
  • SD files started with "P3" was recognized as PPM file instead of SDF. This bug was a result of changes in Marvin version 5.5.

October 18th, 2011: Marvin 5.6.0.3

No changes.

October 5th, 2011: Marvin 5.6.0.2

Bugfix

• Import/Export
  • Sgroups handled implicit hydrogens incorrectly depending on file formats. The bug could prevent matching in case of duplicate search.

September 25th, 2011: Marvin 5.6.0.1

Bugfixes

• Import/Export
  • Data Sgroup was converted incorrectly to cxmiles.
  • Opening PDF files, NullPointerException occured in some cases.

August 31st, 2011: Marvin 5.6.0

New features and improvements

• MarvinSketch GUI
  • New mouse cursors have been introduced.
  • New structure templates have been added (Alpha D sugars, Beta D sugars, Deoxynucleosides, Flavonoids, Nucleobases, Nucleosides, Protoalkaloids, True Alkaloids, Vitamins, Functional Groups).
• MarvinView GUI
  • Atoms can be marked in Marvin View by hovering the cursor over it. This also works even if another atom has already been selected. A property change event is sent on every atom mark.
• Applet
  • New parameters have been introduced:
    • onError
    • alertError
• Import/Export
  • Str2Name
    • New option has been added to generate all common names for a structure, e.g.: molconvert "name:common,all" -s viagra.
    • Less brackets are generated in names in traditional mode. For instance, instead of "{1-[(tert-butoxy)carbonyl]-1H-indol-2-yl}boronic acid" the generated traditional name is now "1-(tert-butoxycarbonyl)indol-2-ylboronic acid".
  • Name2Str
    • MolImporter can now process a PDF file as input and convert the chemical names in the text into structures. Structure images are also converted if OSRA is installed on the computer.
    • Increased support for name to structure conversion (measured between 6% and 30% on certain datasets).
• Calculator Plugins
  • "Marvin Services" has been introduced: Web/local services client, which provides seamless integration of third-party calculations into Marvin Sketch, cxcalc, and via Chemical Terms into Instant JChem or JChem for Excel. Industrial standard solutions like SOAP with WSDL are supported, along with the more lightweight XML-RPC or JSON-RPC protocols. Java based calculations can be called without server, directly from the jar file.
  • A new type of fragmentation has been implemented where the fragments contained in the same S-group are not separated. Fragmentation methods now have fragmentation type as parameter. The three types of fragmentation are:
    • Basic: no S-groups are considered, fragments are separated even if they are in one S-group. Broken S-groups are not added to the fragments.
    • Keeping multicenters: multicenter S-groups are kept in one fragment, other types of S-groups that contain more than one fragment are not added to the fragments, those fragments are separated.
    • Keeping S-groups: all S-groups are kept, fragments in the same S-group are not separated.
    Previous fragmenting methods which did not indicate the type of fragmentation are deprecated; they do the same as before (keep multicenters), but now – correctly – without generating inconsistent molecules with broken S-groups. These methods will be removed in later releases.
• Markush enumeration
  • There is a significant speedup of sequential and random Markush enumerations. (Hundreds of times speedup for average patent Markush structures. Speedup depends on the complexity of Markush structures.)
• Structure Checker
  • New checkers are available:
    • Unbalanced Reaction Checker: reports if there is difference in the total number of atoms or atom types on the two sides of the reaction arrow.
    • Atom Query Property Checker: detects atoms having query properties. A new fixer can remove the identified query properties.
  • New feature: "3D checker" detected issues can be fixed by "Remove Z-Coordinate Fixer". It flattens molecules by setting the z-coordinates of atoms to zero.
  • Structure Checker command line application has greatly improved.
  • Improvements in substructure checker: multifragment molecule handling, implicit hydrogen handling, improved command line access. "Transform" fixer for substructure errors: modifies substructures.
• API
  • New function to get the enantiomer of a molecule has been implemented: chemaxon.calculations.stereo.Stereochemistry.getEnantiomer(MoleculeGraph m).
  • Applet API has been improved with validateMoleculeStr(String str) and validateMoleculeStr(String str, String format) methods.

Bugfixes

• MarvinSketch GUI
  • The double-click selection action did not work after rotating the view in 3D, and then moving/rotating the structure in 3D.
• MarvinView GUI
  • Scale factor was not updated on rescale in MarvinView.
• MarvinView printing
  When multiple structures were printed in PDF with molecule matrix rendering, structures with crossing bonds in the second or further cells were just partially drawn.
• Applet
  • Marvin Applet failed to load changes in a file if the same file url was loaded before and applet started from the legacy cache.
  • Legacy_lfecycle related initialization (parameter loading, event listening, etc.) was fixed in applets.
• Molecule Painting
  • The shadow painting of the sprout drawing feature removed the error highlight of Structure Checker.
  • Atom label was shifted in case of terminal double/aromatic bonds at the end of chains. Double bond was not painted in the centered position when there were no substituents on either sides.
• Import/Export
  • MOL and SDF files including pipe character in the first line were recognized as Chemaxon Extended SMILES.
  • MOLFiles including a caret symbol in the Alias or Sgroup label fields were displayed incorrectly (the caret symbol was not hidden).
  • MOL/SDF files starting with "BM" characters in the first line were recognized as BMP file.
• SMILES/SMARTS
  • ArrayIndexOutOfBoundsException did not work in case of SmilesImport and Chirality calculation.
• Data transfer
  • Copy/paste of Marvin OLE objects from MSOffice applications back to Marvin did not work.
  • OLE image was not updated consistently after editing structure in MsOffice applications on 64 bit environment.
• 2D clean
  • Bad 2D cleaning in case of fused ring system.
• Aromatization/dearomatization
  • Aromata.isDaylightAromatic considered (O=[N+]1C=CC=C1) incorrectly.
• Calculator Plugin
  • logP calculation threw ArrayIndexOutOfBoundsException in some cases.
  • There were incorrect systematic names generated in case of sulfur-based groups with non-standard valence (for instance dihydroxy-lambda6-sulfanone).
  • FindAllRings failed with OutOfMemory error.
• Structure Checker
  StructureCheck command line application did not generate report field in output if checker options are set (e.g. "explicith:isotopic=true").
• Build/Installation
  Marvin Beans installer could not start with 64bit Java 1.6 under OS X 10.5.

July 8th, 2011: Marvin 5.5.1.0

New features and improvements

• Import/Export
  • molconvert: The -T option works with pipes using the fields of the first molecule.
  • Name to structure: Document to Structure also extracts smiles and InChI from the text.
  • CML: CML files now passes the validator at http://validator.xml-cml.org.

Bug fixes

• MarvinSketch
  • Pressing the Shift key when the mouse cursor was on an atom threw an ArrayIndexOutOfBoundsException.
• Chemical structure painting
  • Bond coloring was wrong in 2D if the colors of the neighboring atoms were different.
  • Quick rotation of the 3D view of 2D structures sometimes resulted in the disappearance of the structure.
  • The Java beans and applet parameters for switching the valence property visibility OFF was missing.
• Import/Export
  • MOL/SDF: The coordinate bonds in R-group definitions were wrongly exported.
  • Name to structure: Traditional naming export failed in applet.
  • Name to structure: Document to Structure failed to extract names from PDF documents .
• Calculator Plugins
  • pKa prediction threw ArrayIndexOutOfBoundsException in case of oximes.
  • Tautomerization threw ArrayIndexOutOfBoundsException in case of a few complex aromatic systems.

May 12th, 2011: Marvin 5.5.0.1

Bugfixes

• Calculator Plugins
  • Improved pKa prediction of the "OH" acid in oxim group.
• Structure Checker
  • SubstructureChecker did not work (requires JChem).

May 3th, 2011: Marvin 5.5

New features and improvements

• Marvin Sketch
  • Bold Tool is intended to be used for graphical presentations of molecules. Activate the tool, click on a bond and it will be changed to bold. Bold Tool is located in the Bond Menu, Tools toolbar, and bond PopUp menu by default.
  • The explicit valence setting display (v#) can be switched off.
  • Ctrl + Mouse Wheel zooms in and out on the canvas, while the geometric center of the zoom is defined by the current position of the mouse pointer.
  • To scroll the canvas you can use the mouse wheel or the arrow keys on the keyboard.
  • If there is a selection on the canvas, you can either move the selected object using the arrow keys or move the canvas with Ctrl + Arrow Keys.
  • MarvinSketch canvas is centered to the scaffold after opening R-Group molecules.
  • Atom List and Atom Not List can be entered by simple typing (without opening the Periodic Table).
  • Symbols can be inserted into textboxes. An Insert Symbol dialog with recent symbol list is accessible from the Textbox toolbar.
  • Error messages, warnings, warning details, and error stack trace can be copied to the clipboard.
  • Version and Copyright info can be found in Marvin splash screen.
• Marvin View
  • Printing the molecule matrix view of a multirecord file containing data fields has been improved:
    • Instead of cropping the content of the data fields when the cell is too narrow, they are wrapped into multi-line texts automatically.
    • A minimal size is provided for the molecule structure, so it is visible even if the data fields want to occupy more space than the cell size.
  • The explicit valence setting display (v#) can be switched off.
  • Molecule matrix view is scrollable with mouse wheel.
  • R-groups are visible in MarvinView by default.
• Marvin Space
  • Visualization of aromatic rings and triple bonds have been improved.
• Compatibility
  • Minimum Java requirement of Marvin is 1.6.
• Data Transfer
  • If a selection is made on the structure in the MarvinSketch window that has been opened from the MView pane, the closing of the MarvinSketch window (or clicking on the transfer button) transfers the selection back to the MView pane.
• Chemical structure painting
  • Drawing 2D projected views of 3D aromatic rings.
    • Aromatic rings have ellipses in 3D view as well.
    • Bold bonds and Aromatic Up bonds can be displayed.
    • The display quality of the junctions of Bold and Up bonds with other bonds has been improved.
  • The electron flow arrow display has been improved: Radicals, lone pairs, and negative charges are considered now. If the source is an atom, the electron flow automatically starts from the lone pair, the radical or the charge when they are displayed.
  • The automatic attachment point placement in R-group lists has been improved.
• Electron flow arrow
  • Electron flow arrows are redesigned. It is now separated to logic and display part.
• Import/Export
  • Image Export:
    • JPG, SVG and PNG formats contain the molecule source, so when opening or pasting these images, the molecule source is used (instead of trying to convert the image using OSRA).
    • PNG image color-depth can be specified as bitrate: 1-, 2-, 4-, 8-, 24- and 32-bit PNG image can be created.
  • Syn/Anti and Endo/Exo stereoisomer information is exported into ChemAxonExtended SMILES and SMARTS format.
  • Data fields are exported into SMILES format.
  • Improved SMART representation of generic query atoms (Q, QH, X, XH, etc.).
  • IUPAC Name
    • Major rewrite of the name to structure converter. Higher precision (around 50% improvement) and support for additional names.
    • Import of sulfide has been improved in Name To Structure.
    • Dictionary format improvement in IUPAC naming.
    • Name To Structure supports Alpha and Beta sign in names.
    • Automatic format recognition for CAS Registry Numbers®.
  • IUPAC InChI
    • Inchi converter now uses the IUPAC software API via the jni-inchi instead of the executable. Now it can handle stereochemistry information in 0D.
    • Marvin now uses inchi 1.03.
    • The conversion is much faster now.
    • InChI export does not clean in 0d any more.
• 2D clean / aromatization
  • Keep stereo information at aromatization.
  • Query aromatization considers single/aromatic and double/aromatic.
  • Converting to aromatic form keeps the Bold property of the bond.
• Stereochemistry
  • Syn/Anti and Endo/Exo stereoisomers are recognized.
  • Proper chirality detection in case of topographical differences.
  • Define chirality for adamantane structures.
  • New standardizer action: add implicit parities of bridged systems.
  • NEMA features: atrop isomers, allenes.
• Structure Checker
  • New Checkers:
  • SubstructureChecker detects user defined substructures (requires JChem);
  • RacemateChecker detects tetrahedral stereo centers without specific stereochemistry defined.
  • Improvements:
  • AromaticityErrorChecker searches for aromatic systems that can't be dearomatized or rearomatizing with the given method does not reproduce the initial molecule.
  • Tooltip improvements.
  • Checker status bar indicator can display warning and error icon as well.
  • Rename of specific checkers is supported (affects SubstructureChecker).
• Calculator Plugins
  • Molecular volume calculator plugin has been introduced.
  • Generic tautomer generation ignores all options except "Protect all tetrahedral stereo centers".
  • Preserve exocyclic groups in BMF.
• Chemical Terms
  • Improving initialization speed of Chemical Terms Editor.
  • Enhanced integration of BMF in Chemical Terms.
  • New Chemical Terms function: markushLibrarySize(), markushLibrarySizeAsString(), markushLibraryMagnitude(), matchFirst(), booleanToNumber().
• Automapping
  • Integrate new MCES algorithm into AutoMapper.
• API
  • Implementation of MoleculeGraph.getAtomCount(int atomicNumber). It returns number of atoms in the molecule with the given atomic number.
  • Let user to insert new action into MarvinSketch popup menu.

Bugfixes

• Marvin Sketch
  • A bond to the second attachment point of an Sgroup could not be drawn if it was created by changing a terminal atom of a previously drawn structure.
  • The BzOM group has to be renamed to PhOMe, and its left name should be MeOPh.
  • Selecting every atom and using the "Ungroup" function from the menu caused ArrayInedOutOfBoundsException.
  • Edit source dialog could not be opened after importing SKC.
  • After setting of "Save/Load-default location - Startup directory" in Preferences dialog, Marvin did not navigate to the Startup directory by saving or loading a molecule.
  • The canvas was not scrollable with mouse wheel.
  • When Ala was ungrouped in the R1 definition, the attachment point (which was both an Sgroup and an Rgroup attachment) disappeared.
  • When a reagent was placed over the reaction arrow in abbreviated form, Marvin Sketch became unresponsive.
  • When drawing electron flows to multicenter, Marvin stopped doing anything.
  • Electron flows could cross double and triple bonds when starting from bond.
  • The exception frame was not scrollable when the message was too long.
  • Atoms from periodic table modified bond length when the atom in hand was attached to the end of a bond on the canvas.
  • The aromatization/dearomatization did not run during Directed Merge, therefore if the double bonds were not located at the appropriate positions in case of two aromatizable rings, 5-valence carbon atoms were created.
• Marvin View
  • Scrolling and cleaning 2D in the same time caused CuncurrentModificationException.
  • After clean 2D, Marvin View cells in molecule matrix view were not repainted automatically. You had to click on each cell to refresh them.
• OLE support
  • StandAlone mode could not be set for all users.
• Molecule representation
  • QueryBond cloning did not preserve bond type.
  • Exception related to expanding Sgroups in RgMolecules
  • SuperatomSgroup.attachAtoms was not set automatically during SuperatomSgroup creation.
• Chemical Structure Painting
  • 3D rotation of fragments started to wrong direction.
  • Valence count displayed ugly: on the top of the atom label.
  • The COCl group was not connected through the Carbon label when it was on the left side of a structure.
• Import/Export
  • Smiles did not set arrow for reaction because of it RXNMolecule threw NullPointerException.
  • Molecule.toFormat("smarts") changed the state of Molecule: getAtomCount(), getBondCount() and the unifiedStructure properties of query were null value.
  • Certain MRV files could not be imported where tag included a line break.
  • R-group queries could not be exported to SMARTS as recursive SMARTS in 5.4.x.
  • ArrayIndexOutOfBoundsException was written on System.out by parsing SMILES.
  • IUPAC Name
    • By parsing 2-(o-Toluidino)ethanol IUPAC name, the 'o' was ignored.
    • IUPAC name import did not support correctly poly spiro in the simple case (numbers, not structures).
    • Those IUPAC name could not be parsed from HTML where an &nbsp; preceded the name.
    • By importing certain IUPAC names, the stereo center missed on the created molecule.
    • All IUPAC names with "hydrazon" were wrongly imported.
    • dicarbonimidic diamide and imidodicarbonimidic diamide were not supported.
    • Generate correct name for hydrides of elements in group 1 to 12, for instance "sodium hydride".
  • IUPAC InChi
    • There was a memory leak in the native call, now in the jni-inchi interface it is resolved.
    • InChI failed to export stereochemistry on 0D molecules.
  • Certain CDX files that included graphical arrows and dashed rectangles could not import properly.
• 2D cleaning / Aromatization
  • General aromatization put single-or-aromatic and double-or-aromatic bonds when it shouldn't.
  • Molecule.partialClean(int, int[], String) removed stereo info from molecule when the input was in mrv format.
  • At first attempt, the aromatization did not work after creating a ring with bold double bonds in it.
  • The 2D clean of a molecule with position variation bond caused an error dialog: "Error in module Clean2D".
  • Five membered rings were not converted to aromatic form with single_or_aromatic and double_or_aromatic bonds respectively.
• StereoChemistry
  • Superfluous wedges appeared by importing of certain SMILES.
  • The Phosphorus in phosphines was not recognized as stereo center.
• 3D alignment
  • MCS based alignment bug: bad similarity score was returned for CCC1CCCCC1.CCCCCCC1CCCCC1.
• Calculator Plugins
  • Elemental Analyser result window did not display text fields in single fragment mode.
  • In Naming Plugin result window, the IUPAC name disappeared after scroll down and scroll up by those compounds whose name included special characters (like lambda).
• Chemical Terms
  • When a chem terms column was added in IJC that generated InChI, it occurred a lots of errors and JVM could crash.
• API
  • Molecule.getBondTable() threw exception when a bond with atom index higher than atom count was get.
  • MoleculeGraph.getFormula getMass and getExactMass were not thread-safe.
  • When a new bond with a new end-atom was added to a SelectionMolecule, it was not cloned properly.
  • Serialization threw an EOFException when it was used from MolImporter/MolExporter.

April 8th, 2011: Marvin 5.4.1.2

• Marvin Sketch
  • In the Save As Image dialog, there was a typo in the file type filter list.
  • ArrayIndexOutOfBoundException in template parameter handling.

February 16th, 2011: Marvin 5.4.1.1

Bugfix

• MarvinSketch
  • Fix generic template toolbar removal ability throught ttmpls parameter. Avoid warnings in template related code.

February 9th, 2011: Marvin 5.4.1

New features and improvements

• MarvinSketch
  • Public database search in chemicalize.com.
  • Possibility to change ligand order in MarvinSketch.
• Molecule Painting
  • Fog-effect can be controlled in various ways:
    • There is a slider on the Display tab of the Preferences dialog in the Sketch/View GUI to set the strength of the fog-effect and a checkbox to switch off the automatic fog-effect.
    • Applet and beans parameters are introduced: fogFactor, automaticFogEnabled.
• Molecule Representation
  • Attaching to a group attachment point does not automatically ungroup the Sgroup anymore.
  • Determination of S-group content: multiple and generic S-groups have to contain the whole subgraph between the bonds crossing the brackets.
  • Update of S-group content if bracket positions change: either brackets or the structure is moved.
  • S-group embedding and overlap are checked at molecule consistency checks.
• Import/Export
  • SMARTS import supports aliphatic carbons with double bond.
  • SMILES import/export supports allenes.
  • IUPAC name
    • Generate traditional name for fragments inside a larger compound (e.g. "dextromethorphan hydrobromide").
    • Support for retrieval of CAS Registry Numbers® from publicly available sources hosted by the U.S. National Institutes of Health (“NIH”) and the Wikimedia Foundation.
    • Improved OCR error correction in DocumentExtractor (missing commas, misrecognized parenthesis type, extra spaces, ...).
    • Document Extractor on PDF documents now gives the page number of hits.
    • Improved support for common names in structure-to-name and name-to-structure. The general support for name import increased by around 5% for common and 10% for systematic names. Conversion speed is increased by about 20%.
• Installers
  • JChem and Marvin Beans installers for Windows also extract shell script for cygwin.
• Calculator Plugins
  • Preserve exocycyclic groups in Bemis-Murcko frameworks.
• Markush Enumeration
  • Halogen can have more than one connection during enumeration.
  • Aromatic bonds are considered during calculating the number of double bonds for homology property checking.
• API
  • Lasso selection mode can be set to be the default in MSketchPane.
  • A new function, isChiral has been added to TopologyAnalyzer.
  • New Chmical Terms functions: isQuery(), fieldAsString().

Bugfixes

• MarvinSketch
  • Name box was not updated after group creation because creating a group did not increase graph invariant change count.
  • MarvinSketch application did not understand "-{name}" command line parameter.
  • When the Structure > Find structure online menu was invoked under Linux, the default browser could not be detected to display result.
• Applet
  • The loading of the isotopes.data file from the java cache failed if its uncompressed version was stored in the cache (i.e. if the uncompression was done automatically by the webserver, and not by Marvin).
• Molecule Painting
  • Graphical objects were not displayed in the Geometry Plugin result window.
  • On the electron-flow arrow, the blue box for highlighting was missed.
  • Ligand order was not displayed on the scaffold if the definitions were deleted, even if the "Always" display option was set for "Ligand Orders" on the preferences dialog.
• Import/Export
  • Index of the multicenter atom became corrupt after exporting into MDL Mol format if it was connected to an R-group.
  • Arrow stuck to rectangles was damaged during Mrv import/export.
  • Import of 1-letter peptide failed at a single Histidine.
  • Implicit hydrogens were missing by importing from skc.
  • Null property value of MolAtom was not exported/imported in Mrv format.
  • By importing certain SMARTS, wrong bond type was determined instead of single or aromatic bond.
  • Certain brackets imported from Cdx files drawn in ChemDraw were displayed in the wrong direction.
  • SMARTS export: 1-atom single bond neighbor of an aromatic ring was exported as single bond instead of single/aromatic.
  • Exporting queries with link node and R-groups in SMARTS format were incorrect.
  • The H atom handling was ambiguous in SMARTS expressions.
  • Mol file comment field import failed.
  • Importing of certain SMILES was wrong.
• Clean 2D
  • If the template contains a chain part which can be located in the target as a part of a ring (or ring system) we should ignore that part of the template.
• Molecule Representation
  • The Fine with Hydrogenize option of Clean3D did not ungroup S-groups automatically.
  • Molecule.contractSgroups() messed up the molecule coordinates.
• Stereochemistry
  • Explicit hydrogens were not properly taken into account in Cis/Trans stereochemistry calculation.
• Calculator Plugins
  • Tautomer generator threw ArrayIndexOutOfBoundsException in some cases.
• Markush Enumeration
  • Homology enumeration produced inconsistent molecules for some VMN input.
• Structure Checker
  • Incorrect charge count after applying CovalentCounterion fixer.
  • The log output format of StructureChecker command line differed from output format of the wizard.
  • ChiralFlagErrorChecker did not handle chirality correctly. Instead of calculating chirality from parity data, it used an implementation based on the isChiral method of TopologyAnalyser.

December 17th, 2010: Marvin 5.4.0.1

Bugfixes

• MarvinSketch
  • Highlighting of electron flow arrows was wrong when the base or end point was a bond.
• Applet
  • Serialized menu configuration did not work.
• Import/Export
  • MDL MOL and SDF
    • The index of the multicenter atom was incorrectly created during MDL MOLFile export in case of structures where the R-group was connected to the multicenter atom (position variation bonds).
  • SKC
    • Implicit hydrogens were missing from the atoms after the import or paste of structures in ISIS/Symyx Sketch file format (SKC file format).
  • CDX
    • CDX files including rotated graphical objects exported from old versions of ChemDraw could not be imported.
• Calculator Plugins
  • Tautomer calculation
    • Generic tautomer was not unique enough in some cases. Due to the fix, the generic tautomer is provided aromatic form.
    • Canoncical tautomer calculation has been improved due to the fix of dearomatization.
• cxcalc
  • Certain structures with explicit hydrogens connected with wedge bond gave an exception during generic tautomerization.
  • Volume calculation was missing from cxcalc.
• Structure Checker
  • Structure Checker threw NullPointerException instead of ignoring incorrect configuration file.
• API
  • chemaxon.struc.Molecule.implicitizeHydrogens(MolAtom.ALL_H) did not remove hydrogens.

November 25th, 2010: Marvin 5.4.0

New features and improvements

• MarvinSketch GUI
  • Multiple, ordered R-group attachment points in Markush structures. It is possible to define bond types on the ligands, and change the order of the attachment points as well.
  • PubChem substructure search from Marvin.
  • New 3D transformation options: rotate around various axes, group rotation, horizontal/vertical/group Flip, horizontal/vertical/canvas/group Mirror, and Inversion.
  • 3D Plane option: upon three selected atoms it rotates the structure to have the selected atoms in the drawing plane.
  • Directed Merge option: It merges a fragment (Substituent) to another (Template or Scaffold) based on atom pairs assigned by the Atom Assigner tool.
  • New Substituent option: Opens a separate MarvinSketch window to sketch a new fragment, and transfers it back to the main window.
  • Context based, configurable attached data editing
  • Delete actions have been uniformized, and the Delete tool work differently on terminal atoms when holding the Alt key. The default behavior of delete can be configured on the Preferences dialog.
  • Atom editing procedures have been improved, so the "feature" that automatically deleted a bond when an atom was dragged over it has been removed.
• Applet
  • New parameters have been introduced:
    • disablePluginsLookup
    • defaultDatatransferPolicy
    • isMyTemplatesEnabled
• Molecule Painting
  • Aromatic and double bond display improvements: now it follows the IUPAC recommendation in each case.
  • Ellipses are drawn in asymmetric aromatic rings in 2D.
  • The R-group attachment point display has been changed to follow the IUPAC recommendation. The order of the attachment points is visualized both at the Scaffold and the substituents.
  • R-logic can optionally be displayed on the sketch.
  • The degree of rotation is displayed during rotations having specified axis.
• Molecule Representation
  • S-groups are validated at creation based on the selected (sub)structure: only the chemically meaningful types can be created.The option can be switched off on the Preferences dialog.
  • R-group attachment point representation has been redesigned.
• Import/Export
  • IUPAC Naming
    • Major upgrade of Name To Structure. Reduces wrong conversions by 50% to 70%, and supports about 10% more names.
    • Significant speedup (around 100%) in structure to name generation.
    • Local relative stereo (R* and S*) is supported in name to structure.
    • Pseudo-asymmetric stereo descriptors (r) and (s) are generated.
    • The generated names for salts have been improved.
    • Name generation detects new cases of very complex structures and aborts quickly instead of timing out or locking. All known cases are handled well now.
  • MRV
    • The S-group and the R-group storage has been changed.
  • MOL/SDF
    • The S-group and the R-group storage has been separated: the APO tag stores only the R-group attachment points, and the SAP tag is used for storing the S-group attachment points. The new storage format is not imported properly by older versions of Marvin.
    • A new option, called "skipAtomValues" has been introduced in MolImporter and molconvert to avoid importing lines containing atom values.
    • SDFiles (incorrectly) having an empty line between the CTAB block and the properties block are accepted at import.
  • SMILES/SMARTS
    • SMARTS representation of X.
  • CDX/CDXML
    • CDX/CDXML import has been improved: TLC plates, table objects and r-logic are imported now.
• Datatransfer
  • Configurable clipboard handling in applets: the file formats available for copy and paste can be customized.
  • Marvin OLE object: 64-bit support for windows natives (OLE, EMF generator).
  • Traditional name has been added to the Copy as dialog formats.
• Stereochemistry
  • Graph invariant calculation uses local parity instead of local chirality.
  • Improved stereochemistry (r, s, M, P descriptors).
• Aromatization
  • New aromatization option for ambiguous 5-membered rings.
  • Query aromatization changes single bonds to single_or_aromatic, double bonds to double_or_aromatic in a ring which contains _or_aromatic bond.
• Calculator Plugins
  • logP and logD plugins support multiple logP training parameter files.
  • pKa and logD plugins support multiple pKa correction library files.
  • Fused output option on Markush enumerator GUI
  • Industry standard MMFF94 forcefield options in Conformer Generator and 3D Molecular Properties.
  • Atrop isomers are detected during conformer generation.
  • Canonic tauotomer generation was improved.
  • Performance and accuracy improvements of 3D molecular alignment.
  • Structure Checker functions in Chemical Terms.
  • Chemical Terms uses a new file format for storing predefined molecules. The new format contains also the R-group representation of the molecules, which can be used for visualization.
  • Training and Prediction
    • A new plugin called Predictor enables to train and run the users' own molecular property prediction. 
    • A command line trainer tool has been introduced, called cxtrain.
    • LogP and General (Atomic Contribution Based) Training and Prediction has been refactored (performance improvement and structural changes).
• Structure Checker
  • New checkers are available:
    • Empty Structure Checker
    • Explicit Lone Pair Checker
    • Star Atom Checker
    • Metallocene Checker
    • Covalent Counterion Checker
    • OCR Error Checker
    • Ring Strain Error Checker
  • A command line tool called structurecheck is available for checking files in batch mode.
  • Application based structure checker configuration support has been added to the API. It is also available in the applications that are integrating Structure Checker.
  • Several improvements have been made in the Overlapping Atoms and the Overlapping Bonds checkers: The accuracy of the overlap detection has been improved to avoid fault warnings.
• Licenses
  • All Topology Analysis functions require a valid license.
• Installer
  • Full 64 bit support: 64-bit installers are available for all platforms.
  • Registration of file associations can be turned-off with one checkox.

Bugfixes

• MarvinSketch GUI
  • Delete action sometimes had undesired effect from atom context menu.
  • On Mac OS X, Drag and Drop of names to the canvas did not work.
• Marvin Space GUI
  • The screen flickered and an empty canvas was displayed sometimes.
  • There was a frame closing problem when MarvinSpace was launched for MarvinSketch.
  • The pull-down menus were not displayed properly.
• Applet
  • On Mac OS X, in Safari, the opening of the Periodic Table (or other modal) dialog caused freezing the MarvinSketch applet.
• Molecule Painting
  • Charges disappeared on carbon atoms if carbon labels were hidden and lone pair painting was turned off.
  • Certain MEflow object disappeared when display properties were changed.
  • The second data attached to the same selection using absolute placement overlapped with the first one.
• Molecule Representation
  • RgMolecule.addRgroup(int rl, Molecule m) did not change the grinvCC, therefore the graph union was not updated and had not contained the newly added Rgroup.
  • The bond table representation of the MoleculeGraph has been changed to avoid OutOfMemoryError.
  • There were a few S-groups related bugs: in creating a reaction from a molecule with S-groups, in creating S-groups in reactions, and in merge/unmerge of reaction components containing S-groups.
  • When deleting multiple groups, n-1 occurrences of its content remained.
• Import/Export
  • 0D molfiles can not contain stereo information, therefore Marvin applications apply a 2D clean to 0D molfiles in the future.
  • SMILES/SMARTS
    • Certain SMARTS was imported wrongly.
    • Explicit bond appeared where it was not needed in SMARTS.
• Datatransfer
  • InChi with AuxInfo failed to paste in into Marvin.
• Stereochemistry
  • If only one explicit Hydrogen is attached to one side of the double bond, then it incorrectly got E/Z stereo information.
  • The calculation of chirality/parity for phosphanes was incorrect in some cases.
  • Remove explicit hydrogen removing some stereochemistry.
• Clean 2D
  • Cleaning of ferrocenes created some extremely long bonds.
• Calculator Plugins
  • Moieties (Repeating Units without crossing bonds) were ignored in Markush enumeration.
  • HBDAPlugin threw ClassCastException in some cases.
  • Some bugs were fixed in the tautomer generation.