Markush Editor History of Changes

Only major changes listed here, minor bugfixes, dependency updates, and smaller improvements are not included in the changelog.

Markush Editor 23.8

New Features and Improvements

Migrated Markush Editor to Java 17 from Java 11
The Markush Editor installer bundles Bellsoft Liberica OpenJDK 17
Auto Update doesn't work for this version ! A clean manual installation is required for 23.8. For the following updates Auto Update in Markush Editor will be available again.

Markush Editor 23.4

New Features and Improvements

Several UI related minor improvements are added - like menu button locations or icon appearance changes

Markush Editor 23.2

New Features and Improvements

The grey coverage indicator for position variation bonds will not appear in the exported document
A selection based bug is fixed that caused Markush Enumeration to show a Library size of 1 in Markush Editor

Markush Editor 22.22

New Features and Improvements

Compounds and salts containing counterions and/or solvents are now taken into consideration for the automatically generated Markush structure

Markush Editor 22.19

New Features and Improvements

Homology groups are easier to draw - they are accessible from the HG button on the left side of any editor screen

Markush Editor 22.18

New Features and Improvements

An updated automatic ordering of R-groups is available in the Markush Composer. During the creation of a new Markush structure R-groups are assigned numbers in the following order:
- 1 Ring segment R-groups
- 2 Linker R-groups
- 3 R-groups attached to rings (sequentially for each ring)
- 4 R-groups attached to acyclic atoms

Markush Editor 22.14

New Features and Improvements

New option in document export under Additional settings to chose the image resolution and size of individual exported structure elements (Markush Scaffold, Markush Fragments and Examples). The setting now allows to define the structural element size relative to each other - e.g. setting all three values to 100%, rings appearing as part of the scaffold, as part of an R-group or as part of an example will have the same size.

Markush Editor 22.11

New Features and Improvements

New option in document export under Additional settings to chose the Journal style for the exported structure images (several styles like ACS or Elsevier are supported).
New option in document export under Additional settings to chose the image resolution and size of individual exported structure elements (Markush Scaffold, Markush Fragments and Examples).

Bugfixes

Structure images are exported with correct image parameters - After editing exported structures they are returned with the correct coloring and image aspect ratio (Tested with Marvin, ChemDraw and BioviaDRaw).

Markush Editor 22.10

New Features and Improvements

New option in document export to chose the attachment point indicator symbol for R-groups.
Either wavy line (default) or star symbol can be chosen.

Markush Editor 22.2

New Features and Improvements

Changed the coloring behavior in the Markush tree: Now a new yellow color indicates that the scaffold or R-group is itself matching, but it uses non-matching (red) R-groups.

Markush Editor 22.1

New Features and Improvements

Composer improvement resulting in a more accurate handling of ring systems in the generated Markush, including heteroaromatic rings as well
Markush Editor now supports quick input of homology groups for entering fragment definitions when editing R-groups (by typing the abrreviation for the group in the opened editor window)
Both Chemaxon names and shortcuts defined in the Derwent Markush Reference Manual are recognized for these homology groups

Markush Editor 21.21

New Features and Improvements

New quick text input function for entering fragment definitions in the Markush tree (Reachable through the right click context menu)

Markush Editor 21.20

New Features and Improvements

New Create narrowed claim based on selection function available in validation view
Composer improvement for better handling of ring systems in R-groups in case of an automatically generated Markush
New updated look and feel of Markush Editor

Markush Editor 21.19

New Features and Improvements

Migrated Markush Editor to Java 11
Auto Update doesn't work for this version ! A clean manual installation is required for 21.19. For the following updates Auto Update in Markush Editor will be available again.

Markush Editor 21.17

New Features and Improvements

Added customizable example numbers to show user defined numbers pulled from the input exemplified data file
Added advanced customizable data export features allowing to show additional data (compound ID, assay data, preparation information etc.) present in the example structure file in the exported draft document either as part of the document body or as a comment

Markush Editor 21.16

New Features and Improvements

The automatically generated Markush now shows the Kekulé structures for aromatic rings both in the Editor application and in the exported draft document

Markush Editor 21.15

New Features and Improvements

Fixed exported claim draft language selection when Japanese is the default system language

Markush Editor 21.12

New Features and Improvements

Added automatic generalization of R-groups during the generation of the Markush structure (selectable option on the Compose Markush Structure Window)

Markush Editor 21.10

New Features and Improvements

Added option to select preference between IUPAC name/formula in the exported document for functional group names

Markush Editor 21.9

New Features and Improvements

Major Markush Editor layout changes
Improved freely resizable and reorganizable Validation view (moved from beow Markush tree to the right of it)
Added Example lists window for importing and managing multiple example structure sets for a single Markush
Loaded Example lists are now saved together with the Markush structures
Added Japanese Language support for document preview and export
Example structures can now be aligned to the scaffold from the context menu in Validation view
Nesting view and Preview can now be reached from Markush inspection views on the toolbar

Markush Editor 21.4

New Features and Improvements

Remove confusing attachment order indicators from R-groups in exported documents
Installer now works on MacOS Catalina

Markush Editor 21.2

New Features and Improvements

Claim checker for verrifying the consistency of claim hierarchy
Improved handling of heteroaromatic rings in composer
New replace fragments with more specific/more general feature

Markush Editor 20.19

New Features and Improvements

Basic support of claim hierarchy
Visual editor for custom fragment dictionary

Markush Editor 20.17

New Features and Improvements

Significant improvements in automatic scaffold detection (side changes handling)
Configurable fragment dictionary to overwrite the default fragment names in claim text generation

Markush Editor 20.13

New Features and Improvements

Export the exemplified structures list with structure images and IUPAC names to the generated document.

Markush Editor 20.9

New Features and Improvements

Markush to text export to DOCX format
Significant improvements in the quality of the generated claim draft

Bugfixes

Unnecessary hit coloring removed from exported structure images

Markush Editor 20.5

New Features and Improvements

Major platform update (NetBeans platform version 9.0)

Markush Editor 19.29

Bugfixes

Make Markush required additional license
In some cases, aromatic and non-aromatic fragments are mixed in hit coloring

Markush Editor 19.1

New Features and Improvements

Markush structure to text export in HTML format

Markush Editor 17.5

New Features and Improvements

Version number system change

Markush Editor 17.1.9

New Features and Improvements

Configurable Markush validation options.
Bond length checker removed from the default checker configuration.
Major platform update (Netbeans platform version 8.0)

Markush Editor 15.10.12

New Features and Improvements

Rename R-groups from the tree.

Markush Editor 15.9.28

New Features and Improvements

Save validation result during structure list export.

Markush Editor 15.9.21

New Features and Improvements

The number of matching structures in validation view.
Ignore stereo during Markush validation

Markush Editor 15.9.7

New Features and Improvements

New composer dialog.
Composer input file with non-separated molecules allowed.

Markush Editor 15.8.24

New Features and Improvements

Stereo ignored during Markush validation and Non-Hit coloring.

Markush Editor 15.6.22

New Features and Improvements

logP filter in the biased enumeration.
Save and reset enumeration preferences.
New more-readable estimated library size format.

Bugfixes

R-group aliases are not shown in the enumeration spreadsheet view.
Max. structure count applied before filtering resulting in fewer structures what is expected.

Markush Editor 15.6.15

New Features and Improvements

Markush validation against structure list, with built-in hit and non-hit visualization.
By using Markush Composer wizard validation structures automatically populated with the Composer's input structure list.
Hydrogen bond donors and acceptors filter in the biased enumeration.

Bugfixes

Incorrect fragment size in a case of link node and repeating unit fixed.
A strange look of enumeration panel in Mac and Linux fixed.

Markush Editor 15.6.1

New Features and Improvements

Biased enumeration (directed enumeration based on user-defined parameters).
Molecular weight filter in the biased enumeration.
Unified Mac and Linux installer.

Markush Editor 15.5.18

New Features and Improvements

R-group inline action in Markush tree nodes context menu

Markush Editor 15.5.4

New Features and Improvements

Better display for Composer results.
Improved MCS calculation for R-group nesting.

Markush Editor 15.4.20

New Features and Improvements

Composer capable of generating Markush structures with position variation bonds.
Support of R-groups for user defined scaffold.

Markush Editor 15.4.13

New Features and Improvements

Info dialog if composer creates more than one Markush structures.

Markush Editor 15.4.6

New Features and Improvements

Atom list and bond list support in Composer for user defined scaffold.

Markush Editor 15.3.30

New Features and Improvements

Improved scaffold recognition in Composer..

Markush Editor 15.3.23

New Features and Improvements

Set scaffold function in Markush Composer wizard.

Markush Editor 15.3.16

New Features and Improvements

Display R-group alias instead of R-group number if it exists.

Markush Editor 15.2.23

New Features and Improvements

Smaller, fragment selection handling improvements.

Markush Editor 15.2.16

New Features and Improvements

New selection, hit error and warning visualization in Markush Tree and Fragment view.
Improved undo and redo mechanism, capable of handling structure fixer actions.
Mac and Linux installer..

Markush Editor 15.2.9

New Features and Improvements

A new selection hit error and warning visualization in Markush Tree and Fragment view.
Improved undo and redo mechanism, capable of handling structure fixer actions.

Markush Editor 15.2.2

New Features and Improvements

Support common hotkeys.
Add R-group attachments to fragments automatically in trivial cases.
Make structure fix actions undoable.

Bugfixes

Enumeration exception in a case of undefined R-groups.

Markush Editor 15.1.26

New Features and Improvements

Automatic version update.
Reorganized preview and nesting view components.

Markush Editor 15.1.12

New Features and Improvements

Spreadsheet view for enumeration results with R-group fragments.
Duplicates and infeasible rings filter in the enumeration.
Enumeration results in export.

Markush Editor 14.12.8

New Features and Improvements

If a Markush structure inserted into the scaffold editor it automatically split to scaffold and fragments.

Markush Editor 14.11.24

Bugfixes

Display only explicit R/S labels.
Markush export error in some cases.
Wrong tab display names for files containing multiple structures.

Markush Editor 14.11.17

Bugfixes

Checker panel "invalid checker" warning fixed.

Markush Editor 14.11.10

Bugfixes

In the Markush tree view, scrolling to the selected structure checker result did not work properly.
Fixing only a selected structure checker result did not work properly in some cases.
Enumeration count of hHomologies modified to one regardless to the type of the homology.

Markush Editor 14.10.27

New Features and Improvements

R-group bridging support.

Markush Editor 14.10.6

New Features and Improvements

Dynamic enumeration count calculation.

Markush Editor 14.9.29

New Features and Improvements

Full view removed.
New action icons added.

Markush Editor 14.9.22

New Features and Improvements

Composer standardizer action for removing awkward/superfluous R-groups.
Composer scaffold calculation optimization.

Bugfixes

Minor enumeration related bugfixes.

Markush Editor 14.9.8

New Features and Improvements

Support for open multiple files at once.
Improved re-ordering of fragments and R-groups.

Markush Editor 14.8.25

New Features and Improvements

List atom supports in the composer.
Migrated to Java 8.

Bugfixes

Composer-related minor bugfixes.

Markush Editor 14.8.18

New Features and Improvements

Unnecessary fragment and scaffold cleaning removed.

Markush Editor 14.8.4

New Features and Improvements

MCS optimization for better scaffold recognition.

Markush Editor 14.7.21

Bugfixes

New empty file saving exception fixed.

Markush Editor 14.7.14

New Features and Improvements

"Don't show this message again" option for license warning in viewer mode.

Bugfixes

Fewer Composer warnings.
Memory leak related to closed structures fixed.

Markush Editor 14.7.7

New Features and Improvements

Markush Composer Wizard for generating Markush structures automatically from the list of compounds.
Improved fragment visualization.
Fragments' borders removed.
Random enumeration when only scaffold selected.
The opening sketch window by double clicking.
Improved product info dialog.