Changes

• Improved error message in case of MOL to HELM conversion of oligonucleotides

Bugfixes

• Undo needed to be hit 2 times after expanding or collapsing objects on canvas

Improvements

• Shortcut 'ctrl+alt/option+v' to expand/collapse selected components/sequences, domains and monomers

• Pressing 'ctrl' enables immediate bond drawing

Changes

• In the Secondary View, Sequence View is selected by default

Bugfixes

• Setting molecule using BioEddie API to an invalid HELM representation caused BioEddie crash

• Drag'n'drop/append a CHEM/BLOB monomer to peptide/RNA component caused BioEddie crash

• Expanding/collapsing monomers caused BioEddie crash

• Appending a peptide monomer without the required backbone attachment point caused BioEddie crash

• Cancelled drag'n'drop operation from library sometimes led to a memorized monomer dropped on the canvas

• Replacing a non-terminal monomer with a monomer containing one attachment point by drag'n'drop function caused a flickering preview of the new layout

Improvements

• BioEddie now supports monomers with up to 4 attachment points

Bugfixes

• XSS vulnerability fixed in HELM viewer

Improvements

• modules config parameter, where the user can set exactly which features should be enabled in BioEddie

Changes

• User can switch between local and remote libraries

• 'Library Manager' now can be opened from 'Monomer Library Panel'

• 'Library Manager' can be removed by setting the 'modules.libraryManager' to false

• 'Library Manager' have a new user interface

Bugfixes

• BioEddie license checker failed when the license file contained multiple licenses of other products

Improvements

• Multiple monomer selection on the canvas

• HELM viewer has been introduced next to the details/sequence tab to show the HELM representation of the macromolecule(s). The selected entities are highlighted with red

Changes

• The transparent menu bar is replaced with a non-transparent menu bar with clear border

• Style of the buttons changed

Improvements

• Within inline-chemistry view:

  • Atoms are properly connected to each other

  • Images are scaled based on the spacial need of the chemical structure (results in same image size)

  • Chemical structure images are flipped vertically if it results in a cleaner layout

• Monomer preview:

  • Chemical structure, name and leaving group definition of a monomer can be previewed by hovering over a monomer on the library panel

Improvements

• Monomers can be expanded to check the chemical structure ("inline-chemistry" view)

• biomoleculeToolkitUrl property is added to the Config object, because more-and-more features are depending on the Biomolecule Toolkit, the base url of the Biomolecule Toolkit has been given to BioEddie

Changes

• generateHeadedSVGFromHelm (ImageGenerator) is removed, the preferred way to generate an image is to use the generateSVGFromHelm method which is asynchronous instead of the now-removed generateHeadedSVGFromHelm which generated the image in a synchronous way, but had limitations because of this

Improvements

• Vertical and horizontal scrollbars appear if the macromolecule would not be fully visible on the canvas

Changes

• Image generation became async, the return value of the generation will be a Promise instead of the html itself

Bugfixes

• Image rendering with a single monomer did not work

Changes

• Session format is removed from file format options (through this, SessionImportModule and SessionExportModule modules are also removed from the API)

Bugfixes

• Safari: pasting did not work when new nucleic acid in Add Sequence dialog would be created

• Mac (all browsers): creating a bond from a component dragged away the component

• Domains disappeared when a sequence was moved to a invalid position

• Sequence details was not updated when sequence was edited in sequence editor

• Moving overlapping components on canvas caused errors

Changes

• The name of the MarvinJS html file shipped with BioEddie changed from editor.html to marvinjs.html. Another change here is that BioEddie is unable the pass the license file to MarvinJS, so you need to specify the location of the license file as a query string for marvinjs.html relative to it. So if you have the following folder structure

• Some configuration properties got default value, so you don't need to specify them at configuration time if the default values are sufficient. See the defaultConfig option in the api-doc for more details.

Bugfixes

• Bond drawing with Ctrl/Cmd + left mouse button caused invalid bond to stuck even if the Ctrl/Cmd was released

Improvements

• Internal build number is added to make it easier to test/report problems, it can be found on the Settings/Info panel beside the normal version number between parentheses

• Monomers can be appended to a peptide or RNA sequence on the canvas via drag and drop

• Domain annotations can be seen/edited on the Annotation panel after selecting the domain on the canvas

• Validation of input for domains in the Sequence Editor dialog

• The built-in default database contains more meaningful monomers

• Preview for valid monomer targets when drawing a bond in the canvas

Changes

• BioEddie provides it's own license for MarvinJS, so there is no need for a separate MarvinJS license

• No LicenseLoader anymore

Bugfixes

• Undo of a bond deletion within a domain caused an inconsistent state

• Replacement of a non-terminal monomer in a component with a missing R1 or R2 attachment point containing monomer did not split the component

• HELM export did not export unknown monomers correctly

Changes

• The image generator now generates a container svg element for the image, so from now on it is possible to specify other kind of elements as the parent of the image. Existing applications using the image generator will now have an svg (the generated one) in an svg (the one passed as the parent)

Bugfixes

• Library manager could not load file with same name multiple times

• Undo left sometimes the domain in an inconsistent (half open, half closed) state

• Internet Explorer 11 (Windows 10): in the ad hoc modification dialog the name of the edited monomer did not refresh

• Domain collapse/expand button's position did not always refresh

• Domain name was cropped when opening domain until mouse left the expand button

• Mouse interactions (click, hoover, etc.) with the generated image caused console errors

Improvements

• More informative notifications for users when BioEddie is trying to use JChem WS or BioTK if these are not configured or an error occurs

• 3rd party tools and their licenses included into the bundle by the name of 3rd-party-licenses.txt

Bugfixes

• Internet Explorer 11: application broke when domain name is added via Sequence Editor

• Internet Explorer 11: scrollbar did not appear in annotation panel when the list size exceeded the panel's height

• Safari: user could not type into Sequence Panel and Sequence Editor

Improvements

• onModelChange event listener is added to API. It fires for every macromolecule or annotation related changes

• Macromolecule level annotations can be imported from HELM. Until now the refId was mandatory for each annotations, which linked the annotation to the corresponding component/domain. Now if the refId is not there we treat it as a macromolecule level annotation

• User gets feedback if JChem-web-services is not configured and opens the monomer modification dialog

Changes

Loading helm with monomer abbreviation did not found in library

• previously it yielded the following behaviour:

  • tried to convert the abbreviation to mol via JChem-web-services smiles/mol conversion

  • if it was successful we treated it as an inline smiles, and represented the monomer as an ad-hoc monomer

  • if the conversion failed we treated it as an abbreviation not found in library and represented it as an unknown monomer

• the new solution only tries to convert the abbreviation if it has the extension section of cxSMILES, otherwise treats it as an unknown monomer. If the abbreviation has the extension and still fails to convert it to mol, we display an error message

Bugfixes

• Bond modification within a domain caused errors

• Deletion of the last monomer inside a domain caused errors

• Components could not be dragged infinitely to the left and top directions

• Undoing bond creation and redrawing bonds made the bond originate from the wrong starting point

• Monomer library change via API refreshed the Library Panel UI incorrectly

• Sequence was shown correctly in Sequence Editor in cases where natural analogue was not present (displaying an X for peptide and N for RNA in these cases)

• HELM export was inconsistent for annotations and cyclic macromolecules

• Error message appeared by clicking on monomer on the Library Panel

• Details panel of a bond had styling issues

• After panning/moving a component out of the canvas the component label was still visible

• Bonds to BLOB was not attached correctly (gap between monomer and the end of the bond)

Improvements

• Basic implementation of the chemical structure view of the macromolecule, up to 100 monomers

• Improvements for validating fields in Monomer manager

• Showing-hiding fields in Monomer manager based on the selected type

Bugfixes

• Console warnings/errors occurred

• Hitting enter in the search field of Library panel reloaded the whole page

• Sequence editor removed the correct monomer, when there were three or more same-letter monomers next to each other

• Library panel UI was not updated, when setting monomers via API

• Deleting monomers and bonds inside of a domain on the canvas caused errors

Changes

• Versioning scheme changed in order to use the same version number among the ChemAxon products

Bugfixes

• Monomers were dropped in the wrong position after the Zoom menu item was pressed

Improvements

• Monomer manager application has been introduced with the following features

  • Export the current monomer library into a file

  • Explore and change the monomers directly via the monomer manager

  • It can be accessed directly from BioEddie via the settings menu dropdown

• The current monomer library is persisted into local storage, so if the library is modified through the library manager the changes won't be lost when the user accesses BioEddie later. There is a Reset Library option in the monomer manager which removes the local changes and resets the default library

• API documentation is generated and can be found in the app/api-doc folder

Changes

• We made an effort to make the configuration of BioEddie easier, which resulted in some API changes (see the details in the CHANGELOG.md)

• A new and easier way to provide the chemical drawer (see the details in the CHANGELOG.md)