Examples for the corresponding improvements and changes can be found in CHANGELOG.md file within the downloaded .zip archive
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
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
No changes
SessionImportModule
and SessionExportModule
modules are also removed from the API)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.
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
Undo of a bond deletion within a domain caused an inconsistent state
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)
Library manager could not load file with same name multiple times
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
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
Internet Explorer 11: application broke when domain name is added via Sequence Editor
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
Loading helm with monomer abbreviation did not found in library
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
Bond modification within a domain caused errors
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
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)
Basic implementation of the chemical structure view of the macromolecule, up to 100 monomers
Console warnings/errors occurred
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
Versioning scheme changed in order to use the same version number among the ChemAxon products
Monomers were dropped in the wrong position after the Zoom menu item was pressed
Monomer manager application has been introduced with the following features
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
We made an effort to make the configuration of BioEddie easier, which resulted in some API changes (see the details in the CHANGELOG.md)