Registered monomer attributes are selectable in the monomer's additional data section when the remote library is selected.
Monomers without attachment points can be submitted from the Library Manager interface to the monomer library.
Monomers can be grouped based on their properties that are defined as text or number
Monomer replacement on the canvas caused error in Firefox
BioEddie generated invalid HELM of oligonucleotides if a registered CHEM was attached to the R2/R3 of the sugar on the 3' end
Drag'n'drop operation added monomer attributes to the generated HELM string
Monomers of interest could not be connected when a bond is already selected
Changing monomers and bonds in the 'Edit bond' dialog caused inconsistent state in BioEddie
Drag'n'dropped phosphate linker on the 3' end of RNAs/DNAs could not be connected to other components
Improved error responses upon MOL to HELM conversion of chemical structures containing unknown monomers
Monomers in the Library Manager now can be updated and deleted on the server side
Improved error message upon attempting to convert wildcard 'X' in peptides, and wildcard 'N' in nucleotides to a molfile
Image generation no longer requires a monomer array, thus can be used as follows:
new chemaxon.ImageGenerator().generateSVGFromHelm(domElement, 'PEPTIDE1{C.C}$$$$')
.then(outerhtml => console.log(outerhtml));
Shortcut 'ctrl+alt/option+v' to expand/collapse selected components/sequences, domains and monomers
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
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
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
The transparent menu bar is replaced with a non-transparent menu bar with clear border
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:
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
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
SessionImportModule and SessionExportModule modules are also removed from the API)
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
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
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
BioEddie provides it's own license for MarvinJS, so there is no need for a separate MarvinJS license
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
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
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
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
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
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
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)
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
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
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
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 )