Ketcher 3.11.0¶
What’s Changed¶
New features¶
#8248 – Define nucleotide presets using the monomer creation wizard (POC)
#8254 – Allow for stereo bonds up and down to be a bond between AA and LGA
#8383 – Introduce library searching using HELM aliases, AxoLabs aliases, and modification types
#7915 – Enable flipping of all expanded monomers in a structure
#8363 – Include ‘Arrange as a Ring’ button for Flex mode
Bugfixes and improvements¶
#8386 – Update the help document (3.10.)
#8739 – Migrate to Indigo v1.39.0-rc.1 in-browser module
#4188 – Choosing wedged/hashed bond direction doesn’t work from right-clicking context menu
#7148 – Number of selected elements in context menu is wrong for sense/antisense chain
#7735 – System shows inner circles of aromatized benzene rings from collapsed monomers on Molecules canvas
#6855 – Labels for empty ambiguous monomer categories are present in the library
#7244 – File format name for Sequence is cut off in Save Structure modal dropdown
#5578 – Peptide section for ambiguous monomers should have “Ambiguous Amino Acids” name
#5580 – Order of sections for ambiguous bases is wrong - Ambiguous Bases should come first
#5927 – Font size and label position should be corrected at “Open structure” dialog
#7995 – Unable to create more than one attachment point per atom
#8395 – “Attachment points are set
#5481 – Ambiguous CHEM shown wrong at Sequence mode
#5799 – S-Group properties window should be disabled for monomers
#7385 – Cannot delete and copy microstructures via right-click context menu in macromolecule canvas
#4772 – Fix Platinum valence
#8403 – There is no way to remove HELM alias
#7506 – Tooltip is shown in wrong place for ambigous monomers in popup mode
#8461 – Function calls should not pass extra arguments
#6737 –
5NitIndunsplit nucleotide should be shown as X symbol instead of @ one#8459 – Getters and setters should access the expected fields
#5361 – getInChIKey returns just the InChI string as JSON
#5751 – Establishing connection between ambiguous CHEMs works wrong
#5214 – The tooltip does not appear below the cursor when hovering over the “plus” button and stripe
#6725 – Ambiguous sugars (alternatives and mixed) in sequence shown as % symbol instead of @ symbol
#4891 – When using the “ketcher.setMode(mode)” method, the icon of the “Type mode” drop-down does not change
#8554 – System losts AxoLabs alias while save it KET
#8556 – System losts Modification types values while save it KET
#7372 – “Ghost image” doesn’t satisfy the UX design
#6731 – Ambiguous phosphates (alternatives and mixed) in sequence shown as % symbol instead of @ symbol
#8584 – Tooltip for attachment points appears too far from attachment point
#8397 – Context menu remains visible after creating cyclic structure via right-click menu
#7776 – In Macro mode clicking on Selection tool icon does not open dropdown menu as in Micro mode
#4645 – In the “Modify RNA Builder” mode, when hovering over the buttons “Yes” and “Cancel” in the “Update Sequence” window, tooltips are displayed
#7610 – R-groups are not shown if to Open from file as New project
#7559 – Charge tools doesn’t work for “star” atoms
#7022 – Dropdown for units (Da/kDa/MDa) is not aligned in width with the selector button
#5677 – Preview for chain of CHEMs works wrong in sequence mode
#5664 – Selection circle is different on micro and macro mode
#5469 – Preview tooltips for monomers loaded from HELM with inline smiles are wrong
#7956 – Presence of R32 group in molecule makes impossible to create monomer from it
#5534 – Ambiguous monomer tooltip content doesn’t sorted properly in case of equal quantities
#5382 – System shouln’t allow user to load empty mol file - Add to Canvas should be disabled
#7689 – No tooltip shown and invalid attachments allowed when adding monomers consecutively without moving mouse from arrow button
#5567 – System losts height data during copy/paste operation
#7191 – Change 3SS6 monomer type to Phosphate
#8726 – Name should not be mandatory any more, Symbol value should be used instead if user left it empty
#8723 – User should be able to type ambiguous monomers symbols in edit sequence mode (current sequence type should be taken in to account)
#6730 – System doesn’t unite ambiguous bases (alternatives and mixed) into one @ symbol
#8721 – Create a monomer button remain selected (colored) after user done with monomer creation (creation wizard got closed)
#8720 – Library update event is triggered after API usage
#7578 – Undo/Redo restores partial selection after cancelling monomer creation
#8752 – All types of ambiguous monomers alone represented on sequence canvas as @ symbol should be represented
#7519 – In case of multiple R1 or R2 groups second R1/R2 groups should be assigned to the smallest available Rn (n>2) if available
#5922 – Non-polar amino acid (with W as natural analog) should have shade of green but currently it is violet
#5445 – Labels for ambiguous monomers at Bond Preview tooltip are wrong
#7189 – Unknown unsplit nucleotide looks like chem
#8846 – Unable to create more than one nucleotide monomer - system throws exception
#8845 – Creation nucleortide preset causes som bonds to disappear
#8847 – Former molecule selection causes invalid attachment point creation in Monomer creation wizard
Additional notes:¶
Ketcher 3.11.0 has been built and tested with Indigo version 1.39 (standalone and remote).