What's Changed

New features

• #10173 – Support HELM aliases for CHEMs
• #10166 – Edit all instances of monomers from molecules mode
• #10174 – Align the Ketcher library with the new HELM library
• #6918 – Support for stereo-flags in macromolecules mode
• #10167 – Support S-groups in macromolecules mode
• #10837 – Migrate to Indigo v1.46.0-rc.2 in-browser module

Bugfixes and improvements

• #5576 – System mix up sequences from two files loaded one after another
• #9671 – Context menu works wrong for embedded Ketcher
• #10172 – Update some preset-specific error messages
• #10039 – Nucleotide preset: External AP of a phosphate is not always displayed in the preset tab
• #9750 – RNA Builder: Phosphate position picker is not visible when modifying preset in Sequence mode
• #9780 – Save the polymer type switcher (RNA/DNA/PEP) to browser cache
• #5760 – The type file of module 'ketcher-standalone' cannot be resolved.
• #6013 – System reposition monomers on the canvas if ACS setting were applied
• #8188 – No error if data structure doesn't comply with data structure of sdf and CTFile formats specification
• #399 – Security: shell-quote quote() does not escape newlines in object .op values
• #9715 – No gray arrows appear when hovering on the bond in the direction leading to an already marked component in Monomer Creation Wizard
• #10034 – System doesn't assing added bonds to defined Preset component
• #3882 – Changing at least one atom position causes entire molecule repositioning after Aromatize/Dearomatize
• #8133 – Impossible to restrict adding invalid monomer types (e.g. Unknown base, Micromolecule) through API
• #3963 – After removing a monomer from Favorites tab, its tooltip does not disappear and interferes interaction with other monomers
• #10021 – Hover structure using Structure selection tool shows outline for each atom/bond separately
• #6177 – System losts hydrogen bond connections between monomers
• #3437 – Preview and displaying of Cycloheptane on the canvas doesn't match
• #10095 – Indicator number on an antisense chain
• #7980 – Undo in Sequence mode restores bond detached from monomer abbreviation
• #7822 – Already taken connection points are not marked
• #10238 – Search by IDT alias with position indicator
• #4452 – System doesn't allow to unselect already selected nucleotides
• #10040 – Provide a support for one or several different BIOVIA Specifications
• #7536 – Incorrect preview position when adding monomer via arrow button after Undo operation
• #2198 – Save button enabled when Molecule name contains only spaces
• #9121 – The Attributes panel should be disabled for a non-continuous selection of the Nucleotide (preset) type
• #9555 – Multiple side chain connection linkers
• #6162 – RemoteStructServiceProvider Custom Header does not sent to backend
• #8249 – Prevent hanging hydrogen bond when typing after antisense ove
• #7621 – Fix monomer wizard notification scrolling and stale error state
• #4716 – Individual sequences are merged by replacing the middle sequence in Sequence mode
• #5661 – Carbon label doesn't apper in case of 180 degree angle on macro mode
• #6004 – Stereo flag (ABS) position ignoring text and shapes
• #10196 – Disable the "Open..." and "Save as..." icons in the Creation Wizard mode
• #4663 – Wrong Preset name with technical information while copy/paste Preset name
• #10269 – Incorrect monomer name is loaded into the wizard when using "Edit Instance" option
• #6767 – Dashes (lines) are missing in sense chains
• #8608 – System should not allow to create monomer for molecule that has explicitly defined R-Group connected to non-complient bond
• #10280 – Rotation tool: Rotation center color remains unchanged on hover when whole structure is selected
• #10351 – Replace Chlorophyll A_dative molecule in the library from v3000 format to v2000 one
• #10283 – Rotation tool: Current rotation angle values remain positive beyond 180 degrees instead of switching to negative
• #10322 – Undo operation doesn't work in some cases
• #6826 – Undo/Redo after deleting a sequence via right-click places it incorrectly in the sequence list
• #5442 – Bond preview tooltip layout is wrong for unknown monomers
• #10346 – Update the help document (3.17.)
• #11335 – Errors in console when Reaction Plus tool is active

Additional notes:

• Ketcher 3.18.0 has been built and tested with Indigo version 1.46 (standalone and remote).

What's Changed

• #10833 - Migrate to Indigo v1.45.1 in-browser module

What's Changed

• #10763 - Migrate to Indigo v1.44.1 in-browser module

What's Changed

#10482 - XSS executes if open monomer with vulnerable label in KET file

What's Changed

• #10482 - XSS executes if open monomer with vulnerable label in KET file

What's Changed

New features

• #8855 – Add preset-specific error messages in monomer creation wizard
• #8922 – Add Edit Instance prefill for monomer creation wizard
• #9456 – Add BILN format and monomer alias support
• #6784 – Home and End keys support in Sequence mode

Bugfixes and improvements

• #8779 – Allow moving selected S-groups and monomers in molecules mode
• #9779 – Add an additional amino acid (E*) and assign it and D* a new modification type
• #9757 – App crashes while editing sequence containing particular ambiguous monomers
• #7726 – Bond thickness is less than others on monomer preview
• #8006 – LGAs label numerals are not subscripted
• #9820 – Adding bond to atom could ended with wrong bond angle if user slightly moved mouse during click
• #9692 – RNA Builder: Impossible to specify the phosphate position before any preset components are added
• #9990 – Undo has no effect on bond type changes
• #9738 – Swap stereo labels and stereo atoms when bond is flipped
• #8251 – Monomer should be selected on the canvas after creation
• #9489 – Nucleotide presets: Creating preset with the same component codes replaces properties of the existing preset
• #7546 – Canvas does not reset scroll position after using “Clear canvas” - added monomers appear offset
• #9751 – RNA Builder: Missing "Switch to right/left" tooltips when hovering over the phosphate position picker options
• #9731 – Rotation tool: Rotation center of partially selected structure changes color when hovering over
• #9383 – Rotation tool: After moving the rotation center the rotation handle is not set to the starting position and rotation circle does not cross the dashed line
• #8181 – It is possible to define preset (group) name more than 200 symbols
• #6273 – Thick foreground bonds do not work if the atoms are not carbons
• #9837 – Correct the warning message for unusual base leaving group
• #8199 – System allow to upload monomer that has IDT alises that is longer than allowed (it shouldn't!)
• #4309 – Delete and Backspace hotkeys deletes elements under mouse cursor (hover), but not selected ones
• #8198 – It is possible to add monomer with HELM alias is too long
• #5849 – Expanded monomer inconsistent behaviour
• #8600 – Single Up bond between two monomers painted wrong
• #4093 – Keep loading indicator visible until paste completes
• #9349 – Stereo group labels are overlapped
• #5468 – Multi-Tailed Arrow can't be selected if Structure Selection Tool is used and clicking on tails or head
• #8778 – Only show the possible monomer properties in the attributes panel in the monomer creation wizard
• #8173 – IDT alias could be longer than 10 symbols without slashes
• #10134 – Update the help document (3.16.)
• #9991 – Remove "Highlight" checkbox from monomer creation wizard
• #10054 – Nucleotide preset: R-group labels disappear when switching component tabs
• #9299 – Fixes on new lexical library
• #10102 – Type combobox is empty if S-Group Properties` dialog opened for Copolymer s-group for edit
• #7940 – Export to HELM of monomer with attached micromolecule should cause warning message: The molecule will be exported using inline SMILES, and on load will appear as a CHEM monomer
• #10260 – Warning message for unusual base leaving group incorrectly refers to "hydroxyl" instead of "hydrogen"
• #10146 – Migrate to Indigo v1.45.0 in-browser module

Additional notes:

• Ketcher 3.17.0 has been built and tested with Indigo version 1.45 (standalone and remote).

What's Changed

New features

• #8996 – Show attachment points in the attributes panel when defining presets
• #9310 – Library and autochain support for presets with 5' phosphates

Bugfixes and improvements

• #6603 – Replace AJV with jsonschema in runtime to allow Ketcher work in CSP-strict environment
• #6094 – It is possible to create antisense even if it is not allowed (when base has extra bond out of r1-r3 to sugar)
• #8977 – No focus inside modal confirmation of type changing in monomer creation wizard
• #6093 – Phosphate in antisense chain converted wrong
• #7781 – Inconsistency in fragment selection hover behavior between Micro and Macro modes
• #7204 – Long names and short names of 3D Templates in the Structure Library are swapped and short names are missed
• #7278 – N-methylation option is missing even if monomer in selection is eligible for it
• #5110 – Aromatize the molecules after drawing
• #7083 – Delete operation on Sequence mode causes hanging bonds and undeletable monomers
• #5480 – Ambiguous monomer tooltip covered
• #5934 – Error message is wrong if user tries to establish hydrogen bond if it is already has single one
• #5740 – Establishing connection between ambiguous phosphate and sugar works wrong
• #6090 – Antisense creating doesn't work if ambiguous phosphate present in the chain selection
• #4247 – When pressing the “Open from file” button, the full-screen mode closes
• #9291 – Slow build problem (part 2): reduce circular imports with static-import rollback, mode initialization fixes, and lockfile reset
• #9139 – Incorrect structure while press UNDO aftrer Create Monomer action on the Molecules Mode
• #9730 – Rotation tool: Rotation-angle label overlaps 0° label in Macro mode
• #8332 – cursor flickers between grabbing and pointing hand while dragging a monomer across the cards
• #5543 – Styles from macromolecules mode break global styles
• #9559 – S-Group: Subtype drop-down menu for Copolymer contains an extra option
• #3951 – Aromatizing causes NULL in export to MDL Molfile V2000 format file
• #9709 – It is not correct to have 5' indicator on an antisense chain.
• #6314 – Export to Sequence (3-letter code) and export to IDT doesn't throws an error if user tries to save micromolecule structures
• #8715 – File format dropdown height should be equal to File name edit box
• #6091 – Antisense creating doesn't work if ambiguous sugar present in the chain selection
• #6053 – D peptide with asterik is marked as modified
• #9458 – Add validation for monomer name to ensure valid characters are used
• #7745 – Preview tooltip doesn't appear on the canvas if monomer name too long
• #6907 – Memory leaks for ketcher when it is opened inside modal
• #8389 – Hanging bonds after sequence edit operation
• #7574 – IDT code is missing from preview tooltip on sequence canvas
• #7514 – IDT codes list is wrong for all presets
• #7827 – Some bond types shouldn't be allowed in Create monomer wizard
• #6234 – Thick foreground bond looks wrong on Macro canvas
• #9817 – Double call of context menu for symbol on sequence canvas causes different menu to appear
• #9622 – Update the help document (3.15.)
• #9138 – Update the appearance of the monomer creation wizard
• #9491 – Monomer Creation Wizard: Creating a Nucleotide (preset) allows empty mandatory field natural analogue
• #8203 – System allow to define position IDT aliases with slashes inside
• #8958 – Bond element stays after clear canvas is clicked in Macromolecules canvas
• #8637 – Molecule structure chages made in monomer creation wizard doesn't appear at molecules canvas after monomer creation
• #9887 – Copy paste does not work in Safari
• #10123 – Migrate to Indigo v1.44.0 in-browser module

Additional notes:

• Ketcher 3.16.0 has been built and tested with Indigo version 1.44 (standalone and remote).

What's Changed

New features

• #9118 – Update KET and SDF format to include information about preset phosphate position
• #9129 – Allow 5' position of the phosphate in the monomer creation wizard
• #9310 – Expand RNA Builder presets to support 5' phosphates using preset connections

Bugfixes and improvements

• #9358 – Rotation tool: A dashed bounding box disappears when the focus is moved outside of the browser window
• #9368 – Rotation tool: Rotation handle does not change its view (color and icon) when rotation mode is activated
• #5568 – The "magnet angle" is too large; drawing arrows ±15° of n·90° is impossible; to forbid one third of possible angles is too much.
• #9377 – Right-click on monomer should not only open context menu but select monomer if it was right-clicked
• #9374 – Rotation tool: Current rotation angle is not displayed at starting position in Macro mode
• #9379 – Arrange as a Ring option in context menu should be visible only on Flex mode (Macromolecules canvas)
• #9384 – The layout mode dropdown is overlapped
• #9382 – Rotation tool: It is possible to move the rotation center when part of structure is selected
• #9105 – The monomer is moved after pressing the "Submit" button for any type of monomer
• #7240 – ABS label becomes detached from the structure after horizontal or vertical flip
• #9407 – Labels for monomer natural analog category is missing if filter applied in Ketcher popup mode
• #9060 – Search using some AxoLabs aliases fails
• #9420 – System don't show Fullscreen/window mode in correct state if user switches mode being in fullscreen mode
• #9102 – Incorrect selection a part of structure for phosphate when moving mouse from top to bottom
• #8799 – Changing Implicit H count properties thru Atom properties dialog works wrong
• #9143 – System removes bond between monomers if user removes abbreviation from them on molecules canvas
• #9132 – The “Mark as a…” option is displayed after switching to another type in the Attributes panel
• #8937 – Disable molecules/macromolecules switcher and settings when the monomer creation wizard is active
• #9474 – AxoLabs alias is missing from library preset card preview tooltip and symbol preview tooltip on sequence canvas
• #9141 – System removes atoms that holds unoccopied leaving groups if user removes abbreviation from monomer on molecules canvas
• #9130 – It is not possible to save only the sugar and phosphate in the Nucleotide (preset) type
• #6772 – SYNC mode button is absent if sense/antisense chain pasted from clipboard
• #7021 – Monomer layout inside r-group box become corrupted if user grabs and moves bond between monomers
• #6476 – Unable to paste using Ctrl+V chain from clipboard after clear canvas action
• #9140 – The Structure selection after moving the entire Structure is incorrect.
• #9460 – Implicit H count value doesn't change number of attached hydrogens if applied to canbon (C)
• #9198 – Expand monomer on molecules canvas works wrong if monomer consists of one atom and one leaving group - shows empty structure
• #9542 – Update the hint for preset components defining in the monomer creation wizard
• #8960 – Number associated with symbol is visible
• #8402 – Scrollbar appears unnecessarily in “Create Monomer” attributes panel after selecting Type, and disappears when expanding Aliases
• #4248 – The “File format” drop-down does not open in the “Save Structure” window in the full-screen mode
• #9590 – Fix vite server config error and remove warnings
• #8394 – HELM (and IDT) alias collision should log error in console
• #6616 – Hydrogen bond layouted in flex style on snake mode
• #4675 – It is impossible to cut a structure from a canvas using Ctrl+X
• #9455 – Nucleotide presets: Unable to create preset after adding and removing simple extensions – console error
• #9123 – Monomers disappearing when expanding/collapsing in Molecules Mode after moving in Macromolecules Mode
• #5198 – Added a darker hover state for selected sequence items in Sequence Layout Mode.
• #6239 – Aromatic bond is mirrored if used as inside one on Macro canvas
• #8818 – Add/Remove explicit hydrogens operation inside create monomer wizard causes exception: process is not defined
• #7141 – System shows molecular mass and molecular formula even if few chains on the canvas
• #4694 – Add Hotkeys in Macro Mode Similar to Micro Mode
• #8142 – System allow to load monomers with invalid HELM aliases
• #6851 – Bond to C10H20 superatom rendered wrong if loaded from CDXML
• #9617 – Correct the LGA of meK and meE amino-acids
• #9336 – Update the help document (3.14.)
• #9645 – Migrate to Indigo v1.43.0 in-browser module
• #9774 – Change the structure and the name of Gly-ol amino-acid
• #9828 – Copy functionality is broken on Chrome

Additional notes:

• Ketcher 3.15.0 has been built and tested with Indigo version 1.43 (standalone and remote).

What's Changed

New features

• #8352 – Introducing rotation of monomers in Macromolecules mode
• #6917 – Support for enhanced stereochemistry markings in macromolecules mode

Bugfixes and improvements

• #9113 – The Copolymer S-Group type should not be displayed unless there are at least two structural repeating units (SRUs) in selection
• #9108 – Incorrect valence for nitrogen
• #9126 – Some keyboard shortcuts don't work on Macromolecules canvas
• #8187 – It is possible to create preset with empty name
• #8896 – Unable to load KET file in Molecules mode
• #9328 – Migrate to Indigo v1.42.0 in-browser module
• #9327 – Update the help document (3.13.)

Additional notes:

• Ketcher 3.14.0 has been built and tested with Indigo version 1.42 (standalone and remote).

What's Changed

New features

• #8948 – Add fragment selection tool and rename structure selection tooltip

Bugfixes and improvements

• #8245 – Small molecules positioning rule is not respected when connected to multiple monomers in different chains
• #7927 – Monomer area selection works wrong if user uses mouse wheel to scroll down
• #7729 – “Field value” textbox is active in “S-Group Properties” modal when “Context” field is empty
• #7899 – CIP labels got rendered under the bond after atom selection and move
• #8981 – Stereo bonds between monomers become single bonds if monomer collapsed
• #8986 – ketcher-standalone memory leak
• #8980 – System shows bad valence for atoms that attached to bonds that connects monomers
• #8987 – Labels for monomer natural analog category is missing if filter applied
• #7153 – Molecule from expanded monomer disappears on switching to Macromolecules mode
• #9065 – System shows natural analog category for phosphates
• #9078 – Update the help document (3.12.)
• #9084 – Ketcher saves incorrect attachment points configuration for new nucleotides

Additional notes:

• Ketcher 3.13.0 has been built and tested with Indigo version 1.41 (standalone and remote).