epam/ketcher

✨ New features

• #8777 – Change the logic for activation of 'Arrange as a Ring' tool and context menu item
• #8781 – Change the logic for attachment points editing drop-down in the monomer creation wizard
• #8857 – Monomer saving - presets in the monomer creation wizard
• #8856 – Defining other monomer properties - presets in the monomer creation wizard
• #8866 – Defining the preset - presets in the monomer creation wizard
• #8851 – Highlighting presets in the monomer creation wizard
• #8854 – Defining the preset - presets in the monomer creation wizard
• #8849 – Entering the wizard - presets in the monomer creation wizard
• + 3 more

🐛 Bugfixes and improvements

• #8437 – If no selection made, system doesn't define attachment points for monomer
• #5701 – It is possible to connect all APs to same atom
• #8800 – The hover on a selected atom differs in micro mode and in macro mode
• #7797 – Underline colour for the base counter in the Calculate Properties window doesn't fit the requirement
• #7789 – Fragment selection highlighting inconsistent between Micro and Macro modes
• #7325 – Right-click copy option does not work for microstructures on macro canvas
• #8837 – No bad valence indication on Macromolecules canvas
• #8792 – Rename monomer symbol to monomer code in the monomer creation wizard.
• + 18 more

✨ Additional notes:

• Ketcher 3.12.0 has been built and tested with Indigo version 1.40 ([standalone](https://www.npmjs.com/package/indigo-ketcher/v/1.40.0) and [remote](https://hub.docker.com/layers/epmlsop/indigo-service/1.40.0/images/sha256-865dd73f1ee9c49bcde04f6529ec6f16a3943a7985aa31df691378a27cb98056)).

✨ 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
• + 53 more

✨ Additional notes:

• Ketcher 3.11.0 has been built and tested with Indigo version 1.39 ([standalone](https://www.npmjs.com/package/indigo-ketcher/v/1.39.0) and [remote](https://hub.docker.com/layers/epmlsop/indigo-service/1.39.0/images/sha256-f123ddf09033a88978f0a81f4e3e9bb617fa7034a9c57bea76fae876321ed8fc)).

✨ New features

• #7500 – Update the monomer preview
• #7633 – Allow for setting of modification type in the monomer creation wizard
• #7932 – Add warning messages to the monomer creation wizard in case of unusual leaving group atoms
• #7928 – Allow for setting of HELM alias in the monomer creation wizard
• #8200 – Add parameter to Editor to disable saving new monomers to local storage
• #8281 – Adjust subscription to library update event of Ketcher API
• #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard
• #7970 – Include 'Create cyclic structure' option in the context menu for Flex mode

🐛 Bugfixes and improvements

• #8602 – Migrate to Indigo v1.38.0 in-browser module
• #7971 – Update the help document (3.9.)
• #7887 – Molecule rotation causes error in console: Uncaught TypeError: Cannot read properties of undefined (reading 'pp')
• #4467 – Ket label should be renamed to Ket Format
• #7746 – System replace few spaces in monomer name to one space on monomer preview
• #7421 – "Ghost image" of CHEM is white (different from "ghost image" of other monomer types)
• #7740 – System should not allow to fill Symbol and Name fields if Type is not selected on Monomer creation wizard
• #3742 – Wrong tooltip for "minimize window" button (shows "expand window")
• + 16 more

✨ Additional notes:

• Ketcher 3.10.0 has been built and tested with Indigo version 1.38 ([standalone](https://www.npmjs.com/package/indigo-ketcher/v/1.38.0) and [remote](https://hub.docker.com/layers/epmlsop/indigo-service/1.38.0/images/sha256-40d4d9d732606381a5a3bc9ae5e5ed94a0a948c6e6460e33278285d3d2e71d4a)).

✨ New features

• #7690 – Allow for modification of the structure in the monomer creation wizard
• #7730 – Continuation of attachment points editing in the monomer creation wizard
• #7748 – AxoLabs format support
• #7674 – Add ability to update monomers library API in SDF format
• #7560 – Improving snake layout logic to include small molecules
• #7709 – Update the help document (3.8.)
• #8270 – Migrate to Indigo v1.37.0 in-browser module

🐛 Bugfixes and improvements

• #7572 – "Create a monomer" option is missing in right-click menu when selection meets conditions
• #7443 – Save to SDF button is missed on Salts and Solvents tab in Structure Library dialog
• #7359 – Stereochemistry dialog crashes Ketcher if only one stereo bond on the canvas
• #7697 – IDT alias of CHEM 5TAMRA is displayed wrong
• #7919 – Change the symbol of CHEM Cy5.5 dye
• #5417 – IDT aliases not shown at preview tooltip at Monomer Library
• #5202 – Update visuals in Right-click context menu
• #7395 – Line between Paste option and Create RNA antisense strand option is missing in the context menu
• + 27 more

✨ Additional notes:

• Ketcher 3.9.0 has been built and tested with Indigo version 1.37 ([standalone](https://www.npmjs.com/package/indigo-ketcher/v/1.37.0) and [remote](https://hub.docker.com/layers/epmlsop/indigo-service/1.37.0/images/sha256-51e95fc6d5f2efafc921c5804ff54bbb846c2b4a4739e9419e4a2ef7471d01ef)).

✨ New features

• #6287 – Expanding the snap functionality to monomer groups inside of a structure
• #7441 – Allow for modification of the attachment points in the monomer creation wizard
• #6657 – Bump react to ^19.0.0 in ketcher-react package
• #6358 – Add lasso selection/fragment selection tool in macromolecules mode
• #7554 – Correct existing and add new structures to the library with appropriate IDT codes
• #7221 – Change the colour of nucleobases
• #7384 – Create documentation for hiding toolbar buttons
• #7505 – Update the help document (3.7.)
• + 1 more

🐛 Bugfixes and improvements

• #7222 – Incorrect leaving group atoms for expanded monomers
• #6993 – Atoms and "monomer to atom bonds" are not removed when all other bonds are removed from atom
• #7619 – Pressing ? key at Text Editor form while creation text label opens Macromolecules help link
• #7525 – Specify a target origin for this message. vulnerability
• #6747 – Unnecessary leaving groups (R-groups) appear upon "Removing Abbreviation" of expanded monomer when an attachment point is occupied
• #7571 – Ctrl+M does not open monomer creation wizard when selection meets conditions
• #7683 – Remove Add attachment point functionality
• #7578 – Undo/Redo restores partial selection after cancelling monomer creation
• + 45 more

✨ Additional notes:

• Ketcher 3.8.0 has been built and tested with Indigo version 1.36 ([standalone](https://www.npmjs.com/package/indigo-ketcher/v/1.36.0) and [remote](https://hub.docker.com/layers/epmlsop/indigo-service/1.36.0/images/sha256-a9f6b7cea8e465f097cc36d0dc088a54040439aedbb7ee33da301ae796463344)).

✨ New features

• #6552 – Create a monomer from a selected part of the structure
• #6785 – Support aliases from HELM
• #3253 – Introduce the arrow button on library cards for easy monomer/preset addition to canvas
• #7430 – Adjust sgroup hover rendering to remove overlapping parts
• #6150 – Add the star atom to the special nodes section of the extended table
• #7535 – Add api for switching between macromolecules and molecules modes
• #7660 – Migrate to Indigo v1.35.0 in-browser module

🐛 Bugfixes and improvements

• #7377 – Update the help document (3.6.)
• #7351 – Profiling and optimization for many monomers on molecules canvas
• #6270 – Add "About" (i) and "Help" (?) buttons to the main toolbar in macromolecules mode
• #7222 – Incorrect leaving group atoms for expanded monomers
• #7168 – Opening the 3D Templates section in Structure Library causes multiple errors in the DevTools console
• #7252 – Integrate with SonarQube
• #7273 – System loads micro-macro connected structure on snake canvas and created understandable bond
• #7283 – Context menu is wrong if clicked on top of sequence
• + 40 more

✨ Additional notes:

• Ketcher 3.7.0 has been built and tested with Indigo version 1.35 ([standalone](https://www.npmjs.com/package/indigo-ketcher/v/1.35.0) and [remote](https://hub.docker.com/layers/epmlsop/indigo-service/1.35.0/images/sha256-4c6730c0c6cce76af968317ceecb8b2501a1fefc81211e0ddf881fb58250d9a0)).

✨ New features

• #6404 – Drag and drop for the library elements in macromolecules mode
• #7164 – Introduce marking of nucleotide components
• #7125 – Support for reaction arrows and reaction pluses in macromolecules mode
• #7132 – Update and add icons to right-click drop-down menus in all modes
• #7347 – Migrate to Indigo v1.34.0 in-browser module

🐛 Bugfixes and improvements

• #7231 – Update the help document (3.5)
• #7073 – Unable to create hydrogen bond: Uncaught RangeError: Maximum call stack size exceeded
• #7178 – The tooltip appears behind the context menu options
• #7187 – IDT code shown wrong for SS3 chem
• #6410 – Incorrect bond attachment to micro molecules in Macro Mode
• #7277 – Cannot open multiple instance of Ketcher in one window
• #6986 – Context menu appears on both canvas in molecules mode for several Ketcher instances on same page
• #7207 – Rectangular input field should be wide enough to fit any (at least 4) digit number
• + 8 more

✨ Additional notes:

• Ketcher 3.6.0 has been built and tested with Indigo version 1.34 ([standalone](https://www.npmjs.com/package/indigo-ketcher/v/1.34.0) and [remote](https://hub.docker.com/layers/epmlsop/indigo-service/1.34.0-rc.1/images/sha256-74b6c7d6d5ce454bdf0bbebd5e032e991155434ba6d2ddbf7b589b5d777291a1)).

✨ New features

• #6738 – Ability to change the number of monomers in a line
• #5208 – Allow modifying amino acids on canvas
• #6995 – Smart positioning of CIP stereo labels for atoms
• #6852 – Improve the hydrophobicity graph in the "Calculate Properties" window
• #6589 – API lacks support for 3 letter code sequence export in macro mode
• #7070 – Include the removed versions of some 3D templates in the templates library in addition to the corrected ones
• #7224 – Migrate to Indigo v1.33.0 in-browser module

🐛 Bugfixes and improvements

• #7094 – Update the help document (3.4.)
• #6294 – Hiding toolbar buttons doesn't also hide disable the corresponding keyboard shortcut
• #6930 – Replace File comparison (for MOL files ONLY!) operations with valid helper function - verifyFileExport
• #7032 – Ketcher allows to make changes in sequence while being in nucleotide modification mode
• #5971 – Inconsistent selection sensitivity when highlighting sequences
• #7023 – Hydrophobicity section is missing tooltip icon and description
• #6834 – Clicking on base card in RNA Builder does not scroll to selected base if multiple bases from the same section are selected
• #7031 – Layout shift when entering symbol in sequence mode upon first macromolecules mode initialization
• + 13 more

✨ Additional notes:

• Ketcher 3.5.0 has been built and tested with Indigo version 1.33 ([standalone](https://www.npmjs.com/package/indigo-ketcher/v/1.33.0) and [remote](https://hub.docker.com/layers/epmlsop/indigo-service/1.33.0/images/sha256-e6c8cb1bbede651471b905c927dd1743819ef3025f7c86db13c4aa7db560dc36)).

🐛 Bugfixes and improvements

• #7568 - Unable to use Ketcher in the most basic of Vite projects

✨ New features

• #6832 – Update the help document 3.3
• #6625 – Support of expanded monomer option
• #6271 – Support for CIP stereo labels in macromolecules mode
• #5727 – Add "Calculate Properties" for macromolecules
• #5797 – Highlighting attachment point of expanded monomers on hover in micromolecules mode
• #7237 – Migrate to Indigo v1.32.0 in-browser module

🐛 Bugfixes and improvements

• #4838 – Incorrect structure for Phe-L-Phenylalanine in template library
• #5497 – Refactor (SnakeModePolymerBondRenderer): Create and use `SVGPathDAttributeUtil`
• #6288 – Incorrect numbering in sequence
• #6871 – Connection points become visible and broken if user switch window focus from one app to another and back
• #6870 – Enter key adds undeletable preset to preset section
• #4476 – Tooltips in sequence mode not disappear after right-click on letters
• #6762 – System shows natural analog monomer as modified if source mol file contains only 3-letters natural analog name
• #6791 – Change activation area of the New sequence button
• + 26 more

✨ Additional notes:

• Ketcher 3.4.0 has been built and tested with Indigo version 1.32 ([standalone](https://www.npmjs.com/package/indigo-ketcher/v/1.32.0) and [remote](https://hub.docker.com/layers/epmlsop/indigo-service/1.32.0/images/sha256-d739c8474cea3051354e306320235037a55ab91b207e07eef45f8187b9eceecb)).

✨ New features

• #6508 – Update the logic for recognizing sense and antisense chains
• #6435 – Do not retain snake mode layout when passing though snake mode
• #6519 – Implement the library redesign and modify the RNA builder behavior
• #6620 – Add salts to the "Salts and Solvents" tab in the monomer library
• #6472 – Add "Copy", "Paste", and "Delete" to the r-click drop down menu in sequence mode
• #5999 – Added "Create Antisense Strand" icon on the toolbar
• #6317 – Introducing the snap to distance functionality for monomers connected via bonds
• #6612 – Update the help documentation (3.2)
• + 1 more

🐛 Bugfixes and improvements

• #6293 – Remove base monomer border after selection
• #6573 – Incorrect bond length and angle for non-natural monomers in the library
• #6695 – Unable to create antisense RNA/DNA chain in case of multiple сhain selection (if not eligible for antisense chain selected)
• #6573 – Incorrect bond length and angle for non-natural monomers in the library
• #6842 – Single click on already selected monomer cause monomer sticks to mouse cursor and snapping elements appear on the canvas forever
• #6813 – Click on monomer selection area causes an exception Uncaught TypeError: Cannot read properties of undefined (reading 'drawingEntity')
• #6774 – Modified bases selected via RNA Builder revert to natural analogs in all modes
• #6495 – System replaces A base with always RNA N base (alternatives of A,C,G,U) even if user selected DNA N base (alternatives of A,C,G,T)
• + 21 more

✨ Additional notes:

• Ketcher 3.3.0 has been built and tested with Indigo version 1.31 ([standalone](https://www.npmjs.com/package/indigo-ketcher/v/1.31.0) and [remote](https://hub.docker.com/layers/epmlsop/indigo-service/1.31.0/images/sha256-ca9addbfebcee2ddc858362ce4020f59fd180d4de8a97af1609389e6e9106cdf)).

✨ New features

• #6215 – Introducing the snap to angle and standard bond length for monomers connected via bonds
• #6252 – Allow creation of antisense chains in sequence mode
• #6383 – Introduce the creation of DNA antisense chains
• #6355 – Change attachment points of backbone monomers in automatically created antisense chains
• #6254 – Update the representation of sense and antisense chains in sequence mode (2/2)
• #6284 – Long bonds for uneven double stranded sequences in snake and flex modes
• #6527 – Add ability to pass coordinates to Ketcher addFragment and setMolecule API to position provided structure
• #6357 – Allow insertion of phosphates (p) from the keyboard in sequence mode
• + 1 more

🐛 Bugfixes and improvements

• #6219 – Unable to save to HELM hydrogen connection between micromolecule (with AP) and monomer
• #6005 – Move the dot indicating a modified phosphate in sequence mode
• #4145 – Implement popup versions of Ketcher (and routing)
• #5700 – System allow to establish infinit number of bonds from monomer to microstructure
• #6534 – Adding nucleotide to the last position having phosphate in antisense causes exception: ReferenceError: process is not defined
• #6402 – Hydrogen bonds misaligned due to antisense strand direction change when opening or pasting a structure in Macro Mode
• #6464 – Splitting chain with Enter key doesn't work
• #6425 – Hiding of number indicators while in sync editing mode when the triangle overlaps with the number
• + 29 more

✨ Additional notes:

• Ketcher 3.2.0 has been built and tested with Indigo version 1.30 ([standalone](https://www.npmjs.com/package/indigo-ketcher/v/1.30.0) and [remote](https://hub.docker.com/layers/epmlsop/indigo-service/1.30.0/images/sha256-ec74234c98bbecdab2134efcd04248efa8e69f398991ba29f33c51327c815433)).

✨ New features

• #6167 – Long bonds for linearly displayed circular structures
• #5942 – Update the representation of sense and antisense chains in sequence mode (1/2)
• #5995 – Synchronize the library tab with typing type switcher in sequence mode
• #6222 – New chain tool behavior
• #6246 – Import indigo with EXPORT_ES6 & USE_ES6_IMPORT_META options
• #6417 – Update Indigo to 1.29.0 in browser module

🐛 Bugfixes and improvements

• #6164 – Changing any parameter at Settings cause Undo/Redo work wrong (or delete undo history)
• #6166 – Color schema for Favorites tab at RNA Library is wrong for Peptides
• #6088 – Disable create antisense strand option if antisense-less base present in chain selection
• #5696 – Adding Attachment point to microstructure already connected to monomer - causes problems
• #6201 – Circular hydrogen bond connection between three (or more) chains, those hydrogen bonds isn't considered as side chain connection for layout purposes
• #6195 – Nucleotide wrongly become antisense oriented if have hydrogen connection to sugar
• #6194 – Unknown monomer and CHEM overlap to each other if both are the side chain for same chain
• #6422 – Long bond appears behind monomers when using attachment points
• + 18 more

✨ Additional notes:

• Ketcher 3.1.0 has been built and tested with Indigo version 1.29 ([standalone](https://www.npmjs.com/package/indigo-ketcher/v/1.29.0) and [remote](https://hub.docker.com/layers/epmlsop/indigo-service/1.29.0/images/sha256-e79143bab1b5b96dc8b7b1e10d62612f89e59399c16dba4ecfa56f11fe8fb118)).

🐛 Bugfixes and improvements

• #6563 - Incorrect bond length and angle for some natural monomers

🐛 Bugfixes and improvements

• #6557 - Modified phosphates shift away from main structure during expand in Micro Mode
• #6556 - Expanded macromolecules in Micro Mode causes unintended merging
• #6563 - Incorrect bond length and angle for some monomers

🐛 Bugfixes and improvements

• #6546 - Macro structure duplicated on canvas when using ketcher.getMolfile() and pasting

📋 What's Changed

• 🎉 We’re excited to introduce Ketcher 3.0, featuring the newly available Macromolecules mode!
• Along with this major enhancement, we've included various improvements and bug fixes to enhance performance and usability.

✨ New features

• [#6034](https://github.com/epam/ketcher/issues/6034) – Make macromolecules switcher enabled by default
• [#6029](https://github.com/epam/ketcher/issues/6029) – Enter flex mode when macromolecules mode was not entered in before and there is a drawing on canvas
• [#6027](https://github.com/epam/ketcher/issues/6027) – Support for single atom properties in macromolecules mode
• [#6028](https://github.com/epam/ketcher/issues/6028) – Support all remaining types of bonds from small molecules mode in macro molecules mode
• [#6227](https://github.com/epam/ketcher/issues/6227) – Update indigo to 1.28.0 in browser module

🐛 Bugfixes and improvements

• [#5978](https://github.com/epam/ketcher/issues/5978) – Entire element bounding box should be clickable, not only black dots
• [#6127](https://github.com/epam/ketcher/issues/6127) – Hover mouse over ambiguous monomer on Micromolecules canvas causes app crash
• [#5476](https://github.com/epam/ketcher/issues/5476) – Copy/Cut and Paste using Ctrl+C/X and Ctrl+V doesn't work for static elements in Mozilla Firefox
• [#5317](https://github.com/epam/ketcher/issues/5317) – Some side chain bonds are not shown in Sequence mode for bases, CHEMs, phosphates and sugars
• [#5796](https://github.com/epam/ketcher/issues/5796) – Indigo functions doesn't work if monomer on micro canvas - system throws an error: Error: Cannot deserialize input JSON.
• [#5032](https://github.com/epam/ketcher/issues/5032) – Selection of monomers should disappear when the user moves the cursor
• [#5139](https://github.com/epam/ketcher/issues/5139) – After pressing the Clear Canvas button in sequence-editing view, the Enter button does not start a new sequence but erases it
• [#5231](https://github.com/epam/ketcher/issues/5231) – Canvas should remain in edit mode if we insert monomer from the library
• + 28 more

✨ Additional notes:

• Ketcher 3.0 has been built and tested with Indigo version 1.28 ([standalone](https://www.npmjs.com/package/indigo-ketcher/v/1.28.0) and [remote](https://hub.docker.com/layers/epmlsop/indigo-service/1.28.0/images/sha256-5ac5b4e4b09cc8473ffa7690a412c3cae95bf144521449fac4b296c82b20d028)).
• [How to hide Macromolecules mode](https://github.com/epam/ketcher?tab=readme-ov-file#macromolecules-mode)

✨ New features

• [#5678](https://github.com/epam/ketcher/issues/5678) - Introduce creating antisense chains
• [#5925](https://github.com/epam/ketcher/issues/5925) - Layout for antisense chains in sequence mode
• [#5712](https://github.com/epam/ketcher/issues/5712) - Update snake layout logic taking into account hydrogen bonds
• [#5990](https://github.com/epam/ketcher/issues/5990) - Extend Ketcher API to allow updating monomers library
• [#5630](https://github.com/epam/ketcher/issues/5630) - Mark all modified monomers on canvas (flex and snake modes)
• [#5629](https://github.com/epam/ketcher/issues/5629) - Mark modified amino acids on canvas in sequence mode
• [#5854](https://github.com/epam/ketcher/issues/5854) - Add "Copy to Clipboard" to the export window
• [#5618](https://github.com/epam/ketcher/issues/5618) - Ketcher doesn't trigger change event in macromolecule mode
• + 2 more

🐛 Bugfixes and improvements

• [#5873](https://github.com/epam/ketcher/issues/5873) - Export to ket (and getKET function) change incrementally internal IDs every call
• [#5270](https://github.com/epam/ketcher/issues/5270) - Warning should not displayed for importing CDXML, base64 CDX
• [#5351](https://github.com/epam/ketcher/issues/5351) - Inform User to Apply Layout after Settings Adjustment
• [#5931](https://github.com/epam/ketcher/issues/5931) - Copy/Cut-Paste functionality not working for microstructures in Macro mode
• [#5982](https://github.com/epam/ketcher/issues/5982) - Label shift problem for ambiguous monomers
• [#5954](https://github.com/epam/ketcher/issues/5954) - The reaction with catalysts is displayed incorrect with ACS style setting and after layout
• [#4352](https://github.com/epam/ketcher/issues/4352) - Gap between button and drop-down list of Macro modes
• [#5855](https://github.com/epam/ketcher/issues/5855) - System reset micromolecule canvas settings to default if switched to Macro mode and back
• + 27 more

✨ New features

• #5354 – Apply new hash spacing setting to canvas
• #5579 – Introduce Hand tool for macromolecules mode
• #5590 – Zoom in macromolecules mode should be in relation to the top left corner of the structures
• #5403 – Introduce hydrogen bonds in macromolecules mode
• #5600 – Zoom in automatically upon import of small sequences
• #5637 – Display hydrogen in atom label for molecules in macromolecules mode
• #5556 – Allow import and export of sequences with three letter amino acid codes
• #5640 – Multiple monomers expansion in micro molecules mode
• + 2 more

🐛 Bugfixes and improvements

• #5370 – System should remember the canvas mode on Molecules/Macromolecules mode switch (do not switch to Sequernce by default)
• #5372 – Toggling between Flex and Sequence modes causes loosing layout info
• #5564 – Search of ambiguous monomers doesn't work
• #4475 – Numbers on top of letters are not centered
• #4936 – Applying Enhanced Stereochemistry to monomers causes its disappear from the canvas (and exception in console)
• #4941 – System shows Edit S-Group option for every bond of molecule if it has attachment point
• #5181 – getKet duplicates items when macro molecules are use
• #5398 – Elliptic arrow icons order is wrong at arrow toolbar
• + 10 more

✨ New features

• #5400 – Expand macromolecules in micro mode
• #5359 – Display molecules in macro mode: basic structures with atoms and bonds
• #5325 – Change natural analogue of monomers
• #5324 – Change symbols of monomers
• #5323 – Change names of monomers
• #5195 – Some content problems in monomer library
• #5111 – Change structure of monomers
• #4984 – Highlight atoms and bonds
• + 10 more

🐛 Bugfixes and improvements

• #5430 – Fix ESLint error in selectClearCanvasTool function
• #4983 – Settings for the "attachment point tool" don't update with changed pixel settings
• #4757 – Incorrect stereo-label placement for (E) and (Z)
• #5536 – White screen is displayed after change direction of wedge bond
• #5296 – Save Support for RDF Format
• #5615 – Overlapping UI elements in Query Properties right-click menu
• #4394 – In the Sequence mode, the tooltip “Start new sequence” is shown outside of the canvas
• #5651 – The reaction can't save to MDL RXN V3000 (returns RXN V2000 instead)
• + 50 more

✨ New features

• #4884 – Implement basic preview display for monomer bonds
• #4554 – Support ambiguous monomers in Ketcher (flex mode)
• #5186 – Add ambiguous monomers to the library and allow their addition to the canvas
• #4556 – Support of ambiguous monomers in sequence view
• #4557 – Support of ambiguous monomers in small molecules mode
• #4872 – New approach and UI for switching between types in sequence mode
• #4555 – Preview for ambiguous monomers
• #5224 – Implement basic preview in connection modal for ambiguous monomer
• + 8 more

🐛 Bugfixes and improvements

• #5200 – The users choice is not saved in the settings but is recalculated in px
• #4658 – Some bonds remain selected on export to SVG in Snake mode
• #5201 – it is not possible to enter a value when selecting cm inch pt manually in the settings
• #5454 – Export of variant monomers to Sequence/FASTA doesn't work for presets
• #5425 – Undo-Redo operations over ambiguous monomer causes broken canvas
• #5464 – Undo operation removes ambiguous monomer from the canvas but keep in the KET file export
• #5209 – Cancel of Edit Connection points dialog cause existed connection points eliminated
• #5453 – Circle with monomer number should be few pixels down
• + 13 more

✨ New features

• #4878 – Add/Replace monomer in sequence mode from library
• #4880 – Adjust previews – add APs, show IDT aliases for previews in sequence mode, increase debounce time
• #4888 – Enable editing sequences by click between symbols
• #4887 – Starting new sequences with "Plus" icon on canvas
• #4780 – Remove monomers from the library (Peptides and CHEMs)
• #5167 – Change natural analogue of monomers Peptides and CHEMs)
• #4787 – Change structure of monomers (Peptides and CHEMs)
• #5166 – Change symbols of monomers (Peptides and CHEMs)
• + 8 more

🐛 Bugfixes and improvements

• #4763 – It is possible to create forbidden RNA preset
• #4962 – Bond tool and Erase tool buttons have to be disabled in Sequence mode (since they are not applicable)
• #4659 – Export result SVG contains some labels that are selectable
• #4108 – There are no tooltips when hovering over each of the sequence modes
• #4806 – It is allowed to change bond type between micro and macro
• #4936 – Applying Enhanced Stereochemistry to monomers causes its disappear from the canvas (and exception in console)
• #5090 – The favorites icon overlaps unsplit nucleotide names in the RNA and favorites tab
• #4947 – Distance between unresolved monomer and preview tooltip is too large and it has no IDT alias
• + 13 more

✨ New features

• #4852 – UX support for HELM import/export
• #4846 – Make Sequence view default in Macromolecules mode
• #4431 – Implement support of unresolved IDT monomers
• #4382 – Implement support of unsplit nucleotides
• #3532 – Displaying side chain connections in snake-like mode
• #4856 – Add new CHEM monomers to the library
• #2654 – Improve WASM loading performance
• #5083 – Update indigo to 1.22.0 in browser module

🐛 Bugfixes and improvements

• #4660 – Zero charge shows explicit 0 instead of blank after using A+/A- Tools
• #4801 – Cut operation for attachment points makes canvas inaccessible/unoperational and delete entire molecule
• #4636 – In the Sequence mode, when selecting elements on the canvas, the total number of elements is not displayed in the Right-click menu
• #4686 – After moving the structure in the Macro mode, in the Micro mode the S-group value is displayed separately from the structure
• #4823 – In sequence mode, each press adds two characters and when deleted, also removes two
• #4793 – Context menu for attachment point labels should contain only Delete option
• #4784 – Attachment point enumeration logic works wrong
• #4786 – Keyboard shortcut stops working after adding/removing attachment point
• + 22 more

✨ New features

• #3934 – Support selection entity selection flag in KET format
• #4307 – Migrate Monomer library from MOL V2K to KET format
• #4388 – Allow Nucleoside of sequence edit in RNA builder
• #4427 – Store custom presets in browser local cache by
• #4495 – UI support for IDT import/export
• #4530 – Convert Rx connection points created in molecules mode into chem attachment points in macromolecules mode
• #4531 – Allow moving and connecting "small" structures in macro mode
• #4539 – Export macromolecules canvas as svg image
• + 8 more

🐛 Bugfixes and improvements

• #3943 – System allow to create atoms with Charge value out or range
• #3501 – 3d mol files appear as 2D in Miew
• #4349 – Selection does not work in sequence editing with Shift+Up/Down arrow combination
• #4508 – In the Text-editing mode, when selecting nucleotides linked through phosphates R2-R2, an error appears in the Console
• #4340 – When adding new nucleotides to the beginning of a row, the order of the chains changes in the Sequence mode
• #4470 – Any click on toolbar buttons should cause cancel of "Modify in RNA builder" process
• #4479 – Quick double paste operation from clipboard leads to invalid entities on canvas
• #4488 – System doesn't allow duplicate same preset twice
• + 27 more

✨ New features

• #3734 - Displaying modified nucleotide chains in sequence representation
• #3824 - Modify nucleotides from sequence in RNA builder
• #4374 - RNA builder should be highlighted in Edit mode. Canvas should be disabled
• #3894 - Paste from clipboard in sequence mode

🐛 Bugfixes and improvements

• #4238 - getKet function return ket file without selection flags
• #4174 - Buttons in paste from clipboard window change their position when zoomed more than 175 percent
• #4172 - 'leavingGroup' section does not contain information about number of atoms
• #4144 - Connection of bond to atom inside s-group supergroup cause it connected incorrectly in terms of layout
• #3986 - Selected RNA preset not discards when mouse moved
• #3957 - Atom Query feature export System lost MOST Substitution count values export to Molfile
• #4356 - Clear canvas button doesn't work in Sequence mode
• #4454 - 'Update sequence' modal window: don't close RNA-builder after pressing 'Cancel' in modal window.
• + 13 more

✨ New features

• #3650 - Remove and insert nucleotides in sequences (sequence representation)
• #3861 - Insertion mode for nucleotide entry (switch RNA/DNA/Peptide)
• #4146 - UI for Open/Save As FASTA
• #4109 - UI for Save As Sequence
• #3819 - Selection in sequence representation for view mode
• #3819 - Selection in sequence representation edit mode
• #3876 - Nucleotide preview in sequence representation

🐛 Bugfixes and improvements

• #3005 - Unable to 'undo' the paste action, if there is no reset to Select tool
• #3902 - If open a macro file and put in center of canvas in micro mode then switch to macro, structure is not in center of canvas*
• #3750 - Add search menu clear button
• #4173 - the pop-up window does not appear in fullscreen mode after clicking the “Open” button and the “Save as” button
• #4231 - Maximum call stack size exceeded error appears during snake layout for large chains
• #3663 - After clicking the 'Duplicate and Edit' button and subsequently clicking 'Cancel,' the preset remains saved.
• #4241 - Pasting large cyclodextrins structure cause Ketcher to freeze
• #4271 - The Uncaught TypeError appears in the DevTool Console, when scrolling until it stops, using the Shift+Left arrow, in the Text-editing mode
• + 11 more

✨ New features

• #3648 - Displaying unmodified nucleotide chains in sequence representation
• #3869 - Left-to-right ("Snake-like") layout for RNA
• #3870 - RNA layout change while switching from sequence to flex and snake modes
• #3728 - Add group selection for macromolecules
• #4519 - Macro: Add Pyrro and AspOH peptides to monomer library

🐛 Bugfixes and improvements

• #3827 - Add fixes in group selection for macromolecules
• #3736 - System marks availiable connection point as unavaliable in Select Connection Point dialog
• #2177 - library.svg file for templates does not seem to be used
• #3862 - UI modal window to open and save sequence format
• #4047 - System doesn't save selection state for atom wrapped into R-Group
• #3017 - Using setMolecule with molfile does not rescale bond lengths
• #3891 - Aromatize/Dearomatize of having abbreviation (Salts and Solvents) on the canvas causes spontaneous random de-abbreviation
• #3893 - Remove explicit hydrogens feature changes layout of simple molecules
• + 5 more

📋 What's Changed

• #2370 - erase tool for macromolecules editor
• #2367 - Ability to move items on the canvas
• #2994 - Attachment points should be within S-Group brackets
• #3229 - Run macromolecules e2e tests on ci
• #3276 - Remove 'Edit attachment point...' from right-click context menu
• #3230 - Support parsing KET file for macromolecules on ketcher side
• #3221 - add shortcut shift+tab for switching selection mode
• #3323 - Update schema.json for atom query specific properties
• + 66 more

📋 What's Changed

• #3582 - AP are shown after closing modal
• #3585 - APs are redrawn incorrectly after opening the modal window
• #3583 - selected AP is duplicated while drawing the bond
• #3551 - macro oxygen cannot be a leaving group in a chemical reaction
• #3553 - macro while pulling bond onto monomer a preview is shown when hover monomer
• #3610 - performance issues after selecting and moving large amount of monomers
• #2414 - fix for bonds creation broken after merge of undo/redo task.
• #3604 - macro preview window of micro structure shows pieces of macro structures
• + 75 more

📋 What's Changed

• #3203 - Structure shifting to upper left corner during zoom operations
• #2869 - Preview of monomer structures on canvas
• #3442 - Unused attachment points labels overlaps
• #3554 – Implicit hydrogens for aromatised structures containing Sulphur
• #3544 – option to disable custom query feature
• #3643 - Error appears in DevTool Console after call 'ketcher.setSettings' before templates initialization
• #3636 - Atom display changes to SMARTS notation when any of the Query Properties, such as Aromaticity, Ring membership, Ring size, or Connectivity, is selected.
• #3729 – When merging rings, they are added to canvas at a distorted angle
• + 29 more