Ketcher Web-based chemical structure drawing software

New features

Here’s the converted list with links added for each item:

• #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

Here’s the updated list with links added for each item:

• #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
• #7205 – Layout shift when changing mode from sequence to flex and back upon first macromolecules mode initialization
• #7245 – Missing tooltip for standalone input field in ruler control
• #7440 – Area selection doesn't work till bond/atom reposition
• #7381 – Create documentation for 'change' event subscription
• #7152 – Copy keyboard shortcut works wrong for text content
• #7423 – It is possible to drag monomer from library and drop it to sequence canvas
• #7512 – Library doesn't fit view port in Sequence mode in Popup mode
• #7513 – "Ghost image" doesn't position below mouse cursor if dragged from Library to canvas in popup mode
• #7531 – Arrow icon appears in Sequence mode, violating requirement for Snake and Flex modes only
• #7538 – Unable to add ambiguous monomers via arrow button - no preview and errors in console
• #7539 – No tooltip shown and invalid attachment allowed when adding a monomer without R1 to selected monomer with free R2
• #7548 – Tooltip not shown and addition allowed when multiple monomers with free R2 are selected
• #7551 – Monomer drag-n-drop from Library to the canvas doesn't work for peptides if they were clicked on Sequence canvas
• #7562 – Tooltip overlaps monomers when hovering over arrow button on monomer card
• #7575 – Monomer creation wizard opens despite selection being connected via non-simple bond
• #7576 – Create monomer wizard is available for structures containing S-groups, R-groups, or extended table atoms
• #7577 – "Create a monomer" button becomes active for disconnected structures
• #7563 – Selection after chain/monomer addition (autochain improvement)
• #7580 – Zoom actions in Monomer Wizard throw errors in the console
• #7601 – Wizard allows editing atoms and bonds via right-click menu without showing an error
• #7604 – Name, Symbol, Natural analogue input fields are not highlighted when left empty and Submit is clicked in Monomer Wizard
• #7606 – Pasting text into Symbol or Name fields in Monomer Wizard triggers unrelated "Convert error"
• #7607 – Missing S-group name in KET after saving a monomer via the wizard
• #7609 – Symbol uniqueness validation is missing in Monomer Wizard (no error, no highlight)
• #7612 – Natural analogue is not cleared when monomer type changes
• #7614 – After creating a monomer via wizard, switching to macro mode shows two separate entities instead of one
• #7615 – Phantom structure remains on canvas after closing wizard and is visible in exported files
• #7620 – Creating a monomer from a partial benzene selection causes console errors and no hover highlight on created region
• #7624 – Created Sugars and Phosphates via wizard are not added to Macro library
• #7625 – No validation against existing monomers - newly created monomer with duplicate name overwrites the existing one in the library
• #7627 – Selection tools stop working after creating first monomer via wizard when many structures are on canvas
• #7629 – API does not implement library change subscription
• #7684 – Only selected atoms connected with bonds should be taken into account on monomer creation
• #7714 – System shouldn't allow to create monomer for selected structure that have any non-simple single bonds to non-selected parts of the structure
• #7692 – System shouldn't allow to create monomer for molecules with R-Groups attachment points
• #7691 – System shouldn't allow to create monomer for molecules with R-Groups
• #7725 – Hand tool and Area Selection Tool buttons close Monomer creation wizard if pressed
• #7722 – Connection preview does not follow cursor and AP to AP connection is not possible
• #6581 – Monomer placement offset from cursor when Ketcher runs in a popup with increased browser zoom

Github link: https://github.com/epam/ketcher/releases/tag/v3.7.0

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 Here is the list converted into the desired Markdown format with links:

• #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 instances of Ketcher in one window
• #6986 – Context menu appears on both canvases in molecules mode for several Ketcher instances on the same page
• #7207 – Rectangular input field should be wide enough to fit any (at least 4) digit number
• #7117 – Chemical elements disappear when attempting to Expand the Structure in Micro mode after selecting one in Macro mode
• #7170 – Monomer tooltip appears and remains in place even if the mouse cursor moves away
• #7209 – The ruler is limited to 190 divisions
• #7365 – Console errors appear when using actions on structures with nucleotide component marking
• #7386 – Delete operation causes exception: Uncaught (in promise) Error: Minified Redux error
• #7432 – Security: form-data uses unsafe random function in form-data for choosing boundary
• #7371 – Mouse cursor doesn't position at the top left corner of the preset

Github link: https://github.com/epam/ketcher/releases/tag/v3.6.0

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

Here is the list converted to the desired Markdown format with links:

• #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
• #6958 – Monomers positions are not preserved when pasting macromolecule in MOL format
• #7200 – App crashes after modifying amino acids and switching to Micro mode
• #7203 – N-methylation is shown as available for Hyp even though it shouldn't be
• #7142 – Monomer selection without bonds should work the same as with bonds
• #7251 – Incorrect tooltips for properties and logic for the hydrophobicity graph in the "Calculate properties" window
• #7130 – Incorrect calculation when part of a microstructure is selected - full structure is sent to Indigo
• #7150 – Molecule mass should be calculated for partial selected micromolecule (ketcher part)
• #7202 – Incorrect order of amino acid modification options in context menu
• #7281 – App crashes when closing Ketcher
• #6985 – Structure appears on incorrect canvas in molecules mode for several ketcher instances on the same page
• #7288 – Monomers shift out of visible area when adjusting layout with ruler in sequence edit mode
• #7318 – Bonds are overlapped by CIP labels when moving the structure or when the structure has small bond angles

Github link: https://github.com/epam/ketcher/releases/tag/v3.5.0

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 switches 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
• #6788 – Reduce "Add new sequence" control width
• #7008 – Support of expanded monomer options doesn't work if monomer loaded from file/clipboard
• #7007 – Rotation doesn't work for expanded monomers on Molecules mode
• #5791 – It is possible to expand unknown nucleotide on micromolecules canvas
• #5789 – It is possible to expand ambiguous monomers on micromolecules canvas
• #7014 – No tooltip displayed for the “Calculate Properties” button in main toolbar
• #7019 – Data in “Calculate Properties” window disappears after switching browser tabs, selection remains
• #7030 – Missing Celsius symbol (°C) in “Melting temperature” label
• #7039 – App crashes when adding Ambiguous Amino Acids to peptide sequence with open Calculate Properties window
• #7015 – Alt+C / Option+C hotkey does not open the “Calculate Properties” window
• #7033 – calculateMacroProperties API is called immediately on sequence selection, even when Calculate Properties window is closed
• #7018 – Unable to clear monomer selection after switching browser tabs
• #7026 – Calculate properties for peptides are missing in case of mixed peptide and RNA/DNA chain
• #7017 – “Calculate Properties” shows wrong behavior when sequence is connected to microstructure
• #7062 – Rotation is incorrect upon exporting transformed monomer to SVG or PNG
• #7074 – Formula in "Calculate Properties" window is not updated when selecting monomers with connected microstructure
• #7034 – Unipositive ions default value is shown in nM instead of mM for double-stranded sequence selection
• #7085 – Ketcher does not send bond type to Indigo if connection is different from R2–R1, causing missing data in "Calculate Properties"
• #7027 – Incorrect highlight (missing fill) for leaving-group atoms
• #7028 – Turquoise monomer outline has incorrect gap for attachment points and blue outline too thin
• #7096 – Clearing canvas while "Calculate Properties" window is open causes console errors
• #6974 – System removes monomers from Molecules mode canvas is switched from Macro mode (bonds remain!) if Ketcher is in embedded mode (custom style iframe)
• #7118 – Cannot edit concentration values of unipositive ions and oligonucleotides in "Calculate Properties"
• #7249 – Input fields for ion concentration and oligonucleotides become inactive after clearing or entering zero
• #7266 – Oligonucleotides input field becomes unresponsive after entering zero

Github link: https://github.com/epam/ketcher/releases/tag/v3.4.0

New features

• #6508 – Update the logic for recognizing sense and antisense chains
• #6435 – Do not retain snake mode layout when passing through 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 right-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)
• #6987 – Migrate to Indigo v1.31.0 in-browser module

Bugfixes and improvements Here is the list you provided converted into the desired Markdown format with links:

• #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 chain selection (if not eligible for antisense chain selected)
• #6842 – Single click on already selected monomer causes monomer to stick to mouse cursor and snapping elements to 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)
• #6716 – Cursor can escape to the void after certain actions and break the canvas
• #6671 – Removing dash should turn aligned nucleotide to nucleoside
• #6541 – Undo of clear canvas operation causes molecules bonds to overlap atom labels
• #6712 – Adding RNA/DNA before empty space in sense sequence causes an exception and breaks the canvas
• #6776 – Phosphate does not appear immediately when added via keyboard in SYNC mode
• #6780 – Phosphate always added to sense strand in non-SYNC mode when targeting antisense strand
• #6781 – Phosphates added via keyboard in SYNC mode are not reverted by Undo and cause console errors on hover
• #6779 – Unable to add phosphate to antisense strand in SYNC mode via keyboard
• #6775 – Adding monomer to the first position from the left of antisense chain works wrong and causes exception: Uncaught TypeError: Cannot read properties of undefined (reading 'chain')
• #6863 – Horizontal/Vertical snap to distance doesn't work for hydrogen bonds
• #6814 – System should turn nucleotide to nucleoside on sequence break by Enter
• #6783 – Incorrect cursor jumps after phosphate insertion in the middle or at the end of the sequence
• #6824 – Unable to delete multiple sequences at once via right-click menu in Sequence mode
• #6705 – Antisense complement is not skipped when terminal monomer lacks an attachment point (R1/R2), causing incorrect structure on canvas
• #6833 – Tooltips on monomer cards in all sections instantly disappear on hover in popup Ketcher
• #6830 – RNA Builder section does not highlight the corresponding monomer in library on the first click
• #6828 – Star icon for Favorites tab in monomer library is too small compared to design specification
• #6831 – Last row of monomers in Sugars, Bases, and Phosphates sections is not visible in popup Ketcher
• #6834 – Clicking on base card in RNA Builder does not scroll to the selected base if multiple bases from the same section are selected
• #6816 – Incorrect hotkeys are displayed and triggered for RNA and DNA Antisense strand creation

Github link: https://github.com/epam/ketcher/releases/tag/v3.3.0

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
• #6596 – Update Indigo to 1.30.0 in browser module

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 allows to establish infinite 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
• #6535 – Unable to add nucleoside to the end of sequence if hanging antisense monomer present
• #6561 – Switching to macromolecules changes CSS in the page
• #6369 – System doesn't switch Library tab to proper one if user changes typing type using keyboard shortcuts
• #6627 – Fix invisible snapping drawings after switching to micro mode
• #6621 – Fix monomer snapping wiping monomer labels
• #6608 – API setMolecule moves molecule off-canvas on second call
• #6607 – README missing coordinate units for setMolecule and addFragment API methods
• #6539 – System should add same thing in antisense chain but not connect it with H-bond if it is not nucleotide/nucleoside
• #6624 – Enter key in single-strand edit mode incorrectly breaks both chains instead of only one
• #6632 – New sequence appears gray after clearing the canvas in non-sync mode
• #6631 – Sync mode causes incorrect letter input after adding a monomer in non-sync mode
• #6606 – Adding nucleotide to the last position having phosphate in antisense works wrong
• #6531 – System can't add nucleotide between phosphate and nucleotide in antisense chain
• #6617 – Empty element appears after undoing line deletion in Sequence mode and switching to Flex/Snake mode
• #6609 – System creates ambiguous RNA nucleotides instead of DNA ones in case of DNA antisense stand creation
• #6615 – Missing warning message when deleting all hydrogen bonds between two chains
• #6619 – System doesn't create antisense phosphate if it situated to the left from nucleotide
• #6623 – Sense and antisense chains switch places during editing based on monomer count
• #6443 – System allows to select single antisense symbol that causes an error if it got deleted
• #4002 – getSmiles and getSmarts on query feature containing aromatic ring raises an error
• #6709 – Unable to paste HELM from clipboard to the canvas. System throws an error: Convert error! option manager: Property "sequence-type" not defined
• #6723 – Forbid moving sequence nodes and snapping by select rectangle tool
• #6729 – Create RNA/DNA Strand doesn't work for B, K, Y and S ambiguous bases
• #6750 – Incorrect R1 attachment atom for natural Ribose (R) in the library
• #6759 – Add pruning of the remaining transient views on clear canvas button click
• #6795 – Incorrect properties of some monomers in the library
• #6829 – Add monomers to the library
• #6786 – Add monomers from HELM Core Library to Ketcher Library

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
• #6084 – System doesn't allow select ambiguous monomers from the library
• #6085 – Changing of ambiguous base via RNA Builder on Sequence mode causes sequence corruption
• #6098 – Adding second chain with antisense chain to the canvas cause layout problem
• #6446 – System shouldn't merge two antisense chains if separator monomer got deleted
• #6447 – System doesn't split chain pair on two if - symbol deleted
• #6460 – Troubles with switching to Edit mode if - symbol present in sequence
• #5780 – Connection points appear visually disconnected when moving monomers in Flex and Snake mode
• #6462 – Adding peptide between RNA and - symbol breaks sense/antisense chain
• #6456 – Long bond appears behind the structure after Copy-Paste in Flex Mode
• #6471 – Removing peptide from sense/antisense chain cause unnecessary phosphate removal
• #5780 – Connection points appear visually disconnected when moving monomers in Flex and Snake mode
• #6493 – Undo of deleted bond on sequence mode causes "ghost" monomer appearance on the canvas
• #6505 – Hotkey CTRL+ALT+P does not switch library to Peptides
• #6628 – Add export of ketcher-standalone esm module as cjs
• #6159 – Aromatizing doesn't work for Pyridone and Pyrone (molecules from Template library)
• #6588 – Peptide sequence not pasting directly on canvas
• #6661 – Adjust ketcher-standalone entrypoints to work for all builders

New features

• #6034 – Make macromolecules switcher enabled by default
• #6029 – Enter flex mode when macromolecules mode was not entered in before and there is a drawing on canvas
• #6027 – Support for single atom properties in macromolecules mode
• #6028 – Support all remaining types of bonds from small molecules mode in macro molecules mode
• #6227 – Update indigo to 1.28.0 in browser module

Bugfixes and improvements

• #5978 – Entire element bounding box should be clickable, not only black dots
• #6127 – Hover mouse over ambiguous monomer on Micromolecules canvas causes app crash
• #5476 – Copy/Cut and Paste using Ctrl+C/X and Ctrl+V doesn't work for static elements in Mozilla Firefox
• #5317 – Some side chain bonds are not shown in Sequence mode for bases, CHEMs, phosphates and sugars
• #5796 – Indigo functions doesn't work if monomer on micro canvas - system throws an error: Error: Cannot deserialize input JSON.
• #5032 – Selection of monomers should disappear when the user moves the cursor
• #5139 – After pressing the Clear Canvas button in sequence-editing view, the Enter button does not start a new sequence but erases it
• #5231 – Canvas should remain in edit mode if we insert monomer from the library
• #5795 – Undo operation doesn't work for monomer at micro mode if it was deleted - system throws exception in console
• #6112 – System opens "intellisence"-like dropdown control in unnecessary case
• #5663 – Movement of microstructures on Sequence mode doesn't work
• #4533 – After inserting a nucleotide in the Text-editing mode, the cursor blinks in the wrong place
• #6026 – Bond length is different for monomers loaded from HELM and from the library
• #4723 – When pressing Enter, a user can create new sequences in the “Modify RNA Builder” mode
• #6022 – Side chain attachment point shown in wrong place in Snake mode
• #5341 – Replacing all monomers (or part of them) in edit mode - works wrong - system cuts sequence on two
• #5670 – Structural distortion occurs during multi expand and multi collapse of macromolecule abbreviations in micro mode
• #6021 – Connection between molecule and monomer does not affect an amount of implicit hydrogens
• #5115 – Switching from Sequence mode to Flex mode and back shifts visible area of canvas beyond visible frame.
• #4526 – In the Text-editing mode, the canvas is not moved to make the newly added sequence visible
• #6240 – Export to 3-letter sequence doesn't work
• #6235 – Incorrect representation of hydrogens for alias charge valence and radical properties in macro mode
• #6034 – Combine two editors in ketcher-react package in order to make macro switcher enabled by default
• #6247 – Update the help document
• #3627 – Ketcher requires unsafe-eval in order to run, which contradicts content security policy best practices
• #6344 - Excessive scroll appears in macromolecules mode in canvas if Ketcher is inside dialog window
• #6291 - Super G and Super T monomers do not load from a saved RXN V3000 file
• #6370 - Inconsistent zoom behavior when inserting a molecule via setMolecule and Paste from Clipboard/Open from File
• #6375 - Ketcher renders editor twice in dev mode
• #6379 - Ketcher does not respond if switch to macromolecules, close popup with ketcher and open again
• #6411 - Ketcher structure copy-paste in KET instead of MOL
• #6196 - Ambiguous DNA bases (N, D, H, W) wrongly converted to DNA bases on antisense creation
• #6106 - Two sense chain to one antisense connection render
• #6272 - Cursor position after adding preset in sequence mode causes an incorrect sequence formation
• #6132 - System should not re-layout canvas in case of antisense creation