Add release notes for Ketcher v3.3.0 and v3.4.0

rst/download/ketcher.rst

@@ -7,7 +7,7 @@ Latest release
 .. toctree::
     :maxdepth: 1
 
-    ketcher/ketcher-3.2.0.rst
+    ketcher/ketcher-3.4.0.rst
 
 
 Older releases
@@ -16,6 +16,8 @@ Older releases
 .. toctree::
     :maxdepth: 1
 
+    ketcher/ketcher-3.3.0.rst
+    ketcher/ketcher-3.2.0.rst
     ketcher/ketcher-3.1.0.rst
     ketcher/ketcher-3.0.0.rst
     ketcher/ketcher-2.28.0.rst

rst/download/ketcher/ketcher-3.3.0.rst

@@ -0,0 +1,24 @@
+Ketcher 3.3.0
+--------------
+
+Ketcher distributions
+^^^^^^^^^^^^^^^^^^^^^
+
+`Ketcher 3.3.0 standalone <https://lifescience.opensource.epam.com/downloads/ketcher/ketcher-v3.3.0/ketcher-standalone-3.3.0.zip>`__
+
+`Ketcher 3.3.0 remote <https://lifescience.opensource.epam.com/downloads/ketcher/ketcher-v3.3.0/ketcher-remote-3.3.0.zip>`__
+
+
+NPM packages
+^^^^^^^^^^^^
+
+| `ketcher-core <https://www.npmjs.com/package/ketcher-core/v/3.3.0>`__
+| `ketcher-react <https://www.npmjs.com/package/ketcher-react/v/3.3.0>`__
+| `ketcher-standalone <https://www.npmjs.com/package/ketcher-standalone/v/3.3.0>`__
+| `ketcher-macromolecules <https://www.npmjs.com/package/ketcher-macromolecules/v/3.3.0>`__
+
+
+Source code
+^^^^^^^^^^^
+
+`Source code on GitHub <https://github.com/epam/ketcher/releases/tag/v3.3.0>`__

rst/download/ketcher/ketcher-3.4.0.rst

@@ -0,0 +1,24 @@
+Ketcher 3.4.0
+--------------
+
+Ketcher distributions
+^^^^^^^^^^^^^^^^^^^^^
+
+`Ketcher 3.4.0 standalone <https://lifescience.opensource.epam.com/downloads/ketcher/ketcher-v3.4.0/ketcher-standalone-3.4.0.zip>`__
+
+`Ketcher 3.4.0 remote <https://lifescience.opensource.epam.com/downloads/ketcher/ketcher-v3.4.0/ketcher-remote-3.4.0.zip>`__
+
+
+NPM packages
+^^^^^^^^^^^^
+
+| `ketcher-core <https://www.npmjs.com/package/ketcher-core/v/3.4.0>`__
+| `ketcher-react <https://www.npmjs.com/package/ketcher-react/v/3.4.0>`__
+| `ketcher-standalone <https://www.npmjs.com/package/ketcher-standalone/v/3.4.0>`__
+| `ketcher-macromolecules <https://www.npmjs.com/package/ketcher-macromolecules/v/3.4.0>`__
+
+
+Source code
+^^^^^^^^^^^
+
+`Source code on GitHub <https://github.com/epam/ketcher/releases/tag/v3.4.0>`__

rst/index.rst

@@ -80,7 +80,7 @@ Cheminformatics
       performance, good portability and light weight. You will not need any
       Java or Flash plugins to use it in your browser. Ketcher is completely
       free and open-source, while also available on a commercial basis.
-   -  `Ketcher 2.0 demo <ketcher/demo.html>`__: Edit molecules online
+   -  `Ketcher demo <ketcher/demo.html>`__: Edit molecules online
 
 -  `Indigo Toolkit <indigo/index.html>`__ Universal cheminformatics
    toolkit and API |image3|

rst/ketcher/demo/ketcher_remote.rst

@@ -1,4 +1,4 @@
-Ketcher 3.2.0 Remote
+Ketcher 3.4.0 Remote
 =====================
 
 .. toctree::
@@ -10,6 +10,6 @@ Ketcher demo page was moved. Please use the following link
 
 .. raw:: html
 
-   <a href="/KetcherDemo/index.html?api_path=/v2" target="_blank">Ketcher 3.2.0 Remote</a>
+   <a href="/KetcherDemo/index.html?api_path=/v2" target="_blank">Ketcher 3.4.0 Remote</a>
 
 

rst/ketcher/demo/ketcher_standalone.rst

@@ -1,4 +1,4 @@
-Ketcher 3.2.0 Standalone
+Ketcher 3.4.0 Standalone
 =========================
 
 .. toctree::
@@ -11,6 +11,6 @@ Ketcher demo page was moved. Please use the following link
 
 .. raw:: html
 
-   <a href="/KetcherDemoSA/index.html" target="_blank">Ketcher 3.2.0 Standalone</a>
+   <a href="/KetcherDemoSA/index.html" target="_blank">Ketcher 3.4.0 Standalone</a>
 
 

rst/ketcher/release-notes/index.rst

@@ -48,3 +48,5 @@ Contents:
     ketcher-3.0.0
     ketcher-3.1.0
     ketcher-3.2.0
+    ketcher-3.3.0
+    ketcher-3.4.0

rst/ketcher/release-notes/ketcher-3.3.0.md

@@ -0,0 +1,49 @@
+
+# Ketcher 3.3.0
+
+## What's Changed
+
+### New features
+- [#6508](https://github.com/epam/ketcher/issues/6508) – Update the logic for recognizing sense and antisense chains
+- [#6435](https://github.com/epam/ketcher/issues/6435) – Do not retain snake mode layout when passing though snake mode
+- [#6519](https://github.com/epam/ketcher/issues/6519) – Implement the library redesign and modify the RNA builder behavior
+- [#6620](https://github.com/epam/ketcher/issues/6620) – Add salts to the "Salts and Solvents" tab in the monomer library
+- [#6472](https://github.com/epam/ketcher/issues/6472) – Add "Copy", "Paste", and "Delete" to the r-click drop down menu in sequence mode
+- [#5999](https://github.com/epam/ketcher/issues/5999) – Added "Create Antisense Strand" icon on the toolbar
+- [#6317](https://github.com/epam/ketcher/issues/6317) – Introducing the snap to distance functionality for monomers connected via bonds
+- [#6612](https://github.com/epam/ketcher/issues/6612) – Update the help documentation (3.2)
+- [#6987](https://github.com/epam/ketcher/issues/6987) – Migrate to Indigo v1.31.0 in-browser module
+
+### Bugfixes and improvements
+- [#6293](https://github.com/epam/ketcher/issues/6293) – Remove base monomer border after selection
+- [#6573](https://github.com/epam/ketcher/issues/6573) – Incorrect bond length and angle for non-natural monomers in the library
+- [#6695](https://github.com/epam/ketcher/issues/6695) – Unable to create antisense RNA/DNA chain in case of multiple сhain selection (if not eligible for antisense chain selected)
+- [#6842](https://github.com/epam/ketcher/issues/6842) – Single click on already selected monomer cause monomer sticks to mouse cursor and snapping elements appear on the canvas forever
+- [#6813](https://github.com/epam/ketcher/issues/6813) – Click on monomer selection area causes an exception Uncaught TypeError: Cannot read properties of undefined (reading 'drawingEntity')
+- [#6774](https://github.com/epam/ketcher/issues/6774) – Modified bases selected via RNA Builder revert to natural analogs in all modes
+- [#6495](https://github.com/epam/ketcher/issues/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](https://github.com/epam/ketcher/issues/6716) – Cursor can escape to the void after same actions and broke canvas
+- [#6671](https://github.com/epam/ketcher/issues/6671) – Removing dash should turn aligned nucleotide to nucleoside
+- [#6541](https://github.com/epam/ketcher/issues/6541) – Undo of clear canvas operation causes molecules bonds overlap atom labels
+- [#6712](https://github.com/epam/ketcher/issues/6712) – Adding RNA/DNA before empty space in sense sequence causes exception and broken canvas
+- [#6776](https://github.com/epam/ketcher/issues/6776) – Phosphate does not appear immediately when added via keyboard in SYNC mode
+- [#6780](https://github.com/epam/ketcher/issues/6780) – Phosphate always added to sense strand in non-SYNC mode when targeting antisense strand
+- [#6781](https://github.com/epam/ketcher/issues/6781) – Phosphates added via keyboard in SYNC mode are not reverted by Undo and cause console errors on hover
+- [#6779](https://github.com/epam/ketcher/issues/6779) – Unable to add phosphate to antisense strand in SYNC mode via keyboard
+- [#6775](https://github.com/epam/ketcher/issues/6775) – Adding monomer to first from the left position of antisense chain works wrong and causes exception: Uncaught TypeError: Cannot read properties of undefined (reading 'chain')
+- [#6863](https://github.com/epam/ketcher/issues/6863) – Horizontal/Vertical snap to distance doesn't work for hydrogen bonds
+- [#6814](https://github.com/epam/ketcher/issues/6814) – System should turn nucleotide to nucleoside on sequence break by Enter
+- [#6783](https://github.com/epam/ketcher/issues/6783) – Incorrect cursor jumps after phosphate insertion in middle or at end of sequence
+- [#6824](https://github.com/epam/ketcher/issues/6824) – Unable to delete multiple sequences at once via right-click menu in Sequence mode
+- [#6705](https://github.com/epam/ketcher/issues/6705) – Antisense complement is not skipped when terminal monomer lacks an attachment point (R1/R2), causing incorrect structure on canvas
+- [#6833](https://github.com/epam/ketcher/issues/6833) – Tooltips on monomer cards in all sections instantly disappear on hover in popup Ketcher
+- [#6830](https://github.com/epam/ketcher/issues/6830) – RNA Builder section do not highlight corresponding monomer in library on first click
+- [#6828](https://github.com/epam/ketcher/issues/6828) – Star icon for Favorites tab in monomer library is too small compared to design specification
+- [#6831](https://github.com/epam/ketcher/issues/6831) – Last row of monomers in Sugars, Bases, and Phosphates sections is not visible in popup Ketcher
+- [#6834](https://github.com/epam/ketcher/issues/6834) – Clicking on base card in RNA Builder does not scroll to selected base if multiple bases from the same section are selected
+- [#6816](https://github.com/epam/ketcher/issues/6816) – Incorrect hotkeys are displayed and triggered for RNA and DNA Antisense strand creation
+
+---
+
+### 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)).

rst/ketcher/release-notes/ketcher-3.4.0.md

@@ -0,0 +1,52 @@
+
+# Ketcher 3.4.0
+
+## What's Changed
+
+### New features
+- [#6832](https://github.com/epam/ketcher/issues/6832) – Update the help document 3.3
+- [#6625](https://github.com/epam/ketcher/issues/6625) – Support of expanded monomer option
+- [#6271](https://github.com/epam/ketcher/issues/6271) – Support for CIP stereo labels in macromolecules mode
+- [#5727](https://github.com/epam/ketcher/issues/5727) – Add "Calculate Properties" for macromolecules
+- [#5797](https://github.com/epam/ketcher/issues/5797) – Highlighting attachment point of expanded monomers on hover in micromolecules mode
+- [#7237](https://github.com/epam/ketcher/issues/7237) – Migrate to Indigo v1.32.0 in-browser module
+
+### Bugfixes and improvements
+- [#4838](https://github.com/epam/ketcher/issues/4838) – Incorrect structure for Phe-L-Phenylalanine in template library
+- [#5497](https://github.com/epam/ketcher/issues/5497) – Refactor (SnakeModePolymerBondRenderer): Create and use `SVGPathDAttributeUtil`
+- [#6288](https://github.com/epam/ketcher/issues/6288) – Incorrect numbering in sequence
+- [#6871](https://github.com/epam/ketcher/issues/6871) – Connection points become visible and broken if user switch window focus from one app to another and back
+- [#6870](https://github.com/epam/ketcher/issues/6870) – Enter key adds undeletable preset to preset section
+- [#4476](https://github.com/epam/ketcher/issues/4476) – Tooltips in sequence mode not disappear after right-click on letters
+- [#6762](https://github.com/epam/ketcher/issues/6762) – System shows natural analog monomer as modified if source mol file contains only 3-letters natural analog name
+- [#6791](https://github.com/epam/ketcher/issues/6791) – Change activation area of the New sequence button
+- [#6788](https://github.com/epam/ketcher/issues/6788) – Reduce "Add new sequence" control width
+- [#7008](https://github.com/epam/ketcher/issues/7008) – Support of expanded monomer options doesn't work if monomer loaded from file/clipboard
+- [#7007](https://github.com/epam/ketcher/issues/7007) – Rotation doesn't work for expanded monomers on Molecules mode
+- [#5791](https://github.com/epam/ketcher/issues/5791) – It is possible to expand unknown nucleotide on micromolecules canvas
+- [#5789](https://github.com/epam/ketcher/issues/5789) – It is possible to expand ambiguous monomers on micromolecules canvas
+- [#7014](https://github.com/epam/ketcher/issues/7014) – No tooltip displayed for the “Calculate Properties” button in main toolbar
+- [#7019](https://github.com/epam/ketcher/issues/7019) – Data in “Calculate Properties” window disappears after switching browser tabs, selection remains
+- [#7030](https://github.com/epam/ketcher/issues/7030) – Missing Celsius symbol (°C) in “Melting temperature” label
+- [#7039](https://github.com/epam/ketcher/issues/7039) – App crashes when adding Ambiguous Amino Acids to peptide sequence with open Calculate Properties window
+- [#7015](https://github.com/epam/ketcher/issues/7015) – Alt+C / Option+C hotkey does not open the “Calculate Properties” window
+- [#7033](https://github.com/epam/ketcher/issues/7033) – calculateMacroProperties API is called immediately on sequence selection, even when Calculate Properties window is closed
+- [#7018](https://github.com/epam/ketcher/issues/7018) – Unable to clear monomer selection after switching browser tabs
+- [#7026](https://github.com/epam/ketcher/issues/7026) – Calculate properties for peptides are missing in case of mixed peptide and RNA/DNA chain
+- [#7017](https://github.com/epam/ketcher/issues/7017) – “Calculate Properties” shows wrong behavior when sequence is connected to microstructure
+- [#7062](https://github.com/epam/ketcher/issues/7062) – Rotation is incorrect upon exporting transformed monomer to SVG or PNG
+- [#7074](https://github.com/epam/ketcher/issues/7074) – Formula in "Calculate Properties" window is not updated when selecting monomers with connected microstructure
+- [#7034](https://github.com/epam/ketcher/issues/7034) – Unipositive ions default value is shown in nM instead of mM for double-stranded sequence selection
+- [#7085](https://github.com/epam/ketcher/issues/7085) – Ketcher does not send bond type to Indigo if connection is different from R2–R1, causing missing data in "Calculate Properties"
+- [#7027](https://github.com/epam/ketcher/issues/7027) – Incorrect highlight (missing fill) for leaving-group atoms
+- [#7028](https://github.com/epam/ketcher/issues/7028) – Turquoise monomer outline has incorrect gap for attachment points and blue outline too thin
+- [#7096](https://github.com/epam/ketcher/issues/7096) – Clearing canvas while "Calculate Properties" window is open causes console errors
+- [#6974](https://github.com/epam/ketcher/issues/6974) – System removes monomers from Molecules mode canvas is switched from Macro mode (bonds remain!) if ketcher in embedded mode (custom style iframe)
+- [#7118](https://github.com/epam/ketcher/issues/7118) – Cannot edit concentration values of unipositive ions and oligonucleotides in Calculate Properties
+- [#7249](https://github.com/epam/ketcher/issues/7249) – Input fields for ion concentration and oligonucleotides become inactive after clearing or entering zero
+- [#7266](https://github.com/epam/ketcher/issues/7266) – Oligonucleotides input field becomes unresponsive after entering zero
+
+---
+
+### 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)).

rst/newsfeed.rst

@@ -7,6 +7,44 @@ News
     newsfeed
     release-notes/index
 
+Ketcher 3.4.0 released
+-----------------------
+
+*20 June 2025*
+
+We are glad to announce that a new stable version of Ketcher 3.4.0 is released.
+
+* |ketcher_3_4_0_notes|
+
+* |ketcher_3_4_0_downloads|
+
+.. |ketcher_3_4_0_notes| raw:: html
+
+   <a href="ketcher/release-notes/ketcher-3.4.0.html" target="_blank">Release Notes</a>
+
+.. |ketcher_3_4_0_downloads| raw:: html
+
+   <a href="download/ketcher.html" target="_blank">Downloads</a>
+
+Ketcher 3.3.0 released
+-----------------------
+
+*20 June 2025*
+
+We are glad to announce that a new stable version of Ketcher 3.3.0 is released.
+
+* |ketcher_3_3_0_notes|
+
+* |ketcher_3_3_0_downloads|
+
+.. |ketcher_3_3_0_notes| raw:: html
+
+   <a href="ketcher/release-notes/ketcher-3.3.0.html" target="_blank">Release Notes</a>
+
+.. |ketcher_3_3_0_downloads| raw:: html
+
+   <a href="download/ketcher.html" target="_blank">Downloads</a>
+
 Indigo and Bingo 1.32.0 released
 --------------------------------