From e30dcddbf06df1caa64a4fd9e90e518944a9859c Mon Sep 17 00:00:00 2001 From: Nikita Chistousov Date: Fri, 20 Jun 2025 17:53:14 +0200 Subject: [PATCH 1/2] Add release notes for Ketcher v3.3.0 and v3.4.0 --- rst/download/ketcher.rst | 4 +- rst/download/ketcher/ketcher-3.3.0.rst | 24 ++++++++++ rst/download/ketcher/ketcher-3.4.0.rst | 24 ++++++++++ rst/ketcher/demo/ketcher_remote.rst | 4 +- rst/ketcher/demo/ketcher_standalone.rst | 4 +- rst/ketcher/release-notes/index.rst | 2 + rst/ketcher/release-notes/ketcher-3.3.0.md | 49 ++++++++++++++++++++ rst/ketcher/release-notes/ketcher-3.4.0.md | 52 ++++++++++++++++++++++ rst/newsfeed.rst | 38 ++++++++++++++++ 9 files changed, 196 insertions(+), 5 deletions(-) create mode 100644 rst/download/ketcher/ketcher-3.3.0.rst create mode 100644 rst/download/ketcher/ketcher-3.4.0.rst create mode 100644 rst/ketcher/release-notes/ketcher-3.3.0.md create mode 100644 rst/ketcher/release-notes/ketcher-3.4.0.md diff --git a/rst/download/ketcher.rst b/rst/download/ketcher.rst index ecb0969..e9b6899 100644 --- a/rst/download/ketcher.rst +++ b/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 diff --git a/rst/download/ketcher/ketcher-3.3.0.rst b/rst/download/ketcher/ketcher-3.3.0.rst new file mode 100644 index 0000000..6a74b40 --- /dev/null +++ b/rst/download/ketcher/ketcher-3.3.0.rst @@ -0,0 +1,24 @@ +Ketcher 3.3.0 +-------------- + +Ketcher distributions +^^^^^^^^^^^^^^^^^^^^^ + +`Ketcher 3.3.0 standalone `__ + +`Ketcher 3.3.0 remote `__ + + +NPM packages +^^^^^^^^^^^^ + +| `ketcher-core `__ +| `ketcher-react `__ +| `ketcher-standalone `__ +| `ketcher-macromolecules `__ + + +Source code +^^^^^^^^^^^ + +`Source code on GitHub `__ diff --git a/rst/download/ketcher/ketcher-3.4.0.rst b/rst/download/ketcher/ketcher-3.4.0.rst new file mode 100644 index 0000000..4a39119 --- /dev/null +++ b/rst/download/ketcher/ketcher-3.4.0.rst @@ -0,0 +1,24 @@ +Ketcher 3.4.0 +-------------- + +Ketcher distributions +^^^^^^^^^^^^^^^^^^^^^ + +`Ketcher 3.4.0 standalone `__ + +`Ketcher 3.4.0 remote `__ + + +NPM packages +^^^^^^^^^^^^ + +| `ketcher-core `__ +| `ketcher-react `__ +| `ketcher-standalone `__ +| `ketcher-macromolecules `__ + + +Source code +^^^^^^^^^^^ + +`Source code on GitHub `__ diff --git a/rst/ketcher/demo/ketcher_remote.rst b/rst/ketcher/demo/ketcher_remote.rst index 8ff8d7e..bdb45ba 100644 --- a/rst/ketcher/demo/ketcher_remote.rst +++ b/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 - Ketcher 3.2.0 Remote + Ketcher 3.4.0 Remote diff --git a/rst/ketcher/demo/ketcher_standalone.rst b/rst/ketcher/demo/ketcher_standalone.rst index ebfad90..afa8cf0 100644 --- a/rst/ketcher/demo/ketcher_standalone.rst +++ b/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 - Ketcher 3.2.0 Standalone + Ketcher 3.4.0 Standalone diff --git a/rst/ketcher/release-notes/index.rst b/rst/ketcher/release-notes/index.rst index 88d59f0..8cfbe8a 100644 --- a/rst/ketcher/release-notes/index.rst +++ b/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 diff --git a/rst/ketcher/release-notes/ketcher-3.3.0.md b/rst/ketcher/release-notes/ketcher-3.3.0.md new file mode 100644 index 0000000..cd107d8 --- /dev/null +++ b/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)). diff --git a/rst/ketcher/release-notes/ketcher-3.4.0.md b/rst/ketcher/release-notes/ketcher-3.4.0.md new file mode 100644 index 0000000..d5feb23 --- /dev/null +++ b/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)). diff --git a/rst/newsfeed.rst b/rst/newsfeed.rst index 35e732c..0f3f69b 100644 --- a/rst/newsfeed.rst +++ b/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 + + Release Notes + +.. |ketcher_3_4_0_downloads| raw:: html + + Downloads + +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 + + Release Notes + +.. |ketcher_3_3_0_downloads| raw:: html + + Downloads + Indigo and Bingo 1.32.0 released -------------------------------- From 0045ff80a6f6d40e4167af4ec748d5b82656e190 Mon Sep 17 00:00:00 2001 From: Nikita Chistousov Date: Fri, 20 Jun 2025 18:32:50 +0200 Subject: [PATCH 2/2] Remove Ketcher version from demo link --- rst/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/rst/index.rst b/rst/index.rst index 7ebe972..dd84de2 100644 --- a/rst/index.rst +++ b/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 `__: Edit molecules online + - `Ketcher demo `__: Edit molecules online - `Indigo Toolkit `__ Universal cheminformatics toolkit and API |image3|