Add release notes for Ketcher v3.5.0, v3.6.0 and v3.7.0 (#161)

Author: svvald

rst/download/ketcher.rst

@@ -7,7 +7,7 @@ Latest release
 .. toctree::
     :maxdepth: 1
 
-    ketcher/ketcher-3.4.0.rst
+    ketcher/ketcher-3.7.0.rst
 
 
 Older releases
@@ -16,6 +16,9 @@ Older releases
 .. toctree::
     :maxdepth: 1
 
+    ketcher/ketcher-3.6.0.rst
+    ketcher/ketcher-3.5.0.rst
+    ketcher/ketcher-3.4.0.rst
     ketcher/ketcher-3.3.0.rst
     ketcher/ketcher-3.2.0.rst
     ketcher/ketcher-3.1.0.rst

rst/download/ketcher/ketcher-3.5.0.rst

@@ -0,0 +1,24 @@
+Ketcher 3.5.0
+--------------
+
+Ketcher distributions
+^^^^^^^^^^^^^^^^^^^^^
+
+`Ketcher 3.5.0 standalone <https://lifescience.opensource.epam.com/downloads/ketcher/ketcher-v3.5.0/ketcher-standalone-3.5.0.zip>`__
+
+`Ketcher 3.5.0 remote <https://lifescience.opensource.epam.com/downloads/ketcher/ketcher-v3.5.0/ketcher-remote-3.5.0.zip>`__
+
+
+NPM packages
+^^^^^^^^^^^^
+
+| `ketcher-core <https://www.npmjs.com/package/ketcher-core/v/3.5.0>`__
+| `ketcher-react <https://www.npmjs.com/package/ketcher-react/v/3.5.0>`__
+| `ketcher-standalone <https://www.npmjs.com/package/ketcher-standalone/v/3.5.0>`__
+| `ketcher-macromolecules <https://www.npmjs.com/package/ketcher-macromolecules/v/3.5.0>`__
+
+
+Source code
+^^^^^^^^^^^
+
+`Source code on GitHub <https://github.com/epam/ketcher/releases/tag/v3.5.0>`__

rst/download/ketcher/ketcher-3.6.0.rst

@@ -0,0 +1,24 @@
+Ketcher 3.6.0
+--------------
+
+Ketcher distributions
+^^^^^^^^^^^^^^^^^^^^^
+
+`Ketcher 3.6.0 standalone <https://lifescience.opensource.epam.com/downloads/ketcher/ketcher-v3.6.0/ketcher-standalone-3.6.0.zip>`__
+
+`Ketcher 3.6.0 remote <https://lifescience.opensource.epam.com/downloads/ketcher/ketcher-v3.6.0/ketcher-remote-3.6.0.zip>`__
+
+
+NPM packages
+^^^^^^^^^^^^
+
+| `ketcher-core <https://www.npmjs.com/package/ketcher-core/v/3.6.0>`__
+| `ketcher-react <https://www.npmjs.com/package/ketcher-react/v/3.6.0>`__
+| `ketcher-standalone <https://www.npmjs.com/package/ketcher-standalone/v/3.6.0>`__
+| `ketcher-macromolecules <https://www.npmjs.com/package/ketcher-macromolecules/v/3.6.0>`__
+
+
+Source code
+^^^^^^^^^^^
+
+`Source code on GitHub <https://github.com/epam/ketcher/releases/tag/v3.6.0>`__

rst/download/ketcher/ketcher-3.7.0.rst

@@ -0,0 +1,24 @@
+Ketcher 3.7.0
+--------------
+
+Ketcher distributions
+^^^^^^^^^^^^^^^^^^^^^
+
+`Ketcher 3.7.0 standalone <https://lifescience.opensource.epam.com/downloads/ketcher/ketcher-v3.7.0/ketcher-standalone-3.7.0.zip>`__
+
+`Ketcher 3.7.0 remote <https://lifescience.opensource.epam.com/downloads/ketcher/ketcher-v3.7.0/ketcher-remote-3.7.0.zip>`__
+
+
+NPM packages
+^^^^^^^^^^^^
+
+| `ketcher-core <https://www.npmjs.com/package/ketcher-core/v/3.7.0>`__
+| `ketcher-react <https://www.npmjs.com/package/ketcher-react/v/3.7.0>`__
+| `ketcher-standalone <https://www.npmjs.com/package/ketcher-standalone/v/3.7.0>`__
+| `ketcher-macromolecules <https://www.npmjs.com/package/ketcher-macromolecules/v/3.7.0>`__
+
+
+Source code
+^^^^^^^^^^^
+
+`Source code on GitHub <https://github.com/epam/ketcher/releases/tag/v3.7.0>`__

rst/ketcher/demo/ketcher_remote.rst

@@ -1,4 +1,4 @@
-Ketcher 3.4.0 Remote
+Ketcher 3.7.0 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 3.4.0 Remote</a>
+   <a href="/KetcherDemo/index.html?api_path=/v2" target="_blank">Ketcher 3.7.0 Remote</a>
 
 

rst/ketcher/demo/ketcher_standalone.rst

@@ -1,4 +1,4 @@
-Ketcher 3.4.0 Standalone
+Ketcher 3.7.0 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 3.4.0 Standalone</a>
+   <a href="/KetcherDemoSA/index.html" target="_blank">Ketcher 3.7.0 Standalone</a>
 
 

rst/ketcher/release-notes/index.rst

@@ -50,3 +50,6 @@ Contents:
     ketcher-3.2.0
     ketcher-3.3.0
     ketcher-3.4.0
+    ketcher-3.5.0
+    ketcher-3.6.0
+    ketcher-3.7.0

rst/ketcher/release-notes/ketcher-3.5.0.md

@@ -0,0 +1,40 @@
+
+# Ketcher 3.5.0
+
+## What's Changed
+
+### New features
+- [#6738](https://github.com/epam/ketcher/issues/6738) – Ability to change the number of monomers in a line
+- [#5208](https://github.com/epam/ketcher/issues/5208) – Allow modifying amino acids on canvas
+- [#6995](https://github.com/epam/ketcher/issues/6995) – Smart positioning of CIP stereo labels for atoms
+- [#6852](https://github.com/epam/ketcher/issues/6852) – Improve the hydrophobicity graph in the "Calculate Properties" window
+- [#6589](https://github.com/epam/ketcher/issues/6589) – API lacks support for 3 letter code sequence export in macro mode
+- [#7070](https://github.com/epam/ketcher/issues/7070) – Include the removed versions of some 3D templates in the templates library in addition to the corrected ones
+- [#7224](https://github.com/epam/ketcher/issues/7224) – Migrate to Indigo v1.33.0 in-browser module
+
+### Bugfixes and improvements
+- [#7094](https://github.com/epam/ketcher/issues/7094) – Update the help document (3.4.)
+- [#6294](https://github.com/epam/ketcher/issues/6294) – Hiding toolbar buttons doesn't also hide disable the corresponding keyboard shortcut
+- [#6930](https://github.com/epam/ketcher/issues/6930) – Replace File comparison (for MOL files ONLY!) operations with valid helper function - verifyFileExport
+- [#7032](https://github.com/epam/ketcher/issues/7032) – Ketcher allows to make changes in sequence while being in nucleotide modification mode
+- [#5971](https://github.com/epam/ketcher/issues/5971) – Inconsistent selection sensitivity when highlighting sequences
+- [#7023](https://github.com/epam/ketcher/issues/7023) – Hydrophobicity section is missing tooltip icon and description
+- [#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
+- [#7031](https://github.com/epam/ketcher/issues/7031) – Layout shift when entering symbol in sequence mode upon first macromolecules mode initialization
+- [#6958](https://github.com/epam/ketcher/issues/6958) – Monomers positions are not preserved when pasting macromolecule in MOL format
+- [#7200](https://github.com/epam/ketcher/issues/7200) – App crashes after modifying amino acids and switching to Micro mode
+- [#7203](https://github.com/epam/ketcher/issues/7203) – N-methylation is shown as available for Hyp even though it shouldn't be
+- [#7142](https://github.com/epam/ketcher/issues/7142) – Monomer selection without bonds should work the same as with bonds
+- [#7251](https://github.com/epam/ketcher/issues/7251) – Incorrect tooltips for properties and logic for the hydrophobicity graph in the "Calculate properties" window
+- [#7130](https://github.com/epam/ketcher/issues/7130) – Incorrect calculation when part of a microstructure is selected - full structure is sent to Indigo
+- [#7150](https://github.com/epam/ketcher/issues/7150) – Molecule mass should be calculated for partial selected micromolecule (ketcher part)
+- [#7202](https://github.com/epam/ketcher/issues/7202) – Incorrect order of amino acid modification options in context menu
+- [#7281](https://github.com/epam/ketcher/issues/7281) – App crashes when closing Ketcher
+- [#6985](https://github.com/epam/ketcher/issues/6985) – Structure appears on incorrect canvas in molecules mode for several ketcher instances on same page
+- [#7288](https://github.com/epam/ketcher/issues/7288) – Monomers shifts out of visible area when adjusting layout with ruler in sequence edit mode
+- [#7318](https://github.com/epam/ketcher/issues/7318) – Bonds are overlapped by CIP labels when moving the structure or when the structure has small bond angles
+
+---
+
+### 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)).

rst/ketcher/release-notes/ketcher-3.6.0.md

@@ -0,0 +1,33 @@
+
+# Ketcher 3.6.0
+
+## What's Changed
+
+### New features
+- [#6404](https://github.com/epam/ketcher/issues/6404) – Drag and drop for the library elements in macromolecules mode
+- [#7164](https://github.com/epam/ketcher/issues/7164) – Introduce marking of nucleotide components
+- [#7125](https://github.com/epam/ketcher/issues/7125) – Support for reaction arrows and reaction pluses in macromolecules mode
+- [#7132](https://github.com/epam/ketcher/issues/7132) – Update and add icons to right-click drop-down menus in all modes
+- [#7347](https://github.com/epam/ketcher/issues/7347) – Migrate to Indigo v1.34.0 in-browser module
+
+### Bugfixes and improvements
+- [#7231](https://github.com/epam/ketcher/issues/7231) – Update the help document (3.5)
+- [#7073](https://github.com/epam/ketcher/issues/7073) – Unable to create hydrogen bond: Uncaught RangeError: Maximum call stack size exceeded
+- [#7178](https://github.com/epam/ketcher/issues/7178) – The tooltip appears behind the context menu options
+- [#7187](https://github.com/epam/ketcher/issues/7187) – IDT code shown wrong for SS3 chem
+- [#6410](https://github.com/epam/ketcher/issues/6410) – Incorrect bond attachment to micro molecules in Macro Mode
+- [#7277](https://github.com/epam/ketcher/issues/7277) – Cannot open multiple instance of Ketcher in one window
+- [#6986](https://github.com/epam/ketcher/issues/6986) – Context menu appears on both canvas in molecules mode for several Ketcher instances on same page
+- [#7207](https://github.com/epam/ketcher/issues/7207) – Rectangular input field should be wide enough to fit any (at least 4) digit number
+- [#7117](https://github.com/epam/ketcher/issues/7117) – Chemical elements disappear when attempting to Expand the Structure in Micro mode after selecting one in Macro mode
+- [#7170](https://github.com/epam/ketcher/issues/7170) – Monomer tooltip appears and remain in place even if mouse cursor moved away
+- [#7209](https://github.com/epam/ketcher/issues/7209) – The ruler is limited to 190 divisions
+- [#7365](https://github.com/epam/ketcher/issues/7365) – Console errors appear when using actions on structures with nucleotide component marking
+- [#7386](https://github.com/epam/ketcher/issues/7386) – Delete operation causes exception: Uncaught (in promise) Error: Minified Redux error
+- [#7432](https://github.com/epam/ketcher/issues/7432) – Security: form-data uses unsafe random function in form-data for choosing boundary
+- [#7371](https://github.com/epam/ketcher/issues/7371) – Mouse cursor doesn't positioned at the top left corner of preset
+
+---
+
+### 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)).

rst/ketcher/release-notes/ketcher-3.7.0.md

@@ -0,0 +1,67 @@
+
+# Ketcher 3.7.0
+
+## What's Changed
+
+### New features
+- [#6552](https://github.com/epam/ketcher/issues/6552) – Create a monomer from a selected part of the structure
+- [#6785](https://github.com/epam/ketcher/issues/6785) – Support aliases from HELM
+- [#3253](https://github.com/epam/ketcher/issues/3253) – Introduce the arrow button on library cards for easy monomer/preset addition to canvas
+- [#7430](https://github.com/epam/ketcher/issues/7430) – Adjust sgroup hover rendering to remove overlapping parts
+- [#6150](https://github.com/epam/ketcher/issues/6150) – Add the star atom to the special nodes section of the extended table
+- [#7535](https://github.com/epam/ketcher/issues/7535) – Add api for switching between macromolecules and molecules modes
+- [#7660](https://github.com/epam/ketcher/issues/7660) – Migrate to Indigo v1.35.0 in-browser module
+
+### Bugfixes and improvements
+- [#7377](https://github.com/epam/ketcher/issues/7377) – Update the help document (3.6.)
+- [#7351](https://github.com/epam/ketcher/issues/7351) – Profiling and optimization for many monomers on molecules canvas
+- [#6270](https://github.com/epam/ketcher/issues/6270) – Add "About" (i) and "Help" (?) buttons to the main toolbar in macromolecules mode
+- [#7222](https://github.com/epam/ketcher/issues/7222) – Incorrect leaving group atoms for expanded monomers
+- [#7168](https://github.com/epam/ketcher/issues/7168) – Opening the 3D Templates section in Structure Library causes multiple errors in the DevTools console
+- [#7252](https://github.com/epam/ketcher/issues/7252) – Integrate with SonarQube
+- [#7273](https://github.com/epam/ketcher/issues/7273) – System loads micro-macro connected structure on snake canvas and created understandable bond
+- [#7283](https://github.com/epam/ketcher/issues/7283) – Context menu is wrong if clicked on top of sequence
+- [#7205](https://github.com/epam/ketcher/issues/7205) – Layout shift when changing mode from sequence to flex and back upon first macromolecules mode initialization
+- [#7245](https://github.com/epam/ketcher/issues/7245) – Missing tooltip for standalone input field in ruler control
+- [#7440](https://github.com/epam/ketcher/issues/7440) – Area selection doesn't work till bond/atom reposition
+- [#7381](https://github.com/epam/ketcher/issues/7381) – Create documentation for 'change' event subscription
+- [#7152](https://github.com/epam/ketcher/issues/7152) – Copy keyboard shortcut works wrong for text content
+- [#7423](https://github.com/epam/ketcher/issues/7423) – It is possible to drag monomer from library and drop it to sequence canvas
+- [#7512](https://github.com/epam/ketcher/issues/7512) – Library doesn't fit view port in Sequence mode in Popup mode
+- [#7513](https://github.com/epam/ketcher/issues/7513) – "Ghost image" doesn't positioned below mouse cursor if dragged from Library to canvas in popup mode
+- [#7531](https://github.com/epam/ketcher/issues/7531) – Arrow icon appears in Sequence mode, violating requirement for Snake and Flex modes only
+- [#7538](https://github.com/epam/ketcher/issues/7538) – Unable to add ambiguous monomers via arrow button - no preview and errors in console
+- [#7539](https://github.com/epam/ketcher/issues/7539) – No tooltip shown and invalid attachment allowed when adding a monomer without R1 to selected monomer with free R2
+- [#7548](https://github.com/epam/ketcher/issues/7548) – Tooltip not shown and addition allowed when multiple monomers with free R2 are selected
+- [#7551](https://github.com/epam/ketcher/issues/7551) – Monomer drag-n-drop from Library to the canvas doesn't work for peptides it they were clicked on Sequence canvas
+- [#7562](https://github.com/epam/ketcher/issues/7562) – Tooltip overlaps monomers when hovering over arrow button on monomer card
+- [#7575](https://github.com/epam/ketcher/issues/7575) – Monomer creation wizard opens despite selection being connected via non simple bond
+- [#7576](https://github.com/epam/ketcher/issues/7576) – Create monomer wizard is available for structures containing S-groups, R-groups, or extended table atoms
+- [#7577](https://github.com/epam/ketcher/issues/7577) – "Create a monomer" button becomes active for disconnected structures
+- [#7563](https://github.com/epam/ketcher/issues/7563) – Selection after chain/monomer addition (autochain improvement)
+- [#7580](https://github.com/epam/ketcher/issues/7580) – Zoom actions in Monomer Wizard throw errors in the console
+- [#7601](https://github.com/epam/ketcher/issues/7601) – Wizard allows editing atoms and bonds via right-click menu without showing an error
+- [#7604](https://github.com/epam/ketcher/issues/7604) – Name, Symbol, Natural analogue input fields are not highlighted when left empty and Submit is clicked in Monomer Wizard
+- [#7606](https://github.com/epam/ketcher/issues/7606) – Pasting text into Symbol or Name fields in Monomer Wizard triggers unrelated "Convert error"
+- [#7607](https://github.com/epam/ketcher/issues/7607) – Missing S-group name in KET after saving a monomer via the wizard
+- [#7609](https://github.com/epam/ketcher/issues/7609) – Symbol uniqueness validation is missing in Monomer Wizard (no error, no highlight)
+- [#7612](https://github.com/epam/ketcher/issues/7612) – Natural analogue is not cleared when monomer type changes
+- [#7614](https://github.com/epam/ketcher/issues/7614) – After creating a monomer via wizard, switching to macro mode shows two separate entities instead of one
+- [#7615](https://github.com/epam/ketcher/issues/7615) – Phantom structure remains on canvas after closing wizard and is visible in exported files
+- [#7620](https://github.com/epam/ketcher/issues/7620) – Creating a monomer from a partial benzene selection causes console errors and no hover highlight on created region
+- [#7624](https://github.com/epam/ketcher/issues/7624) – Created Sugars and Phosphates via wizard are not added to Macro library
+- [#7625](https://github.com/epam/ketcher/issues/7625) – No validation against existing monomers - newly created monomer with duplicate name overwrites the existing one in the library
+- [#7627](https://github.com/epam/ketcher/issues/7627) – Selection tools stop working after creating first monomer via wizard when many structures are on canvas
+- [#7629](https://github.com/epam/ketcher/issues/7629) – API does not implement library change subscription
+- [#7684](https://github.com/epam/ketcher/issues/7684) – Only selected atoms connected with bonds should be taken into account on monomer creation
+- [#7714](https://github.com/epam/ketcher/issues/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](https://github.com/epam/ketcher/issues/7692) – System shouldn't allow to create monomer for molecules with R-Groups attachment points
+- [#7691](https://github.com/epam/ketcher/issues/7691) – System shouldn't allow to create monomer for molecules with R-Groups
+- [#7725](https://github.com/epam/ketcher/issues/7725) – Hand tool and Area Selection Tool buttons close Monomer creation wizard if pressed
+- [#7722](https://github.com/epam/ketcher/issues/7722) – Connection preview does not follow cursor and AP to AP connection is not possible
+- [#6581](https://github.com/epam/ketcher/issues/6581) – Monomer placement offset from cursor when Ketcher runs in a popup with increased browser zoom
+
+---
+
+### 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)).