bump indigo version to 1.16.0

rst/download/bingo.rst

@@ -15,7 +15,7 @@ Latest release
 .. toctree::
     :maxdepth: 1
 
-    bingo/bingo-1.16.0.rst
+    bingo/bingo-1.18.0.rst
 
 
 Older releases
@@ -24,6 +24,7 @@ Older releases
 .. toctree::
     :maxdepth: 1
 
+    bingo/bingo-1.16.0.rst
     bingo/bingo-1.14.0.rst
     bingo/bingo-1.13.0.rst
     bingo/bingo-1.12.0.rst

rst/download/bingo/bingo-1.18.0.rst

@@ -0,0 +1,49 @@
+Bingo 1.18.0
+------------
+
+The changelog is available `on this page <../../indigo/release-notes/indigo-1.18.0.html>`__
+
+.. list-table:: 
+   :header-rows: 1
+   :stub-columns: 1
+   :widths: 28 24 24 24
+
+   * - 
+     - |image0| Linux
+     - |image1| Windows
+     - |image2| Mac OS
+   * - Oracle
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.18.0/bingo-oracle-linux-x86_64.zip>`__
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.18.0/bingo-oracle-windows-x86_64.zip>`__
+     - binaries upon request.
+   * - PostgreSQL 15
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.18.0/bingo-postgres-15-linux-x86_64.zip>`__
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.18.0/bingo-postgres-15-windows-x86_64.zip>`__
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.18.0/bingo-postgres-15-macos-x86_64.zip>`__  
+   * - PostgreSQL 14
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.18.0/bingo-postgres-14-linux-x86_64.zip>`__
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.18.0/bingo-postgres-14-windows-x86_64.zip>`__
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.18.0/bingo-postgres-14-macos-x86_64.zip>`__  
+   * - PostgreSQL 13
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.18.0/bingo-postgres-13-linux-x86_64.zip>`__
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.18.0/bingo-postgres-13-windows-x86_64.zip>`__
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.18.0/bingo-postgres-13-macos-x86_64.zip>`__
+   * - PostgreSQL 12
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.18.0/bingo-postgres-12-linux-x86_64.zip>`__
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.18.0/bingo-postgres-12-windows-x86_64.zip>`__
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.18.0/bingo-postgres-12-macos-x86_64.zip>`__   
+   * - PostgreSQL 11
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.18.0/bingo-postgres-11-linux-x86_64.zip>`__
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.18.0/bingo-postgres-11-windows-x86_64.zip>`__
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.18.0/bingo-postgres-11-macos-x86_64.zip>`__   
+   * - Microsoft SQL Server
+     - \-
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.18.0/bingo-sqlserver-windows-x86_64.zip>`__
+     - \-
+
+`Source code on GitHub <http://github.com/epam/indigo>`__
+
+
+.. |image0| image:: ../../assets/Linux.png
+.. |image1| image:: ../../assets/Windows.png
+.. |image2| image:: ../../assets/AppleSZ.png

rst/download/indigo.rst

@@ -15,7 +15,7 @@ Latest release
 .. toctree::
     :maxdepth: 1
 
-    indigo/indigo-1.16.0.rst
+    indigo/indigo-1.18.0.rst
 
 
 Older releases
@@ -24,6 +24,7 @@ Older releases
 .. toctree::
     :maxdepth: 1
 
+    indigo/indigo-1.16.0.rst
     indigo/indigo-1.14.0.rst
     indigo/indigo-1.13.0.rst
     indigo/indigo-1.12.0.rst

rst/download/indigo/indigo-1.18.0.rst

@@ -0,0 +1,98 @@
+
+.. toctree::
+  :hidden:
+  :includehidden:
+
+  ../../indigo/release-notes/index.rst
+
+
+Indigo 1.18.0
+-------------
+
+Language Bindings
+~~~~~~~~~~~~~~~~~
+
+.. list-table:: 
+   :header-rows: 0
+   :stub-columns: 1
+
+   * - |p-icon| Python 
+     - `indigo-python.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.18.0/indigo-python.zip>`__
+   * - |j-icon| Java 
+     - `indigo-java.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.18.0/indigo-java.zip>`__
+   * - |c-icon| .NET 
+     - `indigo-dotnet.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.18.0/indigo-dotnet.zip>`__
+   * - |n-icon| Native Libraries in one archive
+     - `indigo-native-shared-libs.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.18.0/indigo-native-shared-libs.zip>`__
+
+
+Platform/CPU Bindings
+~~~~~~~~~~~~~~~~~~~~~
+
+.. list-table:: 
+   :header-rows: 1
+   :stub-columns: 1
+
+   * - 
+     - |image0| Linux
+     - |image1| Windows
+     - |image2| Mac OS
+   * - |n-icon| Native Libraries x64
+     - `indigo-libs-linux-x86_64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.18.0/indigo-libs-linux-x86_64.zip>`__
+     - `indigo-libs-windows-x86_64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.18.0/indigo-libs-windows-x86_64.zip>`__
+     - `indigo-libs-macos-x86_64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.18.0/indigo-libs-macos-x86_64.zip>`__
+   * - 
+     -
+     - `indigo-libs-windows-mingw-x86_64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.18.0/indigo-libs-windows-mingw-x86_64.zip>`__
+     -
+   * - |n-icon| Native Libraries ARM64
+     - `indigo-libs-linux-aarch64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.18.0/indigo-libs-linux-aarch64.zip>`__
+     - \-
+     - `indigo-libs-macos-aarch64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.18.0/indigo-libs-macos-aarch64.zip>`__
+   * - |n-icon| Native Libraries i386
+     - \-
+     - `indigo-libs-windows-i386.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.18.0/indigo-libs-windows-i386.zip>`__
+     - \-
+   * - |n-icon| Utilities x64
+     - `indigo-utils-linux-x86_64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.18.0/indigo-utils-linux-x86_64.zip>`__
+     - `indigo-utils-windows-x86_64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.18.0/indigo-utils-windows-x86_64.zip>`__
+     - `indigo-utils-macos-x86_64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.18.0/indigo-utils-macos-x86_64.zip>`__
+
+Source code
+~~~~~~~~~~~
+
+`Source code zip <https://github.com/epam/Indigo/archive/indigo-1.18.0.zip>`__
+
+`Repository on GitHub <https://github.com/epam/Indigo>`__
+
+
+NuGet Repository
+~~~~~~~~~~~~~~~~
+
+Indigo .NET packages available at `Nuget <https://www.nuget.org/packages/Indigo.Net/>`__
+
+Just add ``Indigo.Net`` as a dependency into the project.
+
+PyPi package
+~~~~~~~~~~~~
+
+Indigo Python SDK can be found at `PyPi <https://pypi.org/project/epam.indigo/>`__
+
+One can install the Indigo library using *pip* utility
+
+
+.. code-block:: xml
+
+    pip install epam.indigo
+
+
+
+.. |image0| image:: ../../assets/Linux.png
+.. |image1| image:: ../../assets/Windows.png
+.. |image2| image:: ../../assets/AppleSZ.png
+.. |image3| image:: ../../assets/globe.png
+.. |p-icon| image:: ../../assets/indigo/python-icon.png
+.. |j-icon| image:: ../../assets/indigo/java-icon.png
+.. |c-icon| image:: ../../assets/indigo/csharp-icon.png
+.. |n-icon| image:: ../../assets/indigo/native-icon.png
+.. |w-icon| image:: ../../assets/indigo/wasm-icon.png

rst/indigo/release-notes/index.rst

@@ -7,6 +7,7 @@ Contents:
 .. toctree::
     :maxdepth: 2
 
+    indigo-1.18.0
     indigo-1.16.0
     indigo-1.14.0
     indigo-1.13.0

rst/indigo/release-notes/indigo-1.18.0.md

@@ -0,0 +1,63 @@
+# Indigo 1.18.0
+Released 2024-02-29
+
+## Features
+* [#1412](https://github.com/epam/Indigo/issues/1412) Nucleotide splitting for V3000 molfile SCSR  
+* [#1450](https://github.com/epam/Indigo/issues/1450) No naturalAnalogShort in KET for basic aminoacids during conversion MOLV3000 -> KET 
+* [#1436](https://github.com/epam/Indigo/issues/1436) Expose Fold/Unfold hydrogens function in indigo API
+* [#1440](https://github.com/epam/Indigo/issues/1440) Add support for query features in MOL, SDF and RXN formats (Marvin extension)
+* [#1426](https://github.com/epam/Indigo/issues/1426) Import sequence format for RNA, DNA and PEPTIDES 
+* [#1589](https://github.com/epam/Indigo/issues/1589) Apply hydrogens folding/unfolding with respect to selected atoms 
+## Bugs
+* [#1307](https://github.com/epam/Indigo/issues/1307) Error in DevTool console about memory access out of bound when call 'ketcher.getRxn()' 
+* [#1431](https://github.com/epam/Indigo/issues/1431) Crash during parsing query mol-file
+* [#1439](https://github.com/epam/Indigo/issues/1439) Indigo can't parse KET with R-Site as a leaving group 
+* [#1232](https://github.com/epam/Indigo/issues/1232) Multi-line reaction cause access violationg exception.
+* [#1423](https://github.com/epam/Indigo/issues/1423) Common atoms loaded as aliphatic in SMARTS mode
+* Update bug_report.md
+* [#1458](https://github.com/epam/Indigo/issues/1458) Failed UT api\indigo_test.py:test_convert_smarts 
+* [#1460](https://github.com/epam/Indigo/issues/1460) ImplicitH set to zero casue error loading query molecule from ket 
+* [#1446](https://github.com/epam/Indigo/issues/1446) Dearomatization does not work with query features
+* PostgreSQL 11 EOL support 
+* [#1465](https://github.com/epam/Indigo/issues/1465) Unable to load specific mol-file
+* [#1484](https://github.com/epam/Indigo/issues/1484) Query molecule convert implicit/explicit hydrogens cause error 
+* [#1512](https://github.com/epam/Indigo/issues/1512) Broken string-formats support for wasm 
+* [#1452](https://github.com/epam/Indigo/issues/1452) Convert from implicit hydrogens change layout 
+* [#1463](https://github.com/epam/Indigo/issues/1463) Macro: Some molecules are not perfect on preview tooltip 
+* [#1524](https://github.com/epam/Indigo/issues/1524) Dearomatizing doesn't work for molecula with custom query fetures 
+* [#1568](https://github.com/epam/Indigo/issues/1568) Wrong molecule nodes enumeration in KET-file 
+* [#1476](https://github.com/epam/Indigo/issues/1476) Aromatization/Dearomatization wipes out SOME Ring bond count values 
+* [#1478](https://github.com/epam/Indigo/issues/1478) Dearomatization causes exception in case of Implicit H count query feature set to 4 (i.e. more than 2) 
+* [#1525](https://github.com/epam/Indigo/issues/1525) System attach two explicit hydrogens to aromatized ring 
+* [#1573](https://github.com/epam/Indigo/issues/1573) Add/Remove explicit hydrogens can't be applied to fullerene C60 - system throws exception 
+* [#1567](https://github.com/epam/Indigo/issues/1567) System can't copy atom with custom query feature to clipboard 
+* [#1534](https://github.com/epam/Indigo/issues/1534) Presence of stand alone H2 molecule on the canvas breaks Add explicit hydrogens feature (it stops working) 
+* [#1468](https://github.com/epam/Indigo/issues/1468) Valence lost on loading molfile with MRV extension.
+* [#1472](https://github.com/epam/Indigo/issues/1472) Dearomatization wipes out Aromaticity query property
+* [#1504](https://github.com/epam/Indigo/issues/1504) Molfile MRV extension generated for "H count"
+* [#1500](https://github.com/epam/Indigo/issues/1500) Atom Query feature export: System replace "Ring membership" values with "Ring Bond Count" ones for value 0 - export to SDF V2000 file 
+* [#1564](https://github.com/epam/Indigo/issues/1564) Add/Remove explicit hydrogens wanishes "Chirality" value 
+* [#1598](https://github.com/epam/Indigo/issues/1598) Macro: V3000 export: leaving groups are displayed as side chain connections for standard presets added to canvas 
+* [#1533](https://github.com/epam/Indigo/issues/1533) System attach two explicit hydrogens to atoms connected to "any type" bonds 
+* [#1608](https://github.com/epam/Indigo/issues/1608) convert_explicit_hydrogens response doesn't comply with the ket schema 
+* [#1538](https://github.com/epam/Indigo/issues/1538) Add/Remove explicit hydrogens feature doesn't work if atom with problem valence present on canvas (crash happens) 
+* [#1614](https://github.com/epam/Indigo/issues/1614) Adding hydrogens doesn't work for bonds with No center value of Reacting Center 
+* [#1550](https://github.com/epam/Indigo/issues/1550) Add/Remove explicit hydrogens feature doesn't work for "Any Atom" molecule with valence value set
+* [#1593](https://github.com/epam/Indigo/issues/1593) Macro: V3000 import: removed 5' phosphate is displayed in Ketcher
+* [#1483](https://github.com/epam/Indigo/issues/1483) Unable to past empty reaction (arrow only) from clipboard to canvas
+* [#1607](https://github.com/epam/Indigo/issues/1607) Unable to load large base64 CDX content to canvas if remote indigo used`
+* [#1536](https://github.com/epam/Indigo/issues/1536) Add/Remove explicit hydrogens feature doesn't work for reactions on canvas (crash happens)
+* [#1652](https://github.com/epam/Indigo/issues/1652) Unfold hydrogens does not select added bonds 
+* [#1640](https://github.com/epam/Indigo/issues/1640) System adds hydrogens for only one atom among many selected by 
+* [#1634](https://github.com/epam/Indigo/issues/1634) Add/Remove hydrogens doesn't work for atoms with Radical=Triplete if atom with query feature present on the canvas
+* [#1629](https://github.com/epam/Indigo/issues/1629) Add/Rmove hydrogens process should count R-Group attachment point as hydrogen
+* [#1695](https://github.com/epam/Indigo/issues/1695) CDX loader failed if object with zero id follow by reaction 
+* [#1697](https://github.com/epam/Indigo/issues/1697) CDX loader crashed on some files with abbreviations by 
+* [#1684](https://github.com/epam/Indigo/issues/1684) System put on the canvas two arrows (one above other) per each arrow on target CDX 
+* [#1724](https://github.com/epam/Indigo/issues/1724) Fold hydrogen in reaction with selection works wrong by 
+* [#1730](https://github.com/epam/Indigo/issues/1730) UT cano/permutations is too slow by 
+* [#1576](https://github.com/epam/Indigo/issues/1576) Bad molecule layout after adding hydrogens (Chlorophyll A) 
+* [#1685](https://github.com/epam/Indigo/issues/1685) System shows attached abbreviation group in wrong position 
+
+**Full Changelog**: https://github.com/epam/Indigo/compare/indigo-1.16.0...indigo-1.18.0
+

rst/newsfeed.rst

@@ -7,12 +7,37 @@ News
     newsfeed
     release-notes/index
 
+Indigo and Bingo 1.18.0 released
+--------------------------------
+
+*29 February 2024*
+
+We are happy to announce that a new version 1.18.0 of Indigo toolkit and Bingo is released.
+
+* |indigo_1_18_0_notes|
+
+* |indigo_1_18_0_downloads|
+
+* |bingo_1_18_0_downloads|
+
+.. |indigo_1_18_0_notes| raw:: html
+
+   <a href="indigo/release-notes/indigo-1.18.0.html" target="_blank">Release Notes</a>
+
+.. |indigo_1_18_0_downloads| raw:: html
+
+   <a href="download/indigo/indigo-1.18.0.html" target="_blank">Indigo Downloads</a>
+
+.. |bingo_1_18_0_downloads| raw:: html
+
+   <a href="download/bingo/bingo-1.18.0.html" target="_blank">Bingo Downloads</a>
+
 Indigo and Bingo 1.16.0 released
 --------------------------------
 
 *30 January 2024*
 
-We are happy to announce that a new version 1.14.0 of Indigo toolkit and Bingo is released.
+We are happy to announce that a new version 1.16.0 of Indigo toolkit and Bingo is released.
 
 * |indigo_1_16_0_notes|