Update indigo to 1.35.0 #162

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Merged

AlexanderSavelyev merged 1 commit into master from indigo_1.35

Sep 19, 2025

rst/download/bingo.rst

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@@ Expand Up / @@ -15,7 +15,7 @@ Latest release @@
     .. toctree::
         :maxdepth: 1
-        bingo/bingo-1.34.0.rst
+        bingo/bingo-1.35.0.rst
     Older releases
@@ Expand All / @@ -24,6 +24,7 @@ Older releases @@
     .. toctree::
         :maxdepth: 1
+        bingo/bingo-1.34.0.rst
         bingo/bingo-1.33.0.rst
         bingo/bingo-1.32.0.rst
         bingo/bingo-1.31.0.rst
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rst/download/bingo/bingo-1.35.0.rst

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+    Bingo 1.35.0
+    ------------
+    The changelog is available `on this page <../../indigo/release-notes/indigo-1.35.0.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-1.35.0/bingo-oracle-linux-x86_64.zip>`__
+         - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.35.0/bingo-oracle-windows-msvc-x86_64.zip>`__
+         - binaries upon request.
+       * - PostgreSQL 17
+         - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.35.0/bingo-postgres-17-linux-x86_64.zip>`__
+         - \-
+         - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.35.0/bingo-postgres-17-macos-x86_64.zip>`__
+       * - PostgreSQL 16
+         - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.35.0/bingo-postgres-16-linux-x86_64.zip>`__
+         - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.35.0/bingo-postgres-16-windows-x86_64.zip>`__
+         - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.35.0/bingo-postgres-16-macos-x86_64.zip>`__
+       * - PostgreSQL 15
+         - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.35.0/bingo-postgres-15-linux-x86_64.zip>`__
+         - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.35.0/bingo-postgres-15-windows-x86_64.zip>`__
+         - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.35.0/bingo-postgres-15-macos-x86_64.zip>`__
+       * - PostgreSQL 14
+         - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.35.0/bingo-postgres-14-linux-x86_64.zip>`__
+         - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.35.0/bingo-postgres-14-windows-x86_64.zip>`__
+         - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.35.0/bingo-postgres-14-macos-x86_64.zip>`__
+       * - PostgreSQL 13
+         - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.35.0/bingo-postgres-13-linux-x86_64.zip>`__
+         - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.35.0/bingo-postgres-13-windows-x86_64.zip>`__
+         - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.35.0/bingo-postgres-13-macos-x86_64.zip>`__
+       * - Microsoft SQL Server
+         - \-
+         - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.35.0/bingo-sqlserver-windows-latest-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

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@@ Expand Up / @@ -15,14 +15,15 @@ Latest release @@
     .. toctree::
         :maxdepth: 1
-        indigo/indigo-1.34.0.rst
+        indigo/indigo-1.35.0.rst
     Older releases
     --------------
     .. toctree::
         :maxdepth: 1
+        indigo/indigo-1.34.0.rst
         indigo/indigo-1.33.0.rst
         indigo/indigo-1.32.0.rst
         indigo/indigo-1.31.0.rst
@@ Expand Down @@

rst/download/indigo/indigo-1.35.0.rst

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+    .. toctree::
+      :hidden:
+      :includehidden:
+      ../../indigo/release-notes/index.rst
+    Indigo 1.35.0
+    -------------
+    Language Bindings
+    ~~~~~~~~~~~~~~~~~
+    .. list-table::
+       :header-rows: 0
+       :stub-columns: 1
+       * - |p-icon| Python
+         - `indigo-python.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.35.0/indigo-python.zip>`__
+       * - |j-icon| Java
+         - `indigo-java.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.35.0/indigo-java.zip>`__
+       * - |c-icon| .NET
+         - `indigo-dotnet.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.35.0/indigo-dotnet.zip>`__
+       * - |n-icon| Native Libraries in one archive
+         - `indigo-native-shared-libs.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.35.0/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-1.35.0/indigo-libs-linux-x86_64.zip>`__
+         - `indigo-libs-windows-x86_64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.35.0/indigo-libs-windows-x86_64.zip>`__
+         - `indigo-libs-macos-x86_64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.35.0/indigo-libs-macos-x86_64.zip>`__
+       * -
+         -
+         - `indigo-libs-windows-mingw-x86_64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.35.0/indigo-libs-windows-mingw-x86_64.zip>`__
+         -
+       * - |n-icon| Native Libraries ARM64
+         - `indigo-libs-linux-aarch64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.35.0/indigo-libs-linux-aarch64.zip>`__
+         - \-
+         - `indigo-libs-macos-aarch64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.35.0/indigo-libs-macos-aarch64.zip>`__
+       * - |n-icon| Native Libraries i386
+         - \-
+         - `indigo-libs-windows-i386.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.35.0/indigo-libs-windows-i386.zip>`__
+         - \-
+       * - |n-icon| Utilities x64
+         - `indigo-utils-linux-x86_64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.35.0/indigo-utils-linux-x86_64.zip>`__
+         - `indigo-utils-windows-x86_64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.35.0/indigo-utils-windows-x86_64.zip>`__
+         - `indigo-utils-macos-x86_64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.35.0/indigo-utils-macos-x86_64.zip>`__
+    Source code
+    ~~~~~~~~~~~
+    `Source code zip <https://github.com/epam/Indigo/archive/indigo-1.35.0.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

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@@ Expand Up / @@ -7,6 +7,7 @@ Contents: @@
     .. toctree::
         :maxdepth: 2
+        indigo-1.35.0
         indigo-1.34.0
         indigo-1.33.0
         indigo-1.32.0
@@ Expand Down @@

rst/indigo/release-notes/indigo-1.35.0.md

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+    # Indigo 1.35.0
+    Released 2025-09-19
+    ## Features
+    * [2894](https://github.com/epam/Indigo/issues/2894) Saving expanded monomers into MOL-files
+    * Update monomer expand to follow Indigo structure
+    ## Bugfixes and improvements
+    * [2900](https://github.com/epam/Indigo/issues/2900) CIP labels are always rendered from cdxml
+    * [3012](https://github.com/epam/Indigo/issues/3012) Create IUPAC Compliant Chemical Formula
+    * [3050](https://github.com/epam/Indigo/issues/3050), [3047](https://github.com/epam/Indigo/issues/3047), [3048](https://github.com/epam/Indigo/issues/3048), [3054](https://github.com/epam/Indigo/issues/3054), [3051](https://github.com/epam/Indigo/issues/3051) Loading monomer chain from SDF file works wrong - bonds between monomers got lost/Export RNA monomers from MOLv3000 doesn't work for ACCLDraw export
+    * [2928](https://github.com/epam/Indigo/issues/2928) Isoelectric Point calculation should take into account occupied leaving groups (exclude them)
+    * [3053](https://github.com/epam/Indigo/issues/3053) Calculate properties doesn't work for "rich" sequences
+    * [3049](https://github.com/epam/Indigo/issues/3049) Stereo labels got missied on export to SVG result
+    * [3056](https://github.com/epam/Indigo/issues/3056) HELM load fails if it contains more than one instance of monomers with aliasHELM property
+    * [3045](https://github.com/epam/Indigo/issues/3045) Adding substituents to reactants breaks chemical property calculations
+    * [3061](https://github.com/epam/Indigo/issues/3061), [3062](https://github.com/epam/Indigo/issues/3062) System can't recognize single rebose or phosphate if loaded from HELM
+    * [3069](https://github.com/epam/Indigo/issues/3069) Export to RXN doesn't work, system throws exception: Error: memory access out of bounds
+    * [3094](https://github.com/epam/Indigo/issues/3094) Export of expanded CHEMs works wrong (system losts CHEM type)
+    **Full Changelog**: https://github.com/epam/Indigo/compare/indigo-1.33.0-rc.1...indigo-1.34.0

rst/newsfeed.rst

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         newsfeed
         release-notes/index
+    Indigo and Bingo 1.35.0 released
+    --------------------------------
+    *19 September 2025*
+    We are happy to announce that a new version 1.35.0 of Indigo toolkit and Bingo is released.
+    * |indigo_1_35_0_notes|
+    * |indigo_1_35_0_downloads|
+    * |bingo_1_35_0_downloads|
+    .. |indigo_1_35_0_notes| raw:: html
+       <a href="indigo/release-notes/indigo-1.35.0.html" target="_blank">Release Notes</a>
+    .. |indigo_1_35_0_downloads| raw:: html
+       <a href="download/indigo/indigo-1.35.0.html" target="_blank">Indigo Downloads</a>
+    .. |bingo_1_35_0_downloads| raw:: html
+       <a href="download/bingo/bingo-1.35.0.html" target="_blank">Bingo Downloads</a>
     Ketcher 3.7.0 released
     -----------------------
@@ Expand Down @@

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