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Standardizer History of Changes


January 16th, 2026: Standardizer 25.3.6

Bugfixes

  • Fixed custom standardizer configuration file (config.xml) handling in the Standardizer CLI


LTS Release November 28th: Standardizer - Radium 3 (25.2.3)

Bugfixes

  • Fixed an error for stereo handling with flipped structures in the transform schema where for the transform action


October 15th, 2025: Standardizer 25.3.4

Bugfixes

  • The actions "Transform sulfone" and "Transform sulfoxide" were mixed up in Standardizer. Now both actions return correct standardized structures.


August 26th, 2025: Standardizer 25.3.2

Bugfixes

  • Fixed an error for stereo handling with flipped structures in the transform schema where for the transform action


March 4th, 2025: Standardizer 25.1.0

Improvements

  • The Expand Stoichiometry action is improved. The Standardizer multiplied the structures based on the given stoichiometry data, but the components overlapped, so in 2D they were not visible.
  • Fixed inconsistent behavior with Aromatize Standardizer action in CLI
  • The default standardizer transformation for diazonium has been changed from [#6]-[#7:1]=[#7H2+:2]>>[#6][N+:1]#[N:2] to [#6:3]=[N+:1]=[#7-:2]>>[#6:3][N+:1]#[N:2].


LTS Release December 3rd: Standardizer - Platinum 2 (24.4.2)

Bugfixes

  • Fix for the 2D Clean Standardizer action to more precisely maintain the molecule dimensions of the resulting structures.


LTS Release November 29th: Standardizer - Osmium 4 (24.2.4)

Bugfixes

  • Fix for the 2D Clean Standardizer action to more precisely maintain the molecule dimensions of the resulting structures.
  • The default standardizer transformation for diazonium has been changed from [#6]-[#7:1]=[#7H2+:2]>>[#6][N+:1]#[N:2] to [#6:3]=[N+:1]=[#7-:2]>>[#6:3][N+:1]#[N:2].


November 8th, 2024: Standardizer 24.3.2

Bugfixes

  • Fix for the 2D Clean Standardizer action to more precisely maintain the molecule dimensions of the resulting structures.


October 14th, 2024: Standardizer 24.3.1

Improvements

  • Mac machines with ARM architecture can now run Standardizer faster (in case installed with bundled java)


Bugfixes

  • The default standardizer transformation for diazonium has been changed from [#6]-[#7:1]=[#7H2+:2]>>[#6][N+:1]#[N:2] to [#6:3]=[N+:1]=[#7-:2]>>[#6:3][N+:1]#[N:2].


LTS Release September 13th: Standardizer - Platinum 1 (24.4.1)

Bugfixes

  • The default standardizer transformation for diazonium has been changed from [#6]-[#7:1]=[#7H2+:2]>>[#6][N+:1]#[N:2] to [#6:3]=[N+:1]=[#7-:2]>>[#6:3][N+:1]#[N:2].


July 11th, 2024: Standardizer 24.3.0

Bugfixes

  • Improved handling of Markush features (e.g., repeating units) in the Transform standardizer transform action


June 12th, 2024: Standardizer 24.1.3

Bugfixes

  • Improved the handling of Markush features (e.g., repeating units) in the Standardizer Transform action.

LTS Release April 18th, 2024: Standardizer - Osmium 1 (24.2.1)

Bugfixes

  • Tetrahedral stereo information is no longer lost using the Transform action, when a neighbor atom is replaced

March 5th, 2024: Standardizer 24.1.1

Bugfixes

  • Tetrahedral stereo information is no longer lost using the Transform action, when a neighbor atom is replaced

February 19th, 2024: Standardizer 24.1.0

Improvements

  • Custom Transform action can now preserve local parity in cases where bonds next to the stereocenter are affected by the structure modification
  • New Rearrange Reaction action is introduced to clean reaction layouts without changing the components' internal coordinates

LTS Release February 2nd, 2024: Standardizer - Neon 2 (23.15.2)

No changes.

LTS Release January 26th, 2024: Standardizer - Mercury 4 (23.6.4)

No changes.

December 21st, 2023: Standardizer 23.17.0

No changes.

November 17th, 2023: Standardizer 23.16.0

Bugfixes

Standardizer did not lunch on Windows on version 23.14.0

LTS Release November 10th, 2023: Standardizer - Neon 1 (23.15.1)

No Changes.

October 18th, 2023: Standardizer 23.14.0

No changes.

October 6th, 2023: Standardizer 23.13.0

Bugfixes

  • "Ignore errors and continue with next molecule" option on the GUI did not work

August 21st, 2023: Standardizer 23.12.0

No changes.

July 20th, 2023: Standardizer 23.11.0

Bugfixes

  • Automapper ignored timout setting, which caused extremely long running times for certain complex reactions with high symmetry

July 5th, 2023: Standardizer 23.10.0

Improvements:

  • Bundled Java has been updated to Eclipse Adoptium OpenJDK 17.0.7+7

June 28th, 2023: Standardizer 23.9.0

Bugfixes

  • Standardizer was throwing ArrayOutOfBoundsException for certain custom Transform action configurations containing Position Variation bond or Link Node

May 24th, 2023: Standardizer 23.8.0

Improvements

  • New option for the Tautomerize action to generate canonical tautomers is exposed on the desktop UI

May 4th, 2023: Standardizer 23.7.0

Bugfixes

  • Wedge clean worked incorrectly in certain cases containing vicinal chiral centers in ring systems

April 5th, 2023: Standardizer 23.5.0

No changes.

March 10th, 2023: Standardizer 23.4.0

No changes.

February 23th, 2023: Standardizer 23.3.0

Improvements

  • Tautomerize standardizer action has parameter specifying if normal canonical tautomer or canonical tautomer is taken. Documentation

February 8th, 2023: Standardizer 23.2.0

Improvements

  • Improved chirality detection when converting to enhanced stereo.

January 25th, 2023: Standardizer 23.1.0

Improvements

  • Java 17 runtime compatibility is supported.

December 13th, 2022: Standardizer 22.22.0

No changes.

December 1st, 2022: Standardizer 22.21.0

No changes.

November 24th, 2022: Standardizer 22.20.0

Improvements

  • Works with Java 17 as well.

October 27th, 2022: Standardizer 22.19.0

Bugfixes

  • CVE-2022-42889 commons-text vulnerability has been fixed.

September 27h, 2022: Standardizer 22.18.0

Improvements

  • A new option has been added to enforce enhanced abs stereo notation on all unlabelled stereo centers, where applicable.

LTS Release - January 19th, 2023: Standardizer 22.17.4 (Lithium.4)

No changes.

LTS Release - November 29th, 2022: Standardizer 22.17.3 (Lithium.3)

No changes.

LTS Release - November 9th, 2022: Standardizer 22.17.2 (Lithium.2)

Bugfixes

  • CVE-2022-42889 commons-text vulnerability has been fixed.

LTS Release - October 19th, 2022: Standardizer 22.17.1 (Lithium.1)

No changes.

September 27h, 2022: Standardizer 22.18.0

  • No changes

September 8th, 2022: Standardizer 22.16.0

Bugfixes

  • Known issue The applied standardizer actions were not always given back correctly is fixed.

August 9th, 2022: Standardizer 22.15.0

Known issues

  • The applied standardizer actions were not always given back correctly.

August 3rd, 2022: Standardizer 22.14.0

Bugfixes

  • Non-applied standardizer actions were given back as applied ones in the case of molecules with Sgroups.

Known issues

  • The applied standardizer actions were not always given back correctly.

May 22nd, 2020: Standardizer 20.13.0

No changes

LTS Release - March 30th, 2020: 20.9.0 Standardizer (Fermium.1)

No changes

January 13th, 2020 Standardizer 20.1

Bugfixes

  • Charge is not protected using the Standardizer Tautomerize action
  • Preconfigured diazonium transformation causes incorrect structures

LTS Release - October 18th, 2019: 19.21.1 Standardizer (Europium.1)

No changes

October 7th, 2019, Standardizer 19.21.0

Bugfixes

  • HashMap creation in the constructor slowed down standardization and the map wasn't used in most of the use cases

September 2nd, 2019, Standardizer 19.19.0

Bugfixes

  • Cloning Clean2DAction will now create a proper clone of TemplateBasedClean

June 20th 2019, Standardizer 19.14

Bugfixes

  • NullPointerException is thrown for some D-substituted compounds during standardisation
  • Valence checking error causes normal canonical tautomer generation to fail during standardisation of some salt compounds

May 30th 2019, Standardizer 19.12.0

Bugfixes

  • Fixes for the normal canonical tautomer generation

May 3rd 2019, Standardizer 19.10.0

Bugfixes

  • False negative tautomer search hit for some molecules due to incorrect generic tautomer pairs

LTS Release - April 11th, 2019: 19.7.1 Standardizer (Deuterium.1)

No changes

April 8th 2019, Standardizer 19.9.0

Bugfixes

  • Incorrect generic tautomer pairs where generated during tautomer search for certain molecules

March 8th 2019, Standardizer 19.7.0

No changes

February 1st 2019, Standardizer 19.4.0

Bugfixes

  • Improved canonical tautomer generation

December 13th 2018, Standardizer 18.30.0

Bugfixes

  • Incorrect standardized forms of some ChemBL compounds and salts
  • Fixing some Exception in charge calculations during standardization

LTS Release - September 25th, 2018: 18.22.1 Standardizer (Carbon.1)

September 5th 2018, Standardizer 18.22.0

Bugfixes

  • Incorrect Exception is thrown when molecule with valence error is standardized

August 24th 2018, Standardizer 18.21.0

Bugfixes

  • Amine compounds lose stereo flags during tautomerization in standardization processes (in Standardizer)
  • H atom is added to the generated resonant structure of heterocyclic compounds during standardization (in Standardizer)
  • Incorrect standardized (normal canonical tautomer) forms of stereoisomers of sulphur compounds

August 1st, 2018: Standardizer 18.18.0

Bugfixes

  • De-aromatization of a large ring with N fails
  • Standardization (tautomerization) results of the same molecule coming from DB sources are different

February 13th, 2018: Standardizer 18.4.0

Bugfixes

  • Command Line Interface problem: Only the user interface can be started from command prompt.

December 5th, 2016: Standardizer 16.12.5

Bugfixes

  • Strip salts action can be applied to exact matches considering also the explicit H cases.

November 28th, 2016: Standardizer 16.11.28

Bugfixes

  • Strip salts action was changed to remove salts only in case of exact isotope matching.

July 25th, 2016: Standardizer 16.7.25

Bugfixes

  • Error in template based clean of reactions was fixed.

September 14th, 2015: Standardizer 15.9.14

Improvements

  • Standardizer command line application returns proper exit status code if Standardizer license is missing or is invalid.

June 22th, 2015: Standardizer 15.6.22

Bugfixes

  • Strip salts action doesn't remove all components from the molecule. It leaves at least one component, even if it is a salt defined in the salt dictionary.

May 11th, 2015: Standardizer 15.5.11

Bugfixes

  • Mixture brackets were removed when Transform action modified a structure inside the mixture brackets.

April 13th, 2015: Standardizer 15.4.13

Bugfixes

  • Ungroup S-groups action removed coordinate bonds from ferrocene.

February 2nd, 2015: Standardizer 15.2.2

Bugfixes

  • Bugfixes in * Clean 2D* action.

January 19th, 2015: Standardizer 15.1.19

Bugfixes

  • Clean 3D action did not work in Standardizer application and Standardizer command line application. Clean 3D did not work via API when final clean was invoked.

November 17th, 2014: Standardizer 14.11.17

Bugfixes

  • Clean 2D action options were not shown in Standardizer configuration editor.

November 10th, 2014: Standardizer 14.11.10

Bugfixes

  • Renaming Transform actions did not work in some cases. [error report]

August 4th, 2014: Standardizer 14.8.4

Bugfixes

  • Some standardizer actions ( Transform, Strip Salts, Remove Solvents ) required Structure Search license besides Standardizer license.

July 21th, 2014: Standardizer 14.7.21

New features and Improvements

  • Convert Wedge Interpretation standardizer action was removed from Standardizer. Remove it from all of your standardizer configurations.

July 7th, 2014: Standardizer 14.7.7

New features and Improvements

  • More convenient solvent removal with the new *Remove Solvents * action.

Bugfixes

  • Standardizer requires significantly less memory. Occasional out of memory errors were eliminated.
  • GUI layout fixes.

Please visit this page for History of changes relating older JChem versions.