Standardizer History of Changes

October 14th, 2024: Standardizer 24.3.1

Improvements

Macintosh 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]

Long Term Supported 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.

Long Term Supported 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

Long Term Supported Release February 2nd, 2024: Standardizer - Neon 2 (23.15.2)

No changes.

Long Term Supported 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

Long Term Supported 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

Partial 2D clean (Clean 2D action) did not work.
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.