Structure Checker History of Changes

November 20^th, 2025: Structure Checker 25.3.5

Bugfixes

• All original formatting and non-chemical objects are now preserved after structure checking for CDXML input files

October 15^th, 2025: Structure Checker 25.3.4

Bugfixes

• Remove z coordinate fixer now correctly converts structures to 2D

• Metallocene fixer adds now adds coordinate bonds in the correct direction

Long Term Supported Release July 14^th: Structure Checker - Radium 2 (25.2.2)

Bugfixes

• Non stereo wedge bond checker reported false errors on defined stereo centers of large molecules

June 3^rd, 2025: Structure Checker 25.1.4

Bugfixes

• Non stereo wedge bond checker reported false errors on defined stereo centers of large molecules

April 24^th, 2025: Structure Checker 25.1.3

Bugfixes

• The Valence checker did indicate false errors and missed others on structures with aromatic nitrogens. The behavior was further updated following the cahnges of version 25.1.0

March 4^th, 2025: Structure Checker 25.1.0

Improvements

• The Abbreviated Group Structure Checker exclusion list now handles the different abbreviations for the same structure.

For example, excluding OAc will also exclude AcO.

• False valence error was detected for some compounds in which a nitrogen atom was included in two condensed aromatic rings.

• Non-stereo Wedge Bond checker reported error on some structures having r/s labels. Ring tetrahedral centers with 180-degree bonds were flagged as errors.

• Structure checker did not detect some valence errors in reactions and Markush structures.

Long Term Supported Release December 3^rd: Structure Checker - Platinum 2 (24.4.2)

Bugfixes

• False valence error was detected for some compounds in which a nitrogen atom was included in two condensed aromatic rings.

• The Abbreviated Group Structure Checker exclusion list now handles the different abbreviations for the same structure.

For example, excluding OAc will also exclude AcO.

Long Term Supported Release November 29^th: Structure Checker - Osmium 4 (24.2.4)

Bugfixes

• False valence error was detected for some compounds in which a nitrogen atom was included in two condensed aromatic rings.

October 14^th, 2024: Structure Checker 24.3.1

Improvements

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

Bugfixes

• Structure checker did not detect some valence errors in reactions and Markush structures

• Non-stereo Wedge Bond checker reported error on some structures having r/s labels. Ring tetrahedral centers with 180-degree bonds were flagged as errors.

• Incorrect Tetrahedral Stereo Checker didn't check R-group definitions

• False valence error was detected for some compounds in which a nitrogen atom was included in two condensed aromatic rings

• The Abbreviated Group Structure Checker exclusion list now handles the different abbreviations for the same structure.

For example, excluding OAc will also exclude AcO.

Long Term Supported Release September 2^nd: Structure Checker - Osmium 3 (24.2.3)

Bugfixes

• Structure Checker failed on startup having user defined checkers

• The Abbreviated Group Structure Checker exclusion list now handles the different abbreviations for the same structure.

For example, excluding OAc will also exclude AcO.

July 11^th, 2024: Structure Checker 24.3.0

Bugfixes

• Structure checker failed on startup having user defined checkers

• Using Structure Checker in a highly concurrent setup (large number of structures and threads) occasionally caused errors

June 12^th, 2024: Structure Checker 24.1.3

Bugfixes

• Structure Checker failed on startup having user defined checkers

February 19^th, 2024: Structure Checker 24.1.0

No changes.

Long Term Supported Release February 2^nd, 2024: Structure Checker - Neon 2 (23.15.2)

No changes.

Long Term Supported Release January 26^th, 2024: Structure Checker - Mercury 4 (23.6.4)

No changes.

December 21^st, 2023: Structure Checker 23.17.0

No changes.

November 17^th, 2023: Structure Checker 23.16

Bugfixes

Structure Checker did not lunch on Windows on version 23.14.0

Long Term Supported Release November 10^th, 2023: Structure Checker - Neon 1 (23.15.1)

No Changes.

October 18^th, 2023: Structure Checker 23.14.0

No changes.

October 6^th, 2023: Structure Checker 23.13.0

No changes

August 21^st, 2023: Structure Checker 23.12.0

No changes.

July 20^th, 2023: Structure Checker 23.11.0

No changes.

July 5^th, 2023: Structure Checker 23.10.0

Improvements:

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

June 28^th, 2023: Structure Checker 23.9.0

No changes.

May 24^th, 2023: Structure Checker 23.8.0

Bugfixes

• Bond angle checker incorrectly reported problems in certain cases

May 4^th, 2023: Structure Checker 23.7.0

Improvements

• Atom Query Property Checker was extended with an option to detect and remove Recursive SMARTS (SMARTS query)
• New Bond Topology Checker with Remove Bond Topology fixer has been added

Bugfixes

• Attached Data fixer did not remove Attached Data in case of multiple instances

April 5^th, 2023: Structure Checker 23.5.0

No changes.

March 10^th, 2023: Structure Checker 23.4.0

No changes.

February 23th, 2023: Structure Checker 23.3.0

No changes.

February 8^th, 2023: Structure Checker 23.2.0

No changes.

January 25^th, 2023: Structure Checker 23.1.0

Improvements

• Java 17 runtime compatibility is supported.

December 13^th, 2022: Structure Checker 22.22.0

No changes.

December 1^st, 2022: Structure Checker 22.21.0

No changes.

November 24^th, 2022: Structure Checker 22.20.0

Improvements

• Works with Java 17 as well.

October 27^th, 2022: Structure Checker 22.19.0

Bugfixes

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

September 27^th 2022: Structure Checker 22.18.0

No changes.

LTS Release - January 19^th, 2023: Structure Checker 22.17.4 (Lithium.4)

No changes.

LTS Release - November 29^th, 2022: Structure Checker 22.17.3 (Lithium.3)

No changes.

LTS Release - November 9^th, 2022: Structure Checker 22.17.2 (Lithium.2)

Bugfixes

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

LTS Release - October 19^th, 2022: Structure Checker 22.17.1 (Lithium.1)

No changes.

December 22^nd, 2021: Structure Checker 21.20.0

Improvement

• Partial Clean has been added to the Overlapping Atom Checker as a new fixer option

July 16^th, 2021: Structure Checker 21.12.0

Improvement

• Attached Data Checker was extended to accept a list of Attached Data names (or regex) to be excluded from the checking process

May 22^nd, 2020: Structure Checker 20.13.0

Improvement

• Valence error checker was extended to allow traditional pentavalent Nitrogen representation for azides.
  

LTS Release - March 30^th, 2020: 20.9.0 Structure Checker (Fermium.1)

No changes

LTS Release - October 18^th, 2019: 19.21.1 Structure Checker (Europium.1)

No changes

LTS Release - April 11^th, 2019: 19.7.1 Structure Checker (Deuterium.1)

No changes

October 9^th, 2018: Structure Checker 18.24.0

Bugfixes

• Pipe errors of Structure Checker
  

LTS Release - September 25^th, 2018: 18.22.1 Structure Checker (Carbon.1)

No changes

February 13^th, 2018: Structure Checker 18.4.0

Bugfixes

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

August 1^st, 2017: Structure Checker 17.18.0

Bugfixes

• Overlapping Atom Checker does not detect those atoms which are just too close but actually do not overlap.
  

October 3^rd, 2016: Structure Checker 16.10.3

Bugfixes

• Multicenter Checker will not detect the endpoint of a position variation bond as multicenter.
  

September 26^th, 2016: Structure Checker 16.9.26

Improvements

• A list of excluded atom labels can be specified for Pseudo Atom Checker.
  

November 9^th, 2015: Structure Checker 15.11.9

Improvements, deprecations

• Wedge Error Checker was replaced by Incorrect Tetrahedral Stereo, Non-standard Wedge Scheme, and Non-stereo Wedge Bondcheckers.

• Wedge Error Checker is deprecated.
  

August 24^th, 2015: Structure Checker 15.8.24

Improvements

• Additional improvements in * Wedge Error Checker* and Clean Wedge Fixer.
  

August 3^rd, 2015: Structure Checker 15.8.3

API changes

• chemaxon.checkers.runner.BasicCheckerRunner was removed from the public API. Use [AdvancedCheckerRunner](instant-jchem_advanced-structure-checker-button.md).
  

July 6^th, 2015: Structure Checker 15.7.6

Bugfixes

• Wedge Error Checker didn't detect non-stereo wiggly bonds.
  

Improvements

• Clean Wedge Fixer converts non-stereo wiggly bonds to single bonds.
  

June 22th, 2015: Structure Checker 15.6.22

Bugfixes

• Solvent Checker threw exception if input molecule couldn't be converted to SMILES format.
  

April 13^th, 2015: Structure Checker 15.4.13

New features

• New checker: Brackets Checker .
  

January 26^th, 2015: Structure Checker 15.1.26

Bugfixes

• Wedge Error Checker didn't always agree with Wedge Clean Fixer . From now on the molecules fixed by Wedge Clean Fixer * are accepted as correct by * *Wedge Error Checker. *

January 12^th, 2015: Structure Checker 15.1.12

Improvements

• Aromaticity error fixing improvements: Dearomatize and Rearomatize fixers can fix aromaticity errors in heteroaromatic rings (containing only carbons and nitrogens) in unambiguous cases.
  

Bugfixes

• Bond Angle Checker did not accept some bond angles as correct. Bonds connected to a ring were affected.
  

January 5^th, 2015: Structure Checker 15.1.5

Bugfixes

• From now on * Rare Element Checker* will not detect deuterium (D) and tritium (T) as rare element.
  

November 17^th, 2014: Structure Checker 14.11.17

Bugfixes

• Chiral Flag Error Checker did not report invalid chiral flag on achiral molecules.
  

October 27^th, 2014: Structure Checker 14.10.27

New features and Improvements

• New checker: R-group Bridge Error Checker.

• R-group Attachment Error Fixer improvements:

  * removes superfluous attachment points,

  * can fix errors in R-group definitions having multiple equivalent candidates for the addition or removal of the attachment point(s),

  * can fix structures containing contracted abbreviated groups,

  * can handle R-group bridges.
  

October 6^th, 2014: Structure Checker 14.10.6

Bugfixes

• Circular R-group Reference Checker failed to identify some circular references

• Missing R-group Checker did not identify unnumbered R-group as missing
  

July 21th, 2014: Structure Checker 14.7.21

New features and Improvements

• OCR Error Checker was improved, now it identifies optical structure recognition errors better

• "Discard OCR errors" option was removed from Structure Checker application and structurechecker command line application. Use OCR Error Checker.
  

Bugfixes

• Overlapping Bond Checker detected some non-overlapping bonds as overlapping [error report]
  

July 7^th, 2014: Structure Checker 14.7.7

New features and Improvements

• Less invasive fix of bond length errors and bond angle errors with newly introduced Bond Length Fixer and Bond Angle Fixer .

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