sugarremoval - Sugar Removal Utility v1.5

• The Sugar Removal Utility (SRU) algorithm source code was moved to the Chemistry Development Kit (CDK) library. This repository now only contains the command-line application and some additional documentation about the algorithm! Listed below are the changes done to the SRU during migration to CDK:
  • The SRU can now process disconnected structures (e.g. ion and counter-ion) as well, even if only terminal sugars are removed
  • Saturating open valences of the extracted substructures with implicit hydrogen atoms (or R labels / pseudo atoms) must be done externally now (open valences result from bond breakages, e.g. between aglycone and sugar moiety)
  • PreservationModeOption enum was renamed to PreservationMode
  • The functionality to tag molecules as sugar-containing via CDK IAtomContainer properties has been removed. Use the hasSugar() methods of the class instead
  • Many constants were made protected that were formerly public (e.g. the sugar pattern lists but they can still be accessed via public getter methods)
  • Switched to CDK LoggingTool
  • Fewer RuntimeExceptions are thrown now (e.g. NullPointerExceptions, IllegalArgumentExceptions)
  • Cloning of input atom containers must be done externally now! Check the documentation of the specific method you are using and if need be, clone your input molecule before deglycosylation if you also want to keep the unaltered structure!
  • Some static utilities like selectBiggestUnconnectedFragment(), selectHeaviestUnconnectedFragment(), and partitionAndSortUnconnectedFragments() have been removed
  • Some futher minor API changes

Auto-generated Release Notes

What's Changed

• March 2025 Updates by @JonasSchaub in https://github.com/JonasSchaub/SugarRemoval/pull/8
• SRU v1.5 by @JonasSchaub in https://github.com/JonasSchaub/SugarRemoval/pull/10

Full Changelog: https://github.com/JonasSchaub/SugarRemoval/compare/v1.4...v1.5

- Java
Published by JonasSchaub 12 months ago

sugarremoval - Sugar Removal Utility v1.4

Updated some dependencies, added JavaDoc page, automated Maven artifact release, and some other minor adjustments.

Full Changelog: https://github.com/JonasSchaub/SugarRemoval/compare/v1.3.2...v1.4

- Java
Published by JonasSchaub over 2 years ago

sugarremoval - Sugar Removal Utility v1.3.2

Update of dependencies: Java, CDK, JUnit, Maven JAR plugin, and Maven assembly plugin

- Java
Published by JonasSchaub over 3 years ago

sugarremoval - Sugar Removal Utility v1.3.1

• CMD app now outputs absolute SMILES with stereo-chemical information
• fixed minimum Java version check

- Java
Published by JonasSchaub over 3 years ago

sugarremoval - Sugar Removal Utility v1.3

New in this version:

• The Chemistry Development Kit (CDK) version has been updated to 2.6 to fix a security issue with the contained Log4J library
• Small bug fixes and documentation updates

- Java
Published by JonasSchaub about 4 years ago

sugarremoval - Sugar Removal Utility v1.2

New in this version:

• The SugarRemovalUtility publication has now finally been published and can be accessed here: https://jcheminf.biomedcentral.com/articles/10.1186/s13321-020-00467-y

• A new option has been added to allow the detection of potential circular sugar moieties with keto groups. It can be used via the command-line application and the SugarRemovalUtility source code. See detailed description below.

• Fixed the ambiguity that sugar-like spiro rings were detected in linear sugar detection if the detection of linear sugars in rings was turned on and the detection of these cycles in the circular sugar detection turned off. Now, sugar-like spiro rings are always excluded from linear sugar detection, along with all potential sugar cycles.

• Extended the illustrative test of a known problem with the linear sugar detection using the SRU: In a few cases, the detection of a linear sugar candidate can fail if the circular sugars are removed from the molecule. The particular linear sugar is in most cases part of a ring and detected when the molecule still has its original structure. After removing the circular sugars, the linear sugar is not detected anymore. (specificTest35WithDepiction() in SugarRemovalUtilityTest.java)

• Extended the 'handpickednp.txt' set with the additions made to the test cases for the three changes above.

More detailed description of the new option for circular sugar detection (and removal):

The general rule specified in the original algorithm description is that every potential sugar cycle with an exocyclic double or triple bond is excluded from circular sugar detection. If this option is turned on, an exemption to this rule is made for potential sugar cycles having keto groups. Also, the double-bound oxygen atoms will then count for the number of connected oxygen atoms and the algorithm will not regard how many keto groups are attached to the cycle (might be only one, might be that all connected oxygen atoms are double-bound). If this option is turned off, every sugar-like cycle with an exocyclic double or triple bond will be excluded from the detected circular sugars, as it is specified in the original algorithm description. Per default, this option is turned off. Therefore, nothing changes compared to prior versions when using the default settings. In the command-line application, this new option can be configured by using '-circSugKetoGroups' or '--detectCircularSugarsWithKetoGroups' as parameter key with a boolean argument. See usage instructions for more information.

- Java
Published by JonasSchaub over 5 years ago

sugarremoval - Sugar Removal Utility v1.1

New in this version: - The command-line argument management of the SRU CMD application has been completely revised. Now, Apache Commons CLI v1.4 is used for this purpose. See updated usage instructions and documentation for further details. - The JAR used for deployment of the SRU CMD application has been made lighter by only importing the actually needed CDK modules in the pom.xml file. - Note: The Sugar Removal Utility algorithm and its implementation has NOT changed in this new release.

- Java
Published by JonasSchaub over 5 years ago

sugarremoval - Sugar Removal Utility v1.0

Initial public release of the Sugar Removal Utility algorithm implementation and the accompanying command line application, as described in the publication preprint undergoing review: Schaub J, Zielesny A, Steinbeck C, Sorokina M. Too sweet: cheminformatics for deglycosylation in natural products, 02 August 2020, PREPRINT (Version 1), available at Research Square [DOI:10.21203/rs.3.rs-50194/v1]

- Java
Published by JonasSchaub over 5 years ago