Sugar Removal Utility v1.4

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

Full Changelog: v1.3.2...v1.4

Sugar Removal Utility v1.3.2

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

Sugar Removal Utility v1.3.1

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

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

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 'hand_picked_np.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.

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.

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]