2. New option for keto groups on circular sugars

In version 1.2, a new option has been added to allow the detection (and subsequent removal) of potential circular sugar moieties with keto groups. It can be used via the command-line application and the Sugar Removal Utility source code.
The general rule specified in the original algorithm description (see article) 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 the application for more information.