Table 1 Summary of available settings and options for fine-tuning the sugar detection and removal in the SRU, along with their impact, default, and availability

Type of sugar moieties to remove

Circular/linear/both

Sugar removal

(None)

Web application, command-line application, source code

Remove only terminal sugars

Yes/no

Sugar removal

Yes

Web application, command-line application, source code

Preservation mode

Preserve all/judge by heavy atoms / judge by molecular weight

Sugar removal

Judge by heavy atoms

Command-line application, source code

Preservation mode threshold

Any number of heavy atoms or a molecular weight ≥ 0

Sugar removal

5 heavy atoms

Command-line application, source code

Detect circular sugars only with O-glycosidic bond

Yes/no

Circular sugar detection (and removal)

No

Web application, command-line application, source code

Detect circular sugars only with enough exocyclic oxygen atoms

Yes/no

Circular sugar detection (and removal)

Yes

Command-line application, source code

Exocyclic oxygen atoms to atoms in ring ratio threshold

Any ratio ≥ 0

Circular sugar detection (and removal)

0.5 (five- and six-membered sugar rings need at least 3 connected oxygen atoms)

Command-line application, source code

Detect spiro rings as circular sugars

Yes/no

Circular sugar detection (and removal)

No

Command-line application, source code

Detect linear sugars in rings

Yes/no

Linear sugar detection (and removal)

No

Command-line application, source code

Linear sugar candidate minimum size

Any number of carbon atoms ≥ 1

Linear sugar detection (and removal)

4 carbon atoms

Command-line application, source code

Linear sugar candidate maximum size

Any number of carbon atoms ≥ 1

Linear sugar detection (and removal)

7 carbon atoms

Command-line application, source code

Detect linear acidic sugars

Yes/no

Linear sugar detection (and removal)

No

Command-line application, source code

Circular/linear sugar patterns

Adding/removing patterns

Circular/linear sugar detection (and removal)

Pre-compiled set of circular and linear sugars (see Figs. 5 and 6)

Source code