CyDexID Generator: This tool generates unambiguous nomenclature for cyclodextrin monomers

This application generates CyDexID nomenclature for cyclodextrin molecules through an interactive interface:

1. Basic Setup:
   • Select the number of glucopyranoside units (residues) using the control panel (4-15)
   • The circular diagram shows the cyclodextrin structure where each hexagon represents a glucose residue
2. Adding Modifications:
   • Drag functional groups from the sidebar to the red circles in the diagram, corresponding to the primary alcohol (position 6, pointing inward) or secondary alcohols (positions 2 and 3, pointing outward)
   • Create custom functional groups using the "Add New Functional Group" field
3. Managing Chirality:
   • Double-click on the red circles (positions 2, 3, and 6) to toggle chirality changes for the carbon atoms supporting the corresponding functional groups
   • Smaller circles at positions 1 and 4 represent additional chiral centers. Double-click these circles to modify the chirality of their respective carbon atoms
   • By default, all chiral centers retain the native chirality found in unmodified cyclodextrins
   • When chirality is altered, the circle's color changes to visually indicate the modification
4. Editing & Output:
   • To remove substituted functional groups, activate the cleaning mode (trash bin icon) and click on the substitution you want to remove
   • The nomenclature updates automatically in three formats below
   • Use the copy buttons to easily transfer the generated codes

Tip: Refer to the collapsible help panels in the sidebar for detailed information about position codes and chiral center configurations.

The position code follows a 1-digit system for three possible substitution positions (2, 3 and 6) at each glucopyranoside ring:

By default, all glucopyranoside units in the sequence retain their natural chirality. Chirality changes at specific carbon atoms are encoded using a position-specific 1-digit code. Each unit in the sequence is represented by a single digit, and the code is prefixed with RS236 or RS14, depending on the positions being modified.

RS236: Chirality Changes at Positions 2, 3, and 6

The prefix RS236 indicates modifications at positions 2, 3, and 6 of the glucopyranoside units. Each code represents a specific combination of chirality changes.

RS14: Chirality Changes at Positions 1 and 4

The prefix RS14 is used for chirality changes at positions 1 (anomeric center) and 4 (ring position) of the glucopyranoside units.