Atom Properties Dialog

By using the Atom properties dialog, you can set values to atoms.

Atomic charges, isotopes, radicals, enhanced stereo specifications, atom maps, aliases can be set in the Basic tab and query properties in the Advanced tab.

Atom properties dialog window is available from the context menu after a right-click on the atom.

{info} It is possible to set atom properties for several atoms at once. In the dialog, only properties that are permitted for every selected atom type are available. If the selected atoms have attached previously defined properties, you can delete them by inactivating their input field by clicking the Padlock icon. See how to set atom properties for more than one atom here.

The appearance of this dialog depends on the context. You can see the summary of the available properties below:

Basic Tab

• Atom: The chemical symbol of the element (the atom number appears automatically next to the text field). In the case of hydrogen isotopes (deuterium and tritium), their specific atomic symbols (D and T) can be used as well.
• Alias: A text (a label to an atom). Please, note that the other properties (except query atom properties) will be hidden, however, this information is preserved.
• Isotope: A positive integer.
• Charge: (+) or (-), and an integer (other numbers will be rounded to an integer).
• Radical: None, monovalent, divalent, divalent singlet, trivalent quartet, 4 radical.
• Enhanced stereo: Off (default), Absolute, And, Or. In the latter two cases, a number must accompany the identifier. If you leave the number field empty, number 1 will be associated with the group identifier automatically.
• Map: An integer.

Advanced Tab

Additional Properties

• List/NOT list: Elements can be added to the list by entering their corresponding chemical symbols, separated by commas.
• Homology Group: Homology groups can be chosen by using the Group field. Their alias can also be selected by using the Display field. See the table below, for the complete list of homology groups.