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:

    Context (Change to) Type Alias Isotope Charge Radical Enhanced Stereo Map Additional properties Advanced Panel
    Element Atom ✔️ ✔️ ✔️ ✔️ ✔️ ✔️ ✔️
    Query Atom ✔️ ✔️ ✔️ ✔️ ✔️ ✔️
    R-group R ✔️ ✔️
    List/NOT list List type ✔️ ✔️ ✔️ ✔️ Elements ✔️
    Pseudo Pseudo ✔️ ✔️ ✔️ ✔️
    Homology Group Group ✔️ ✔️ ✔️ (Group) Display ✔️
    Abbreviation N/A ✔️

    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

    Property name and notation** Property Possible Values
    Total H (H) The total number of hydrogen substituents. 0-254
    Implicit H (h) The number of implicit hydrogen substituents. 0-254
    Bond orders (v) Total bond order. In some cases, it is referred to as valence. 0-254
    Connections (X) The number of substituents including hydrogens. 0-254
    Ring count (R) The number of rings the atom is a member of. 0-254 R (>0)
    Smallest ring size (r) Size of the smallest ring the atom is a member of. 3-254
    Ring bond (rb) Number of ring bonds next to the atom. 0-254 rb0, rb2-rb3: exact ring bond count; rb4: 4 or more ring bonds. "as drawn" (rb*)
    Substitutions (s) Substitution count: the number of non-hydrogen substituents plus the number of isotopic hydrogen substituents. 0-254 s0-s5: exact substitution count s6: 6 or more substitutions "as drawn" (s*)
    Unsaturated (u) Unsaturated atom: an atom that has a double, triple, or aromatic bond. Unsaturated (u)
    Aromaticity (a/A) It defines whether the atom has at least one aromatic bond (a) or only aliphatic (A) bonds. Aromatic (a) Aliphatic (A

    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.
    Homology Group Alias
    Actinide ACT
    AlkaliMetal AMX
    Alkenyl CHE
    Alkyl CHK
    Alkynyl CHY
    Any group XX
    AnyAtom -
    Carboalicyclyl CYC
    Carboaryl ARY
    CarbonTree acyclicCarbon
    Cyclyl anyring
    FusedHeterocyclyl HEF
    Haloalkyl -
    Halogen HAL
    Heterocyclyl Heterocycle
    Heteromonoalicyclyl HET
    Heteromonoaryl HEA
    HeteroSubstitutedAlkyl HSA
    Hydroxyalkyl -
    Lanthanide LAN
    Metal MX
    OtherMetal A35
    Protecting PRT
    RingSegment -
    TransitionMetal TRM
    Unknown group UNK