Atom properties dialog in Marvin JS

    In 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 Panel.

    Atom properties dialog window is available from the pop-up menu after a right-click on the atom. images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/lightbulb_on.svg Set atom properties for several atoms at once

    In the dialog only the properties which 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 via the "Padlock" icon.

    images/download/attachments/5309968/Video_new_30.pngSee 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 - - - - - - + - -

    Basic Tab


    Possible values

    Atom: the chemical symbol of the element (the atom number appears automatically next to the text field).

    In 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

    Ehanced stereo: Off (default), Absolute, And, Or. In the latter two cases a number should accompany the identifier. If you leave the number field empty, number 1 will be associated with the group identifier automatically.

    Map: integer

    Advanced Tab

    Property name and notation Property Possible Values
    Total H (H) Total number of hydrogen substituents. 0-254
    Implicit H (h) Number of implicit hydrogen substituents. 0-254
    Bond orders (v) Total bond order. (Some cases it is referred as valence.) 0-254
    Connections (X) Number of substituents including hydrogens. 0-254
    Ring count (R) 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 number of isotopic hydrogen substituents. 0-254 s0 - s5: exact substitution count s6: 6 or more substitutions "as drawn" (s*)
    Unsaturated (u) Unsaturated atom: atom that has double, triple or aromatic bond. Unsaturated (u)
    Aromatcity (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


    Homology group

    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

    Related pages

    Atom drawing

    Atom Context menu

    Bond properties dialog

    ... back to Dialogs