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.

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

-

-

-

-

-

-

+

-

-

Basic Tab

Possible Values

  • 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.

images/download/attachments/1803068/Basic_Atom_Properties.png

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

images/download/attachments/1803068/Advanced_Atom_Properties.png

Additional Properties

List/NOT List

images/download/attachments/1803068/List_NOT_List.png

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

images/download/attachments/1803068/Homology_Group.png