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. 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.

See how to set atom properties for more than one atom here.

• Basic Tab

• Advanced Tab

• Additional properties

  • List/NOT list

  • Homology group

• Related pages

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

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