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_GB/7201/e9483755159fbecaf5aef9b1eebd094ee4430d2f/_/images/icons/emoticons/lightbulb_on.png 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/41125638/Video_new_30.png 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

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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

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

images/download/attachments/41125882/image2015-3-23_14_57_43.png

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

images/download/attachments/41125882/image2015-4-22_14_16_48.png

Homology group

images/download/attachments/41125882/image2015-3-23_14_43_56.png

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