Query atoms

Query atom represents a group of elements which has common properties.

Create them in Marvin JS: you can find them on the Atom toolbar. See the available query atoms, and more details in the Query Atoms... page in the Editor Overview section.
Usage in Marvin JS: you can create and manipulate the query atoms as other atoms. For more details, please check the Atom page in the Drawing features section.

Query atom properties

Add them to atoms in Marvin JS: you can find them in the Atom properties dialog or you can get quick access to these via the Atom query properties dialog.
Usage in Marvin JS: you can add these properties to atoms by right clicking on them then choosing the Atom properties dialog from the list, or by pushing . keyboard button (or click its icon on the toolbar) to open the Atom query properties dialog.

Atom Lists and NOT Lists

An Atom List query atom indicates any atom that is part of the list; similarly, a NOT List query atom can represent any atom that is not part of the list.

Create them in Marvin JS: Atom Lists and NOT Lists can be defined using the Periodic Table.

Usage in Marvin JS: After creation, you can modify the elements in Atom properties dialog, otherwise, you can handle them as other atoms (move, delete, overwrite etc.). For more details, please check the Atom page in the Drawing features section.

Homology groups

Built-in homology groups of Marvin JS represent series of chemical compounds with the same specific structural properties. Click here for the list of the available homology groups.
(If you need more information about the properties or search conditions of the homology groups, please, check the corresponding pages of JChem Base documentation or just click here.)

Create them in Marvin JS: Homology groups can be created via Atom properties dialog, after a right-click on an atom. At the top of the dialog, change 'Element' to 'Homology Groups' then select the appropriate group from the list and choose either its full name or its alias at the 'Display' option.

Usage in Marvin JS: On the canvas you can manipulate the homology groups as other atoms (move, delete, overwrite etc.). For more details, please check the Atom page in the Drawing features section

Query bonds

Bond query represents that the actual bond can be more than one type.

Create them in Marvin JS: You can find these kind of bonds in the Bonds combo-box on the Tools toolbar. Just click on the desired bond, and it will appear on the tip of the cursor. Now, you can put it anywhere on the canvas as many times as you want.

Usage in Marvin JS: You can edit these bonds, as the others. See in details here.

Position Variation Bond (variable point of attachment)

Position variation bond represents a variable connection pointing from a group of atoms to an atom.

Create them in Marvin JS: Find these kind of bonds in the Bonds combo-box on the Tools toolbar. Detailed description how to draw position variation bond here.

Usage in Marvin JS: After creation, several properties of this bond is changeable, such as bond type, topology, location on the canvas, etc. You can see a detailed description about editing the bonds here.

See how to use the Position variation tool here.

Bond properties

In Marvin JS bond type, topology and reacting center can be set to bonds.

Add these to bonds in Marvin JS: You can find these properties in the Bond properties dialog.

Usage in Marvin JS: These can be set and change via Bond properties dialog.

R-groups

A query with an R-group represents substitution variation on the same root structure.The molecule containing an R-group is the so called scaffold. An R-group query can involve several derivatives which differ in one or more substituents (fragments).

Absolute stereo information

The "Absolute" chiral flag on a molecule indicates that every chiral center marked with wedge bonds has a known absolute configuration, in other words the structure represents a single, well-defined stereoisomer.

Create them in Marvin JS: The chiral flag can be added to a molecule through the Empty space or the Selection pop-up menu.

Display: The visibility of the chiral flag can be turned on/off in the View Settings dialog window.

Enhanced stereo specifications

Marvin JS supports the MDL enhanced stereo representation. Enhanced stereo specifications refer to several stereoisomers of a molecule by drawing only one structure. Adding these notations to chiral centers makes it possible to represent stereochemical information: whether we know the absolute configuration of a stereogenic center or we have information only about the relative configuration of two or more chiral atoms.
Each group label consists of an identifier, and – in some cases – of a number. Each and every stereocenter belongs to only one stereogenic group.

The following table contains the available identifiers.

Set and modify these properties in Marvin JS: You can add these properties to the chiral atoms via Atom properties dialog.

You can find a more detailed description of enhanced stereo representation along with a set of examples in the JChem Query Guide.