Query Structures in Marvin JS

    Query Atoms

    Query atoms represent a group of elements that have common properties. You can find them on the atom toolbar. You can create and manipulate the query atoms as other atoms.

    Query Atom Properties

    You can find them in the[Atom properties] dialog or you can get quick access to these through the Atom query properties dialog. You can add these properties to atoms by right-clicking on them then choosing the Atom properties dialog from the list, or by pushing the . 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. Atom Lists and NOT Lists can be defined using the Periodic table dialog. After creation, you can modify the elements in Atom properties dialog, otherwise, you can handle them as other atoms (move, delete, overwrite, and so on).

    Homology Groups

    Built-in homology groups of Marvin JS represent a series of chemical compounds with the same specific structural properties. For a list of the available homology groups, see Atom properties dialog. For more information about the properties or search conditions of the homology groups, see Homology Groups in Markush Structures.

    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. On the canvas, you can manipulate the homology groups as other atoms (move, delete, overwrite, and so on).

    Query Bonds

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

    Bond type Representation
    Any Any query bond icon
    Single or double Single or double query bond icon
    Single or aromatic Single or aromatic query bond icon
    Double or aromatic Double or aromatic query bond icon
    Double Cis or Trans Double cis or trans query bond icon
    Double C/T or Unspecified Double CT or unspecified query bond icon
    Single Up or Down Single up or down query bond icon

    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. You can edit these bonds, like the others.

    Position Variation Bond

    The position variation bond represents a variable connection pointing from a group of atoms to an atom. Find these kinds of bonds at the Bond tools on the tools toolbar. After creation, several properties of this bond are changeable, such as bond type, topology, location on the canvas, and so on.

    Bond Properties

    In Marvin JS bond type, topology and reacting center, stereo search flag can be set to bonds. For more information about stereo search flag usage, see Stereochemistry JCB. You can find these properties in the Bond properties dialog. These can be set and change via Bond properties dialog.


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

    R-group Label

    You can add R-groups to your root structure in the following ways; by the [R-group] tool or through a Keyboard shortcut. Change the number by clicking repeatedly with the Smart R-group tool; change the label and add other properties in the Atom properties dialog.

    R-group Definition

    To create the definition for an R-group, first, draw the substituents from which the R-group should stand for, then enframe them with the Smart R-group tool or after selection use the R+Space keyboard shortcut. You can manipulate the R-group definitions by the Smart R-group tool or by the context menu.

    Attachment Points

    You can add attachment points to the fragments in an R-group definition by using the R-group Attachment button or from the context menu. The attachment points on every separate fragment are automatically numbered beginning with 1. The bond type of the R-group attachment points can be changed using either the R-group attachment point tool or any of the bond tools.

    {info} R-group definition import and export are supported only in ChemAxon Marvin Document (MRV) format in Marvin JS; besides, you can choose other formats if the relevant web service is available.


    Adding R-logic to an R-group query is possible via R-logic Dialog, which is available from the Empty space, the Atom, and also the R-labelcontext menus if there is at least one R-group definition on the canvas. You can do any modifications in the R-logic Dialog.

    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. The chiral flag can be added to a molecule through the Empty space or the Selection pop-up menu. If there is a reaction on the canvas, the chiral flag can be assigned to every component independently through the Selection pop-up menu. The visibility of the chiral flag can be turned on/off in the View settings dialog.

    Depending on the file format, a molecule which has wedge bonds without a chiral flag means one of the following:

    • In MDL file types (MOL, SDF, and so on): Wedge bonds describe the relative configuration of chiral centers; the structure is a racemic mixture of two enantiomers.
    • In Daylight file types (SMILES, SMARTS): Wedge bonds describe the absolute configuration of chiral centers; the structure represents a single enantiomer.

    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 stereocenter belongs to only one stereogenic group. The following table contains the available identifiers.

    Identifier Description
    Off We have no information about the configuration of the chiral atom.
    Abs We know the absolute configuration of the chiral center.
    Or We only know the configuration of the atom relative to another chiral center, but we do not have information about the absolute configuration. For a molecule with two chiral centers, it either refers to the structure as drawn (for example, 1R, 2R configuration) or to its enantiomer, which has opposite configuration on its chiral atoms (1S, 2S).
    And We use the „And" notation if we want to represent a mixture of stereoisomers which can contain specified enantiomers/diastereomers or even every optical isomer.

    You can add these properties to the chiral atoms through Atom properties dialog dialog. You can find a more detailed description of enhanced stereo representation and handle along with a set of examples in the JChem Query Guide.

    {info} Importing and exporting enhanced stereo notations are not possible in MDL Molfile V2000 format. It is only possible in the extended MDL Molfile (V3000) format ( requires the relevant web service ).