Query Structures in Marvin JS

    Query structures are generalized structures representing a group of similar molecules which differ only in some structural elements.

    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 theAtom 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.

    Type Bond type Representation
    Generic Any images/download/thumbnails/5311097/image2015-4-23_17_8_48.png
    Single or double images/download/thumbnails/5311097/image2015-4-23_17_10_1.png
    Single or aromatic images/download/thumbnails/5311097/image2015-4-23_17_11_2.png
    Double or aromatic images/download/thumbnails/5311097/image2015-4-23_17_11_54.png
    Stereo Double Cis or Trans images/download/thumbnails/5311097/image2015-4-23_17_15_49.png
    Double C/T or Unspecified images/download/thumbnails/5311097/image2015-4-23_17_17_13.png
    Single Up or Down images/download/thumbnails/5311097/image2015-4-24_11_41_35.png

    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.

    images/download/attachments/5309968/Video_new_30.pngSee how to use the Position variation tool here.

    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 JChem Base documentation here.)

    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.


    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).

    R-group label

    Creating R-groups in Marvin JS: You can add R-groups to your root structure in three ways: by the Smart R-group tool or viaKeyboard shortcut.

    Managing R-groups: Change the number by clicking repeatedly with the Smart R-group tool; change the label and add other properties in the Atom Properties menu.

    R-group definition

    Creating R-group definitions in Marvin JS: In order to create the definition for an R-group, firstly, 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.

    Modify R-group definitions: You can manipulate the R-group definitions by the Smart R-group tool or by Context menu. See detailed description here.

    Attachment points

    Creating R-group attachment point in Marvin JS: 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".

    Change attachment's properties: 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. 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.


    Creating R-logic in Marvin JS: 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-label context menus if there is at least one R-group definition on the canvas.

    Modify R-logic: You can do any modifications in the R-logic dialog.

    Create and usage in Marvin JS: Here you can read a detailed description about how to manage R-group queries in Marvin JS.

    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. If there is a reaction on the canvas, chiral flag can be assigned to every component independently via Selection pop-up menu.

    Display: The visibility of the chiral flag can be turned on/off in the View Settingsdialog window. images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/lightbulb_on.svg Depending on the file format, a molecule which has wedge bonds without a chiral flag has either of the following meanings:

    • In MDL file types (MOL, SDF, ...): 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 and every stereocenter belongs to only one stereogenic group.

    The following table contains the available identifiers.

    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 ( e.g. , 1 R , 2 R configuration) or to its enantiomer, which has opposite configuration on its chiral atoms ( 1 S , 2 S )
    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.

    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 and handling along with a set of examples in the JChem Query Guide.

    Please, note that import and export of enhanced stereo notations are not possible in MDL Molfile V2000 format, only in the extended MDL Molfile (V3000) format (provided that the relevant webservice is available).

    Related Page

    JChem Base Query GuideQuery Guide