Substructure Groups in MarvinSketch

    How to Create Groups

    Create Group button

    • Select the molecule or a part of the molecule. Click the Create Group button in the Tools toolbar and edit the group properties in the dialog window.

    • Click the Create Group button in the Tools toolbar then select the group atoms and bonds. Upon releasing the mouse button, the Group dialog pops up.

    Alternatively the Create Group dialog can be reached using

    In the dropdown list of the group type only those types can be selected which are enabled for the actual selection in the molecule.

    To enable all types: go to Edit > Preferences > Structure tab and uncheck the ' Validate S-groups at creation ' box.

    Enabling/disabling a group type depends on:

    • the number of crossing bonds

    • the embedding of groups into each other: several conditions are checked here for the group to be created

      • whether it can be embedded into the groups which would contain it,

        e.g. polymer S-groups can not be embedded into multiple S-groups

      • whether it can embed all the groups which would be contained by it,

        e.g. structural repeating unit S-groups (SRU) can not embed monomers

      • whether it can be embedded directly into the group which would be its direct embedder,

        e.g. component S-groups can be directly embedded only into ordered or unordered mixtures

      • whether it can directly embed the groups which would be embedded by it directly,

        e.g. mixtures can directly embed only components.

    • Expandable S-groups are not allowed to be embedded into each other.

    Since those group types which are allowed only for whole fragments (mixtures, components and monomers) are always extended to whole fragments, thus these types are allowed even if only fragment parts where selected, if they are correct when extended to the whole fragment.

    Extension to whole fragment is not allowed if the group type is changed by editing an existing group: in this case mixtures (etc.) are not allowed for fragment parts.