Remove Solvents

    This action removes predefined fragments from multifragment molecules (regarded as solvents), and saves the information of the removed fragments in SDF property fields. In case all fragments are solvents the action keeps only the largest solvent based on the heavy atomnumber. A built-in solvent dictionary is used by default, but custom solvent definitions can be used by setting it in place during action configuration.

    Custom solvent definition : You can edit your custom list of solvent definitions after you placed action "Remove solvents" to the right side panel of "Configure Actions" window. Select the action on the right side panel and edit the solvent definitions on the lower panel.

    Below column "Name", you can type a desired solvent name or select one from the drop-down list.

    Edit the appropriate structure by double clicking on the field below column "Structure" (a MarvinSketch window will appear).

    You can delete any table element as follows: Click on the relevant structure field; the row will be highlighted. Click on images/download/attachments/1803711/remove16.png.

    Built-in solvent dictionary : You can load the elements of built-in solvent dictionary by clicking on button images/download/attachments/1803711/open16.png.

    Example :

    Action Input Output
    Remove Solvents (removesolvents) images/download/attachments/1803711/input_remove_solvent.jpg images/download/attachments/1803711/remove_solvent_output.jpg

    The action never removes all components (fragments) from the molecule. If all components of the molecule are defined in the solvent dictionary then the largest (based on molecular weight) is not removed.

    The removed solvent are stored in the "Solvent-" property.