Chemaxon Integration

RSpace uses Chemaxon MarvinJS structure editor for chemical structure drawing and display.

You can use MarvinJS to draw chemical structures and reactions, and import from or export to standard formats such as ChemDraw, mol, SMILES, etc. MarvinJS supports 3D rotation of structures and sophisticated structure search.

The full documentation for this service can be found here. The following is a quick-start guide about how to start using the Chemistry editor in RSpace.

Enabling Chemaxon Integration

First of all, make sure that the Chemistry feature is enabled. Go to the Apps tab and enable Chemistry:

Creating Chemical Structures

To draw or import a chemical structure into a document start editing a text field, then click on the benzene ring icon in the Text Editor toolbar, or clicking ‘Insert’ > ‘Structural formula’.

A Chemaxon Marvin sketcher tool will appear. You can draw molecules and reactions out of combinations of elements, or you can import a file containing a structure in common format such as mol or ChemDraw (use the 'Import' button in the top toolbar).

After drawing or importing a structure insert it to your RSpace document, where an image of it will be placed in the text where the cursor was placed when opening the editor. To edit an existing chemical structure, select it in the document, then click on the benzene-ring icon to open the editor again. The structure remains fully editable at all times.

Properties of a Chemical Structure

After saving the document the chemical element will have its basic properties calculated and displayed next to it. You can also click on the image to see larger preview of the molecule or reaction.

Using Marvin Sketcher you can also export structures in various standard formats - use the ‘Export’ button in the Marvin Sketcher toolbar.

Searching for Chemical Structures

Chemical structures, or elements used in them, can be searched for using ChemAxon’s structure search feature. The search mechanism is located in the drop-down options of the main Workspace search, at the top right of the Workspace view.

There are various types of chemical search, the default is substructure search. Chemaxon’s documentation gives full information about the characteristics of each search type.When you open the Chemical Search dialog, draw the structure (whole or part) query, then click Search:

Documents that contain chemical search hits are listed, together with an image of the search hit. You can click on the document to open it. The screenshot below shows some example search results.

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