ChemAxon & ChemDraw Integration

ChemDraw

RSpace fully supports the ChemDraw format: you can easily import, manipulate, export, and search for ChemDraw files in RSpace. Operations on ChemDraw files work in the same way as for other chemistry file formats: instructions for enabling and using this feature are included in the sections below.

Overview

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.

Note on Drawing Chemical Structures in Word

It is not possible to draw chemical structures in Word without using an external plugin, such as JChem or Chem4Word. We recommend drawing the structures in the RSpace document editor instead, using our ChemAxon integration, as this will make them easily searchable within RSpace.

Enabling ChemAxon Integration

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

Importing Chemical Structures by drag & drop

If you have a file, or multiple files containing chemical structures saved in a standard format (e.g. ChemDraw, mol, SMILES), you can drag & drop them to text editor to have them imported as a chemical drawings.

Just open the document for editing, then select chemical files from your computer's desktop and start dragging them into the text field editor. The drop area will show up:

Dropping chemical files into the import file area will convert them into Marvin format and draw them as chemical structures in the document. It will also save a copy of the file to a separate 'Chemistry' section in the gallery:

Chemical Structure that appears as a result of dragging and dropping a chemical file into the editor

Uploaded Chemical File in the new 'Chemistry' Gallery section

Chemistry files uploaded via dragging and dropping into the editor, or by uploading them to the gallery and inserting them into a document have different properties to those created and inserted via the Marvin sketcher tool:

• Chemical structures created by upload of a chemical file can only be viewed in the Marvin Sketcher tool and cannot not edited.
• Chemical structures created in the Marvin Sketcher tool can be edited. You can upload and edit chemical structures from your computer this way.

Drawing Chemical Structures

To draw a chemical structure 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

RSpace displays metadata on chemical structures and reactions, both in view mode and edit mode.

When you select a chemical structure when editing (by clicking on it), a column appears on the right-hand side of the editor pane, with a series of cards displaying the metadata of each selected chemical structure. Each card has small thumbnail of the structure to help distinguish multiple structure cards apart. If you prefer to use the full expanse of the editor pane, you can hide these cards easily by clicking on "Close all".

Chemical Structures

Chemical Reaction (shows chemical metadata for each reactant and product)

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, or click on the download icon to download a PNG image of the structure.

Exporting structures

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 and chemistry files stored in the gallery that contain chemical search hits are listed, together with an image of the search hit. You can click on the document link to open it, or the gallery link to see the chemical file in the gallery. The screenshot below shows some example search results.

Uploading New Versions of Chemical Files

Chemical structures that have been uploaded through drag and drop into the editor or directly to the Gallery have a file associated with them. This file is stored in a separate Chemistry section in the Gallery. From the Gallery or a document, a new version of this chemical file can be uploaded, replacing any structures present in the system with the new one. This workflow is shown below, where we upload a chemical file called caffeine.mol, then upload a new version called amphetamine.mol using "Upload new version"; we can see that after the update, the chemical is noted as being on Version 2 in the info panel.