ChemAxon & ChemDraw Integration
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.
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:
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. Two drop-areas will show up:
Drop chemical files into the right-side area to convert them into Marvin format and draw them as chemical structures editable in the document.
Alternatively, you can drag the files into left-side area - that'll import the files into RSpace Gallery and add them to the document as standard file attachments. There will be no file conversion, but also no chemical preview.
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 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.
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.