Purpose
The App converts a worksheet column containing either SMILES or InChI strings into images of the molecules the strings represent. SMILES and/or InChI strings can optionally be loaded into a worksheet from various chemical data files using the Import Chem Data App (http://www.originlab.com/fileexchange/details.aspx?fid=337) or by any other means applicable to loading data into a worksheet.
NOTE: The current version does not support rendering "Reaction SMILES". Support will be added for them in a release in the near future.
Installation
Drag and drop the SMILES to Image.opx file into Origin workspace (installation may take a little while). The first time the App is run from the App Gallery, you will be prompted to register on the OriginLab website (an internet connection is required only on first run). You must register prior to using the App.
Operation
To render images of molecules, select an entire column of SMILES or InchI strings in the active worksheet. In the Apps Gallery, click on the SMILES to Image icon. In the dialog, select one or more Rendering Options (you may need to expand the control branch) and click OK to replace the strings in the column with images.
To remove the images from a column and restore the strings, select the entire column of images in the active worksheet. Reopen the App from the Apps Gallery. In the dialog, select Remove Images from Column when click OK and click OK.
Errors that may be generated when images of molecules are rendered can be suppressed using the Suppress Image Rendering Syntax Errors control (not pictured in screenshot).
Rendering Options:
Note: How molecules are rendered and how rendering options behave is highly dependent on how the SMILES or InChI string was originally encoded. Subtle variations in the SMILES or InChI can alter the rendered molecule. Also note that SMILES or InChI strings generated molecule drawing applications may not always reflect the exact presentation of the molecule as drawn in the application.
- Display Colored Atoms: On or off; default off. Render atoms in molecule in color.
- Background Color: Color; default None. Background color of rendered image.
- Molecule Color: Color; default Black. Color of molecule including atoms and bonds. Display Colored Atoms will override atom colors if on.
- Relative Thickness: Number between 0 and 2; default 1. Thickness/weight of atoms and bonds. 1 (default) is generally the best setting.
- Label Mode: One of: all, terminal-hetero, hetero; default terminal-hetero. See screenshot for effect.
- Display Stereochemistry: On or off; default off. Display stereochemistry indicators if applicable. See screenshot for effect.
Sample OPJ File
The App ships with a sample OPJ file. In the Apps Gallery, right-click on the SMILEs to Image icon and select Show Samples Folder. From the window that opens, drag and drop SMILES to Image Sample.opj into Origin to open the project. The project includes a page of information and instructions. Note: If saving the OPJ after changing it, it is best to save it to a different location than the one it was opened from (e.g. save to your User Files Folder).