Validating Mol String

Is there a way to determine if a mol string is valid or not? Before attempting to display the molecule via MarvinView, I would like to be able to detect whether or not the mol string is valid (will actually display), and when it is not going to be displayed, display a message to our users instead of a blank box (applet with nothing displayed). Thanks!

To test the molecule string, I suggest to convert it into another format. If MolConverter does not indicate error, the molecule may be correct.

I need to do the validation 'programmatically' (i.e. not interactively). Specifically, it needs to be done either via C# on the server, or maybe via Javascript on the client. This is part of a .NET, browser-based application.

You can use the MolImporter API (that is part of the Marvin Beans package) to read molecule source. MolImporter will throw exception if you try to import an invalid molecule.

Code:

MolImporter importer; try { importer = new MolImporter(args[0]); Molecule mol = importer.read(); } catch(MolFormatException mex) {     // invalid molecule format } catch(IOException ioex) {    // invalid molecule or any other read error }

Via, JNBridge you can access the full Marvin Beans API. See the details in the following document: .NET support

You can put the above code into a JSP page, so that it runs upon compilation and display to the user; it doesn't need to be in a separate back-end file.