Reading Molecules From a File

IJC can read a variety of molecule file types, handled via MolImporter. MolImporter automatically recognizes file structures, making import a very simple process. The scriptlet below sets up a while loop, one of the most common uses of MolImporter in scripts. This cycles through a SD file, echoing the raw molecule. While it is not echoed, the grabbed molecule (String molStr) is a marvin structure, which is the format to use when inserting into a structures table.

            import chemaxon.formats.MolImporter
            
            String file = 'C:/data/import.sdf'

            importer = new MolImporter(file)
            importer.grabbingEnabled = true
            mol = importer.createMol()
            
            while (importer.read(mol)) {
                String molStr = importer.grabbedMoleculeString
                print "Molecule is $mol \n"   
                 }                
        

Files can be specified in the code themselves (as above), or you can use JFileChooser to prompt the user for a file.

            import javax.swing.*
            
            def chooser = new JFileChooser()
            chooser.setDialogTitle('Select file')
            if (chooser.showOpenDialog(null)==JFileChooser.APPROVE_OPTION) {
                fileName = chooser.selectedFile.canonicalPath
                // fileName is then used when creating a MolImporter
            } else {
                return 
            }