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"   
}

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 
}