MolConvert script/AppleScript for manipulating ~1000 files

Hello, I am trying to convert files from .mol to .inchi using MolConvert. For one file I simply type: /Applications/ChemAxon/MarvinBeans/bin/molconvert inchi ~/myFile.mol > ~/myFile.inchi

I also make an image: /Applications/ChemAxon/MarvinBeans/bin/molconvert -o ~/myFile.png png ~/myFile.inchi 

Quality of image is not very good. Most probably I am doing something wrong.

But I have way to many files to do it all manually, so I wanted to automate the process, either using AppleScript or any other possible solution.

Here is my attempt (non-working so far, unfortunately) using AppleScript:

tell application "Finder"

    set folder to files of folder POSIX file "/Users/user/myFolderWithFiles/" as alias list

end tell

repeat with file in folder

if fileExtension is "mol" then

tell application "/Applications/ChemAxon/MarvinBeans/bin/molconvert" to inchi f > f.inchi

end tell

end if

end repeat

On this 'f' execution of the script fails: 'Expected end of line but found identifier.' Which is most probably due to my 0 AppleScript skill, which I actually have never used before.
What can I do in this case? How to write a script? 

Hi,

According to AppleScript I can not provide a solution but I attach a small code that would do the job for you written in Java. Also I would like to mention that the generated pictures were not so good looking because they were "cleaned" in 3D. In the provided code I've inserted a "clean" call that transforms the molecule to it's 2D view. I suppose you would need it also while exporting into png.

Here is the code snippet:

public static void main(String[] args) throws IOException {
    File folderOfMolFiles = new File("/absolute/path/to/mol/files/folder");
    File folderToExportInchis = new File("/absolute/path/to/export/inchi/files");
    for (String fileName : folderOfMolFiles.list()) {
        if (fileName.endsWith("mol")) {
            File molFile = new File(folderOfMolFiles, fileName);
            MolImporter importer = new MolImporter(molFile);
            Molecule mol = importer.read();
            importer.close();
            Cleaner.clean(mol, 2);
            File inchiFile = new File(folderToExportInchis, fileName.replaceAll("mol$", "inchi"));
            MolExporter exporter = new MolExporter(new FileOutputStream(inchiFile), "inchi");
            exporter.write(mol);
            exporter.close();
        }
    }

Regards, Domi

Thanks a lot, now I see, how I should write such things)