User a9d76a1173
17-12-2011 18:07:16
Hi ,
I have a sdf file that is not properly formatted. When I open it with marvin view and save as a sdf I get a properly formatted sdf. I am trying to replicate this functionality using api. Reading part works fine. Writing does not work. I get an empty file.
Here is the code
private void marvinSDFWrite()
{
try
{
FileInputStream fileInputStream = new
FileInputStream(Settings.getCurrentDirectory()+sep+Settings.getJobName()+"_filtered.sdf");
FileOutputStream os = new FileOutputStream(Settings.getCurrentDirectory()+sep+"molconnIn.sdf");
MolImporter molImporter = new MolImporter(fileInputStream);
MolExporter molExporter = new MolExporter(os,"sdf");
Molecule molecule;
while ((molecule = molImporter.read()) != null) {
molExporter.write(molecule);
}
molImporter.close();
molExporter.close();
}
catch (Exception e)
{
System.out.println(e.toString());
}
}
What am I doing wrong?? I am getting java.lang.NullPointerException Is there anything else marvin does to reformat sdf? standardization perhaps ?