@Test
public void testDragonShell() throws Exception {
DragonShell shell = new DragonShell();
shell.setDescriptors(new String[] {"MW", "MLOGP", "Constitutional indices"});
IIteratingChemObjectReader reader =
FileInputState.getReader(
getClass().getClassLoader().getResourceAsStream("ambit2/dragon/test/structure.sdf"),
"structure.sdf");
Assert.assertTrue(reader != null);
while (reader.hasNext()) {
Object o = reader.next();
IAtomContainer mol = (IAtomContainer) o;
mol = shell.process(mol);
Assert.assertTrue(mol.getProperties().size() > 0);
}
reader.close();
}
/** @param args the command line arguments */
public static void main(String[] args) throws IOException, CDKException {
BufferedOutputStream writer = new BufferedOutputStream(new FileOutputStream(output));
int j = 0;
File f;
SmilesGenerator sg;
f = new File(input);
System.out.println(input);
IteratingSDFReader reader =
new IteratingSDFReader(new FileInputStream(f), DefaultChemObjectBuilder.getInstance());
sg = SmilesGenerator.generic().aromatic();
sg.setUseAromaticityFlag(true);
// List<IAtomContainer> mols = new ArrayList<IAtomContainer>();
IAtomContainer mol;
long totalMemory = 0;
while (reader.hasNext()) {
mol = (IAtomContainer) reader.next();
// mols.add(mol);
j++;
String smiles = sg.create(mol);
if (!smiles.equals("")) {
writer.write(sg.create(mol).getBytes());
writer.write(";".getBytes());
writer.write("https://www.ebi.ac.uk/chembl/compound/inspect/".getBytes());
writer.write(((String) mol.getProperties().get("chembl_id")).getBytes());
writer.write("\n".getBytes());
} else {
System.out.println("HUUUUGE");
}
System.out.println("done" + j);
}
// totalMemory = MemoryUtil.deepMemoryUsageOfAll(mols, MemoryUtil.VisibilityFilter.ALL);
// System.out.println("Average memory: " + (totalMemory/j));
/*a a = new a();
a aa = new a();
a.c = new c();
aa.c = a.c;
System.out.println("a " + MemoryUtil.deepMemoryUsageOf(a, MemoryUtil.VisibilityFilter.ALL));
System.out.println("aa " + MemoryUtil.deepMemoryUsageOf(aa, MemoryUtil.VisibilityFilter.ALL));
System.out.println("a.c " + MemoryUtil.deepMemoryUsageOf(a.c, MemoryUtil.VisibilityFilter.ALL));
List<a> ll = new ArrayList<a>();
ll.add(a);
ll.add(aa);
System.out.println(MemoryUtil.deepMemoryUsageOfAll(ll, MemoryUtil.VisibilityFilter.ALL));*/
System.out.println("done" + j);
writer.close();
}