/**
* @return
* @throws Exception
*/
public int process() throws Exception {
if (file == null) throw new Exception("File not assigned! Use -f command line option.");
if (!file.exists()) throw new FileNotFoundException(file.getAbsolutePath());
int records_read = 0;
int records_processed = 0;
int records_error = 0;
InputStream in = new FileInputStream(file);
/**
* cdk-io module http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-
* search;classname~IteratingMDLReader
*/
IteratingSDFReader reader = null;
SDFWriter writer = new SDFWriter(new OutputStreamWriter(System.out));
try {
reader = new IteratingSDFReader(in, DefaultChemObjectBuilder.getInstance());
LOGGER.log(Level.INFO, String.format("Reading %s", file.getAbsoluteFile()));
while (reader.hasNext()) {
/** Note recent versions allow IAtomContainer molecule = reader.next(); */
Object object = reader.next();
IAtomContainer molecule = null;
if (object instanceof IAtomContainer) molecule = (IAtomContainer) object;
else break;
records_read++;
try {
/** cdk-standard module */
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
// CDKHueckelAromaticityDetector.detectAromaticity(molecule);
for (IAtom atom : molecule.atoms())
if (atom.getImplicitHydrogenCount() == null) {
LOGGER.fine(
atom.getSymbol()
+ "\t"
+ atom.getAtomTypeName()
+ "\t"
+ atom.getImplicitHydrogenCount());
atom.setImplicitHydrogenCount(0);
}
molecule = AtomContainerManipulator.copyAndSuppressedHydrogens(molecule);
/** Generate SMILES and assign as properties */
assignSMILES(molecule);
molecule.setProperty("REACTION", "REACTANT");
molecule.setProperty("SMIRKS", "");
/** Apply reactions */
writer.write(molecule);
for (int r = 0; r < smirks.length; r++) {
if (reactions[r] == null) {
reactions[r] = smrkMan.parse(smirks[r][1]);
}
IAtomContainer reactant = molecule.clone();
if (smrkMan.applyTransformation(reactant, reactions[r])) {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactant);
reactant.setProperty("REACTION", "PRODUCT OF " + smirks[r][0]);
reactant.setProperty("SMIRKS", smirks[r][1]);
try {
assignSMILES(reactant);
} catch (Exception x) {
LOGGER.log(Level.WARNING, x.getMessage());
}
writer.write(reactant);
}
}
records_processed++;
;
} catch (Exception x) {
System.err.println("*");
records_error++;
LOGGER.log(
Level.SEVERE,
String.format("[Record %d] Error %s\n", records_read, file.getAbsoluteFile()),
x);
}
}
} catch (Exception x) {
LOGGER.log(
Level.SEVERE,
String.format("[Record %d] Error %s\n", records_read, file.getAbsoluteFile()),
x);
} finally {
try {
reader.close();
} catch (Exception x) {
}
try {
writer.close();
} catch (Exception x) {
}
}
LOGGER.log(
Level.INFO,
String.format(
"[Records read/processed/error %d/%d/%d] %s",
records_read, records_processed, records_error, file.getAbsoluteFile()));
return records_read;
}
/** @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();
}