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import java.io.*;
import java.util.ArrayList;
import java.util.List;
import java.util.Arrays;
import java.util.Vector;
import java.util.Map;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.ISimpleChemObjectReader;
import org.openscience.cdk.io.ReaderFactory;
import org.openscience.cdk.qsar.DescriptorEngine;
import org.openscience.cdk.qsar.IDescriptor;
import org.openscience.cdk.qsar.IMolecularDescriptor;
import org.openscience.cdk.qsar.result.DoubleArrayResult;
import org.openscience.cdk.qsar.result.DoubleArrayResultType;
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.qsar.result.IDescriptorResult;
import org.openscience.cdk.qsar.result.IntegerArrayResult;
import org.openscience.cdk.qsar.result.IntegerArrayResultType;
import org.openscience.cdk.qsar.result.IntegerResult;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
import org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor;
import org.openscience.cdk.smiles.SmilesGenerator;
public class ApplyCDKDescriptors
{
public ApplyCDKDescriptors(String inpath, String outpath, String descNamesStr) throws java.io.IOException
{
getDescriptorCSV(inpath,outpath,descNamesStr);
}
private static DescriptorEngine ENGINE = new DescriptorEngine(DescriptorEngine.MOLECULAR);
private static int getSize(IMolecularDescriptor descriptor)
{
IDescriptorResult r = descriptor.getDescriptorResultType();
if (r instanceof DoubleArrayResultType)
return ((DoubleArrayResultType) r).length();
else if (r instanceof IntegerArrayResultType)
return ((IntegerArrayResultType) r).length();
else
return 1;
}
private static String getName(IDescriptor descriptor)
{
return ENGINE.getDictionaryTitle(descriptor.getSpecification()).trim();
}
//public static void main(String args[]) throws java.io.IOException
//{
// String inpath = "hamster_3d.sdf";
// String outpath = "hamster_desc.csv";
// getDescriptorCSV(inpath,outpath,"KappaShapeIndicesDescriptor");
//}
public static void getDescriptorCSV(String sdfInputPath, String csvOutputPath, String descNamesStr) throws java.io.IOException {
List<IMolecule> mols = readMolecules(sdfInputPath);
System.out.println("read " + mols.size() + " compounds");
List<IDescriptor> descriptors = ENGINE.getDescriptorInstances();
System.out.println("found " + descriptors.size() + " descriptors");
List<String> descNames = Arrays.asList(descNamesStr.split(","));
ArrayList<String> colNames = new ArrayList<String>();
ArrayList<Double[]> values = new ArrayList<Double[]>();
for (IDescriptor desc : descriptors) {
if (desc instanceof IPMolecularLearningDescriptor)
continue;
String tname = desc.getClass().getName();
String[] tnamebits = tname.split("\\.");
if (!descNames.contains(tnamebits[tnamebits.length-1]))
continue;
String[] colNamesArr = desc.getDescriptorNames();
colNames.addAll(Arrays.asList(colNamesArr));
List<Double[]> valuesList = computeLists(mols, (IMolecularDescriptor) desc);
values.addAll(valuesList);
}
int ncol = values.size();
int nrow = mols.size();
FileWriter fstream = new FileWriter(csvOutputPath);
BufferedWriter out = new BufferedWriter(fstream);
out.write("SMILES,");
for (int c=0; c<ncol; c++) {
if (c!=0) out.write(",");
out.write(colNames.get(c));
}
out.write("\n");
for (int r=0; r<nrow; r++) {
String smi = getSmiles(mols.get(r));
out.write(smi + ",");
for (int c=0; c<ncol; c++) {
if (c!=0) out.write(",");
out.write(""+values.get(c)[r]);
}
out.write("\n");
}
out.flush();
}
public static String getSmiles(IMolecule m)
{
Map<Object, Object> props = m.getProperties();
for (Object key : props.keySet()) {
if (key.toString().equals("STRUCTURE_SMILES") || key.toString().equals("SMILES"))
return props.get(key).toString();
}
SmilesGenerator g = new SmilesGenerator();
return g.createSMILES(m);
}
public static List<Double[]> computeLists(List<IMolecule> mols, IMolecularDescriptor desc )
{
//System.out.println("computing descriptor " + getName(desc));
List<Double[]> values = computeDescriptors(mols, (IMolecularDescriptor) desc);
return values;
}
public static List<IMolecule> readMolecules(String filepath)
{
Vector<IMolecule> mols = new Vector<IMolecule>();
File file = new File(filepath);
if (!file.exists())
throw new IllegalArgumentException("file not found: " + filepath);
List<IAtomContainer> list;
try
{
ISimpleChemObjectReader reader = new ReaderFactory().createReader(new InputStreamReader(
new FileInputStream(file)));
if (reader == null)
throw new IllegalArgumentException("Could not determine input file type");
IChemFile content = (IChemFile) reader.read((IChemObject) new ChemFile());
list = ChemFileManipulator.getAllAtomContainers(content);
reader.close();
}
catch (Exception e)
{
e.printStackTrace();
return null;
}
for (IAtomContainer iAtomContainer : list)
{
IMolecule mol = (IMolecule) iAtomContainer;
mol = (IMolecule) AtomContainerManipulator.removeHydrogens(mol);
try
{
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
}
catch (Exception e)
{
e.printStackTrace();
}
try
{
CDKHueckelAromaticityDetector.detectAromaticity(mol);
}
catch (Exception e)
{
e.printStackTrace();
}
if (mol.getAtomCount() == 0)
System.err.println("molecule has no atoms");
else
mols.add(mol);
}
return mols;
}
public static List<Double[]> computeDescriptors(List<IMolecule> mols, IMolecularDescriptor descriptor)
{
List<Double[]> vv = new ArrayList<Double[]>();
for (int j = 0; j < getSize(descriptor); j++)
vv.add(new Double[mols.size()]);
for (int i = 0; i < mols.size(); i++)
{
if (mols.get(i).getAtomCount() == 0)
{
for (int j = 0; j < getSize(descriptor); j++)
vv.get(j)[i] = null;
}
else
{
try
{
IDescriptorResult res = descriptor.calculate(mols.get(i)).getValue();
if (res instanceof IntegerResult)
vv.get(0)[i] = (double) ((IntegerResult) res).intValue();
else if (res instanceof DoubleResult)
vv.get(0)[i] = ((DoubleResult) res).doubleValue();
else if (res instanceof DoubleArrayResult)
for (int j = 0; j < getSize(descriptor); j++)
vv.get(j)[i] = ((DoubleArrayResult) res).get(j);
else if (res instanceof IntegerArrayResult)
for (int j = 0; j < getSize(descriptor); j++)
vv.get(j)[i] = (double) ((IntegerArrayResult) res).get(j);
else
throw new IllegalStateException("Unknown idescriptor result value for '" + descriptor + "' : "
+ res.getClass());
}
catch (Throwable e)
{
System.err.println("Could not compute cdk feature " + descriptor);
e.printStackTrace();
for (int j = 0; j < getSize(descriptor); j++)
vv.get(j)[i] = null;
}
}
for (int j = 0; j < getSize(descriptor); j++)
if (vv.get(j)[i] != null && (vv.get(j)[i].isNaN() || vv.get(j)[i].isInfinite()))
vv.get(j)[i] = null;
}
return vv;
}
}
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